AMBER Archive (2007) - By Author

Starting: Mon Jan 01 2007 - 04:25:56 CST
Ending: Mon Dec 31 2007 - 15:27:41 CST

• $BJ}b}(B
  • Re: AMBER: About the problem of the PMEMD and cutoff (Mon Jan 15 2007 - 06:45:29 CST)
  • AMBER: About the problem of the PMEMD and cutoff (Sun Jan 14 2007 - 21:56:17 CST)
• #NGUYEN CONG TRI#
  • RE: AMBER: Troubling with installing Amber8 (Thu Dec 13 2007 - 08:19:47 CST)
  • AMBER: Troubling with installing Amber8 (Sun Dec 09 2007 - 06:06:18 CST)
• A Box
  • Re: AMBER: how to modify map.DG-AMBER file? (Tue Apr 10 2007 - 18:56:21 CDT)
  • AMBER: Amber9 Sander Error (Thu Mar 29 2007 - 20:26:21 CST)
  • AMBER: Prepgen (Wed Feb 14 2007 - 22:15:21 CST)
  • AMBER: LeaP: Mol2 files (Tue Feb 13 2007 - 19:44:08 CST)
  • AMBER: Antechamber Charge Calculation Method (Mon Jan 29 2007 - 18:46:42 CST)
• Aaron Greenwood
  • Re: AMBER: mdfil: Error unknown flag: -p4pg (Tue Oct 30 2007 - 06:03:29 CST)
  • AMBER: mdfil: Error unknown flag: -p4pg (Mon Oct 29 2007 - 13:38:44 CST)
  • AMBER: Portland Group vs. Intel Compilers. (Tue Oct 23 2007 - 12:03:43 CDT)
  • AMBER: Beowulf cluster from PSSC Labs (Tue Oct 23 2007 - 11:22:33 CDT)
• Aaron Virshup
  • AMBER: Converting AMBER-format force fields for tinker (Fri Aug 31 2007 - 14:04:12 CDT)
• ABEL Stephane 984007
  • RE : AMBER: Atom types for polyunsaturated lipids (Sun Nov 18 2007 - 13:40:24 CST)
  • AMBER: Atom types for polyunsaturated lipids (Sun Nov 18 2007 - 11:14:14 CST)
  • AMBER: 2 double bond in AMBER ffield (Tue Nov 13 2007 - 11:00:08 CST)
• Abhilash
  • Re: AMBER: Problem related simulation of dimer (Thu Mar 15 2007 - 10:03:06 CST)
• Abi Ghanem josephine
  • AMBER: ANGVE/TORAVE (Thu Oct 25 2007 - 10:58:11 CDT)
  • Re: AMBER: regarding energy calculation (Wed Sep 26 2007 - 04:13:38 CDT)
  • AMBER: Restraining valence angles (Wed Jun 06 2007 - 03:35:12 CDT)
• Achuth Prabhu
  • AMBER: Ptraj hbond analysis (Tue Jun 05 2007 - 09:51:54 CDT)
  • AMBER: ambpdb gives empty cpin (Mon May 21 2007 - 03:27:16 CDT)
  • Re :Re: AMBER: multiple excecution of sander (Fri May 18 2007 - 01:03:23 CDT)
  • AMBER: multiple excecution of sander (Thu May 17 2007 - 10:55:47 CDT)
  • AMBER: polymer (Mon May 14 2007 - 07:55:12 CDT)
  • AMBER: leap problem (Wed May 09 2007 - 07:48:33 CDT)
  • AMBER: leap problem (Wed May 09 2007 - 07:28:01 CDT)
  • AMBER: leap problem (Wed May 09 2007 - 07:03:51 CDT)
• adelene_at_Stanford.EDU
  • Re: AMBER: Temperature Drift in MD (NAB) (Fri May 18 2007 - 18:56:39 CDT)
  • AMBER: Temperature Drift in MD (NAB) (Fri May 18 2007 - 17:49:25 CDT)
  • Re: AMBER: NAB Average Structure (Thu May 17 2007 - 13:59:42 CDT)
  • AMBER: NAB Average Structure (Thu May 17 2007 - 11:12:47 CDT)
  • AMBER: Energy Spread using GB & Langevin Dynamics (NAB) (Mon May 14 2007 - 15:17:28 CDT)
  • AMBER: Electrostatic Energy in MD Simulation (GB) (Thu May 10 2007 - 12:20:32 CDT)
  • AMBER: NAB MD Output (Mon May 07 2007 - 17:30:51 CDT)
  • AMBER: GB Energy Spreads for MD Structures (Mon May 07 2007 - 14:19:47 CDT)
• Adrian Roitberg
  • Re: AMBER: replica exchange out files continually overwritten (Fri Dec 14 2007 - 12:33:23 CST)
  • Re: AMBER: Minimization amber9 segmentation fault (Sat Dec 01 2007 - 13:44:16 CST)
  • Re: AMBER: Minimization amber9 segmentation fault (Sat Dec 01 2007 - 10:17:15 CST)
  • Re: AMBER: questions about smd of amber 9 (Thu Nov 29 2007 - 10:56:15 CST)
  • Re: AMBER: RE: FF94 or FF99? (Thu Nov 22 2007 - 09:20:22 CST)
  • Re: AMBER: invalid digit '*' in the input file (Mon Nov 12 2007 - 09:17:43 CST)
  • Re: AMBER: TIP5P water simulation using AMBER7 (Sun Nov 11 2007 - 10:29:11 CST)
  • Re: AMBER: Compiling single programs (Fri Nov 02 2007 - 12:08:44 CST)
  • Re: AMBER: &dipoles output in QM/MM simulations (Fri Nov 02 2007 - 07:06:28 CST)
  • Re: AMBER: Umbrella sampling (Fri Oct 26 2007 - 09:11:14 CDT)
  • Re: AMBER: AMBER 9 - Force Field Options - Question (Thu Oct 18 2007 - 13:56:23 CDT)
  • Re: AMBER: AMBER 9 - Force Field Options - Question (Wed Oct 17 2007 - 13:26:56 CDT)
  • Re: AMBER: constant-pH MD with replica exchange (Thu Oct 11 2007 - 13:55:18 CDT)
  • Re: AMBER: constant-pH MD with replica exchange (Thu Oct 11 2007 - 10:33:30 CDT)
  • Re: AMBER: effective step period for constant pH simulations (Mon Sep 24 2007 - 13:31:05 CDT)
  • Re: AMBER: Targeted MD (Sat Sep 08 2007 - 17:35:22 CDT)
  • Re: AMBER: Running mpirun -np 1 on different processors (Tue Sep 04 2007 - 08:45:11 CDT)
  • Re: AMBER: heating up system (Tue Aug 28 2007 - 13:45:26 CDT)
  • Re: AMBER: SCC convergence failure in QM-MM DFTB (Sat Aug 25 2007 - 13:10:35 CDT)
  • Re: AMBER: SMD simulation (Fri Aug 24 2007 - 07:43:35 CDT)
  • Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj). (Thu Aug 23 2007 - 08:32:28 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 07:44:01 CDT)
  • Re: AMBER: xleap and amber7 (Mon Jul 02 2007 - 09:20:28 CDT)
  • Re: AMBER: Re: Strange shape in my MD simulations (Tue Jun 19 2007 - 09:16:17 CDT)
  • Re: AMBER: Re: Strange shape in my MD simulations (Tue Jun 19 2007 - 07:57:07 CDT)
  • Re: AMBER: Pi-pi interactions (Mon May 21 2007 - 08:56:51 CDT)
  • Re: AMBER: Is the simulation reasonable ? (SMD : dissocation antibody-antigen) (Thu May 17 2007 - 10:06:49 CDT)
  • Re: AMBER: need help to calculate IR spectra from amber trajectory (Thu May 10 2007 - 14:16:59 CDT)
  • Re: AMBER: Chemical shift: simulation vs. experiment (Fri May 04 2007 - 01:42:55 CDT)
  • Re: AMBER: Steered MD & Jarzynski's equality (Wed May 02 2007 - 02:26:30 CDT)
  • Re: AMBER: qm/mm ti (Fri Mar 02 2007 - 08:02:49 CST)
  • Re: AMBER: Sander slower on 16 processors than 8 (Thu Feb 22 2007 - 15:25:15 CST)
  • Re: AMBER: units in hessian matrix (Thu Feb 15 2007 - 11:35:07 CST)
  • Re: AMBER: Protonation of Aspartate (Thu Feb 08 2007 - 11:17:11 CST)
• Age.Skjevik_at_student.uib.no
  • AMBER: Electron density profile (Thu Dec 20 2007 - 06:13:56 CST)
  • AMBER: RED III (Mon Oct 15 2007 - 05:06:49 CDT)
  • AMBER: ntt parameter in vacuum (Mon Sep 03 2007 - 08:40:15 CDT)
• Akansha Saxena
  • AMBER: implicit solvent simulations with calcium ion (Mon Dec 10 2007 - 15:19:01 CST)
• Akshay Patny
  • RE: AMBER: Problem with anisotropic pressure scaling (Fri Mar 16 2007 - 10:37:22 CST)
  • AMBER: Difference in Equilibration & Production MD in Amber (Wed Feb 28 2007 - 14:33:56 CST)
  • RE: AMBER: Box dimensions (Fri Feb 16 2007 - 10:34:40 CST)
  • AMBER: Density of a system in MD (Thu Feb 15 2007 - 14:45:27 CST)
  • RE: AMBER: Membrane Simulation: NPT Issues (Thu Feb 15 2007 - 10:54:02 CST)
  • RE: AMBER: Membrane Simulation: NPT Issues (Mon Feb 12 2007 - 09:33:40 CST)
  • RE: AMBER: antechamber for topology file (Thu Feb 08 2007 - 00:28:50 CST)
  • AMBER: Membrane Simulation: NPT Issues (Wed Feb 07 2007 - 11:28:05 CST)
  • AMBER: Membrane Simulation: NPT issues (Wed Feb 07 2007 - 12:29:36 CST)
  • AMBER: RESP Charges for Charged Carboxylate in Organic Ligand (Fri Feb 02 2007 - 10:05:35 CST)
  • RE: AMBER: ADDIONS do not neutralize to ZERO (Mon Jan 29 2007 - 11:04:58 CST)
  • RE: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand (Mon Jan 29 2007 - 10:57:45 CST)
  • AMBER: Ligand-Protein Distance Restraints during MD Simulation (Fri Jan 26 2007 - 18:06:26 CST)
  • RE: AMBER: ADDIONS do not neutralize to ZERO (Fri Jan 26 2007 - 17:38:48 CST)
  • RE: AMBER: NVT/NPT equilibration issue in GPCR-membrane simulation (Fri Jan 26 2007 - 17:27:56 CST)
  • AMBER: NVT/NPT equilibration issue in GPCR-membrane simulation (Fri Jan 26 2007 - 16:23:46 CST)
  • RE: AMBER: Defining BOX INFO during TLEAP (Wed Jan 24 2007 - 13:54:37 CST)
  • AMBER: Defining BOX INFO during TLEAP (Mon Jan 22 2007 - 21:02:15 CST)
  • RE: AMBER: ADDIONS do not neutralize to ZERO (Mon Jan 22 2007 - 20:10:47 CST)
  • AMBER: ADDIONS do not neutralize to ZERO (Mon Jan 22 2007 - 19:19:20 CST)
  • AMBER: RESP Charges for Charged Carboxylate in Organic Ligand (Fri Jan 19 2007 - 02:34:58 CST)
  • RE: AMBER: Leap adding extra atoms (Thu Jan 11 2007 - 15:38:37 CST)
  • AMBER: Leap adding 3 extra atoms (Thu Jan 11 2007 - 11:35:00 CST)
• Alana Canfield
  • AMBER: rms and rms nofit (Sat Sep 08 2007 - 16:23:39 CDT)
• Alberto Perez
  • AMBER: dna forcefield: PARMBSC0 (Wed Mar 14 2007 - 01:14:36 CST)
• Alessandro Nascimento
  • Re: AMBER: closest water molecules with 8 angstroms (Wed Dec 19 2007 - 04:49:56 CST)
  • Re: AMBER: Troubles installing amber (Fri Dec 07 2007 - 13:55:54 CST)
  • Re: AMBER: About RAMD (Thu Nov 29 2007 - 04:54:02 CST)
  • AMBER: EXCEEDED MAXLESADJ in sander.LES.MPI (amber9) (Sat Nov 17 2007 - 15:24:58 CST)
  • AMBER: mm_pbsa and energy decomposition (missing BELE for MM in 1) (Tue Jul 31 2007 - 16:34:12 CDT)
  • AMBER: Improving pmemd parallel scaling (Thu Jun 28 2007 - 11:07:15 CDT)
• Alexandar T Tzanov
  • Re: RE: AMBER: Portland Group vs. Intel Compilers. (Tue Oct 23 2007 - 13:35:25 CDT)
  • Re: AMBER: Portland Group vs. Intel Compilers. (Tue Oct 23 2007 - 12:11:46 CDT)
  • AMBER: Re: RE: Problems with Ifort 9.1.047 on Altix (Was: RE: Re: AMBER: $AMBERHOME on PATH) (Fri Jun 29 2007 - 09:48:13 CDT)
  • Re: RE: Re: AMBER: $AMBERHOME on PATH (Thu Jun 28 2007 - 10:39:57 CDT)
• Alexander Rubinstein
  • AMBER: Energy calculation by Anal (Thu Feb 08 2007 - 14:11:16 CST)
  • AMBER: Energy calculation by Anal (Thu Feb 08 2007 - 14:11:16 CST)
• Alexander Steudle
  • AMBER: MAXGRP error message (Mon Feb 05 2007 - 08:03:45 CST)
• alfredoq_at_fcq.unc.edu.ar
  • AMBER: Problem using Ptraj (Mon Apr 23 2007 - 10:41:56 CDT)
• alfredoq_at_mail.fcq.unc.edu.ar
  • Re: AMBER: Problem with xLeap (Tue Nov 13 2007 - 12:11:31 CST)
  • Re: AMBER: Problem with xLeap (Tue Nov 13 2007 - 11:07:40 CST)
  • AMBER: Problem with xLeap (Tue Nov 13 2007 - 09:34:46 CST)
• Allen, Thomas W., Ph.D. [RO BIOCHM]
  • AMBER: umbrella sampling and WHAM (Mon Nov 05 2007 - 14:03:31 CST)
• Amarda Shehu
  • Re: AMBER: equilibration in explicit solvent (Thu Feb 08 2007 - 13:48:23 CST)
  • Re: AMBER: equilibration in explicit solvent (Thu Feb 08 2007 - 11:37:39 CST)
  • Re: AMBER: equilibration in explicit solvent (Sun Feb 04 2007 - 12:32:05 CST)
  • AMBER: equilibration in explicit solvent (Sun Feb 04 2007 - 11:40:12 CST)
• Amit Kumar
  • AMBER: vlimit error (Fri Mar 16 2007 - 17:10:06 CST)
  • Re: AMBER: extracting coordinate from crd file (Sat Feb 10 2007 - 09:31:35 CST)
  • AMBER: addions (Sat Feb 03 2007 - 07:17:57 CST)
  • Re: AMBER: issues with restrt file (Thu Jan 18 2007 - 12:27:12 CST)
  • Re: AMBER: issues with restrt file (Thu Jan 18 2007 - 11:59:40 CST)
  • AMBER: issues with restrt file (Thu Jan 18 2007 - 10:15:52 CST)
• Anamika Awasthi
  • AMBER: Pre-requisites for AMBER software (Thu Oct 25 2007 - 07:05:19 CDT)
• Andrea - Tisacali
  • AMBER: MM-PBSA calculation with GB dynamic (Wed May 16 2007 - 08:56:15 CDT)
• Andrea Bortolato
  • Re: AMBER: is possible to compile pmemd using scali MPI? (Mon Apr 23 2007 - 07:31:53 CDT)
  • Re: AMBER: is possible to compile pmemd using scali MPI? (Fri Mar 30 2007 - 13:48:12 CST)
  • AMBER: is possible to compile pmemd using scali MPI? (Thu Mar 29 2007 - 10:17:05 CST)
• Andreas Svrcek-Seiler
  • Re: AMBER: website problems (Sun Dec 09 2007 - 11:25:12 CST)
  • Re: AMBER: compilation error in SGI Altix 4700 with Intel Fortran 10.1.008 and IMKL 10.0.1.014 (Thu Dec 06 2007 - 09:49:34 CST)
  • Re: AMBER: gb minimization using nab (Tue Nov 13 2007 - 05:58:05 CST)
  • Re: AMBER: Portland Group vs. Intel Compilers. (Tue Oct 23 2007 - 15:24:29 CDT)
  • Re: AMBER: What is the best computer for running AMBER simulations? (Thu Aug 16 2007 - 17:51:06 CDT)
  • RE: AMBER: Any experience on Dell two quad core system? (Mon Aug 13 2007 - 15:46:58 CDT)
  • Re: AMBER: Any experience on Dell two quad core system? (Mon Aug 13 2007 - 12:21:39 CDT)
  • RE: AMBER: Any experience on Dell two quad core system? (Mon Aug 13 2007 - 10:12:15 CDT)
  • Re: AMBER: Any experience on Dell two quad core system? (Thu Aug 02 2007 - 23:18:42 CDT)
  • Re: AMBER: configure question (Thu Jun 28 2007 - 11:49:38 CDT)
  • Re: AMBER: Math libraries (Thu Jun 28 2007 - 11:27:28 CDT)
  • Re: AMBER: NAB normal mode output (Fri May 25 2007 - 04:15:46 CDT)
  • Re: AMBER: NAB Average Structure (Thu May 17 2007 - 14:40:26 CDT)
  • Re: AMBER: Energy Spread using GB & Langevin Dynamics (NAB) (Tue May 15 2007 - 04:20:16 CDT)
  • Re: AMBER: NAB MD Output (Tue May 08 2007 - 05:09:18 CDT)
  • Re: AMBER: Problems installing Amber9 (Fri Apr 27 2007 - 07:52:05 CDT)
  • Re: AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8 (Fri Feb 23 2007 - 05:02:52 CST)
  • Re: AMBER: question about the testing of AMBER9 (Mon Jan 08 2007 - 05:15:58 CST)
• Andres Palencia
  • AMBER: atomicfluct (Mon Oct 01 2007 - 13:12:20 CDT)
  • AMBER: atomicfluct (Tue Sep 25 2007 - 12:45:50 CDT)
• Andrew Borgert
  • AMBER: Integrating the alpha-helix bias correction into ff94 (Mon Aug 06 2007 - 14:18:58 CDT)
  • Re: AMBER: Cutoff list exceeds largest sphere in unit cell (Fri Jul 13 2007 - 11:27:44 CDT)
  • AMBER: Cutoff list exceeds largest sphere in unit cell (Fri Jul 13 2007 - 11:18:05 CDT)
  • AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8 (Wed May 30 2007 - 12:35:51 CDT)
• Andrew Purkiss-Trew
  • RE: AMBER: Restraintmask syntax (Wed Dec 05 2007 - 04:39:08 CST)
• andy ng
  • Re: AMBER: refinement of NMR struture using AMBER (Fri Sep 07 2007 - 08:42:44 CDT)
  • Re: AMBER: refinement of NMR struture using AMBER (Wed Sep 05 2007 - 04:59:00 CDT)
• Andy Purkiss
  • Re: AMBER: request for hardware recommendations (Sat Oct 06 2007 - 12:53:23 CDT)
• Andy Purkiss-Trew
  • Re: AMBER: problems using TIP4PBOX (Wed Jun 13 2007 - 07:36:14 CDT)
  • RE: AMBER: problem running parallel jobs (Thu Jun 07 2007 - 04:53:34 CDT)
  • Re: AMBER: .prmtop entries (Mon Apr 23 2007 - 06:13:18 CDT)
  • Re: AMBER: Problem with anisotropic pressure scaling (Fri Mar 16 2007 - 09:47:19 CST)
• Anela Ivanova
  • AMBER: Generation of ESP(ind) within atomic charges derivation for polarizable force field (Wed Jul 04 2007 - 07:26:02 CDT)
• Anju Sharma
  • AMBER: How to carry out drug-dna complex simulations (Tue Aug 14 2007 - 03:50:04 CDT)
  • Re: AMBER: Problem while carrying out minimisation of drug molecule using sander (Tue Aug 07 2007 - 00:32:43 CDT)
  • AMBER: Problem while carrying out minimisation of drug molecule using sander (Sun Aug 05 2007 - 22:51:11 CDT)
  • Re: AMBER: Problem with antechamber (Thu Aug 02 2007 - 04:03:36 CDT)
  • AMBER: Problem with antechamber (Thu Aug 02 2007 - 01:34:39 CDT)
  • Re: AMBER: Problem while saving .top and .crd files. (Thu Aug 02 2007 - 00:25:19 CDT)
  • AMBER: Problem while creating input files in antechamber (Tue Jul 31 2007 - 00:33:12 CDT)
  • AMBER: Problem while saving .top and .crd files. (Mon Jul 30 2007 - 22:47:39 CDT)
  • AMBER: Needed help regardng Simulated Annealing (Thu Apr 12 2007 - 00:07:14 CDT)
  • Re: AMBER: Prblm rgrdng Simulated Annealing (Wed Apr 11 2007 - 06:46:08 CDT)
  • Re: AMBER: Prblm rgrdng Simulated Annealing (Wed Apr 11 2007 - 06:33:03 CDT)
  • AMBER: Prblm rgrdng Simulated Annealing (Wed Apr 11 2007 - 05:06:08 CDT)
  • Re: AMBER: Problem while using antechamber (Tue Apr 10 2007 - 04:18:07 CDT)
  • AMBER: Problem while using antechamber (Tue Apr 10 2007 - 01:15:47 CDT)
  • AMBER: Regarding Simulated Annealing (Tue Apr 03 2007 - 07:27:18 CDT)
  • AMBER: Problem while running Antechamber (Wed Mar 21 2007 - 03:35:28 CST)
  • AMBER: Problem while loading Pdb in xleap (Tue Mar 20 2007 - 22:12:55 CST)
  • AMBER: Problem!! (Mon Mar 19 2007 - 00:38:15 CST)
  • AMBER: Problem while creating structure in xLeap (Sun Mar 18 2007 - 22:30:03 CST)
  • AMBER: hi (Sun Mar 18 2007 - 21:56:22 CST)
  • AMBER: hi (Fri Mar 16 2007 - 04:50:44 CST)
  • AMBER: hii (Thu Mar 15 2007 - 03:28:47 CST)
  • AMBER: How to build organic compound in Amber (Wed Mar 14 2007 - 22:24:09 CST)
  • AMBER: Need help in Analysis (Wed Mar 14 2007 - 03:13:03 CST)
  • Re: AMBER: problem while analysing result (Wed Mar 14 2007 - 00:27:20 CST)
  • AMBER: problem while analysing result (Tue Mar 13 2007 - 23:38:37 CST)
  • AMBER: Problem Solved (Tue Mar 13 2007 - 22:19:57 CST)
  • Re: AMBER: problem while running minimisation (Tue Mar 13 2007 - 22:19:03 CST)
  • AMBER: problem while running minimisation (Tue Mar 13 2007 - 22:10:15 CST)
  • Re: AMBER: hi.. (Tue Mar 13 2007 - 06:29:28 CST)
  • Re: AMBER: hi.. (Tue Mar 13 2007 - 06:28:23 CST)
  • Re: AMBER: hi.. (Tue Mar 13 2007 - 06:15:27 CST)
  • AMBER: hi.. (Tue Mar 13 2007 - 05:59:24 CST)
  • AMBER: unable to run test (Sun Mar 11 2007 - 23:14:03 CST)
  • Re: AMBER: hi (Tue Feb 13 2007 - 22:44:45 CST)
  • Re: AMBER: hi (Tue Feb 13 2007 - 22:50:16 CST)
  • Re: AMBER: hi (Tue Feb 13 2007 - 22:48:36 CST)
  • AMBER: hi (Tue Feb 13 2007 - 04:08:01 CST)
  • AMBER: Fwd: help me out... (Mon Feb 12 2007 - 06:22:57 CST)
  • AMBER: help me out... (Mon Feb 12 2007 - 06:21:00 CST)
• anna duraj
  • AMBER: Problem with Sander (Thu Sep 13 2007 - 17:42:29 CDT)
  • AMBER: docking ability (Wed Aug 15 2007 - 12:34:37 CDT)
  • Re: AMBER: Problem with Antechamber and point charges (Fri Aug 03 2007 - 14:47:17 CDT)
  • AMBER: Problem with Antechamber and point charges (Wed Aug 01 2007 - 14:40:44 CDT)
• Anna Díaz Cirac
  • AMBER: xleap question (Fri Sep 14 2007 - 11:26:33 CDT)
  • AMBER: secstruct command (Thu Jul 19 2007 - 12:35:42 CDT)
• anna.schrey_at_gmx.de
  • Re: AMBER: topology for postprocessed files? (Wed Apr 18 2007 - 12:40:51 CDT)
  • Re: AMBER: topology for postprocessed files? (Thu Apr 12 2007 - 05:42:41 CDT)
  • AMBER: topology for postprocessed files? (Thu Apr 12 2007 - 04:57:28 CDT)
  • AMBER: supplement ptraj:problems with time correlation calculation (comp. with NMR experiments) (Sun Apr 08 2007 - 09:15:22 CDT)
  • AMBER: ptraj:problems with time correlation calculation (comp. with NMR experiments) (Sun Apr 08 2007 - 07:21:38 CDT)
• Anselm Horn
  • Re: AMBER: pmemd: same rst, different result? (Tue Dec 18 2007 - 03:10:20 CST)
  • AMBER: pmemd: same rst, different result? (Mon Dec 17 2007 - 03:54:20 CST)
  • AMBER: Polarizable Force Field: Ligand Parameterization et al. (Thu Oct 25 2007 - 04:00:03 CDT)
  • AMBER: FF02: sander problem with irstdip=1 (Fri Sep 14 2007 - 05:31:19 CDT)
• Anthony Cruz
  • Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! (Fri Oct 05 2007 - 07:44:50 CDT)
  • Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! (Wed Sep 26 2007 - 11:03:41 CDT)
  • AMBER: Simulation continuation problem. Cant read restart file!!!!!! (Wed Sep 26 2007 - 09:55:45 CDT)
• Anthony Cruz Balberdi
  • AMBER: S-nitrocysteine (Wed Jun 13 2007 - 08:12:00 CDT)
• Antonio Morreale
  • Re: AMBER: MM_PBSA No radius found for Br!! (Mon Aug 13 2007 - 06:39:52 CDT)
  • AMBER: protein-rna interaction & mmpbsa (Thu Apr 26 2007 - 03:28:19 CDT)
  • AMBER: mm_pbsa_statistics.pl (Tue Jan 16 2007 - 06:28:52 CST)
• Anupam Nath Jha
  • AMBER: calculation of angle between helices (Mon Oct 29 2007 - 00:06:37 CST)
• Arvind Marathe
  • Re: AMBER: AMBER9 installation error on dual core AMD Opteron(tm) processor 275 (Fri Apr 13 2007 - 10:59:35 CDT)
  • AMBER: AMBER9 installation error on dual core AMD Opteron(tm) processor 275 (Fri Apr 13 2007 - 05:23:38 CDT)
• Asim Okur
  • Re: AMBER: hybrid remd (Wed May 09 2007 - 14:07:59 CDT)
• Atila Iamarino
  • Re: AMBER: working with Antechamber (Wed Apr 11 2007 - 13:59:03 CDT)
  • AMBER: working with Antechamber (Wed Apr 11 2007 - 12:45:20 CDT)
• Austin B. Yongye
  • RE: AMBER: Calculating dipole moments (Thu Nov 29 2007 - 09:40:51 CST)
  • AMBER: Calculating dipole moments (Wed Nov 28 2007 - 13:33:41 CST)
  • Re: AMBER: calculating charges to modified 4GA unit (Wed Nov 07 2007 - 08:26:57 CST)
  • AMBER: restarting REMD simulations (Thu Sep 27 2007 - 09:21:43 CDT)
  • Re: AMBER: Re: how to create an O linked N-acetylglucosamine in a (Tue Jul 17 2007 - 01:22:12 CDT)
  • Re: AMBER: Ptraj: reading PDB files (Thu Jun 07 2007 - 09:16:10 CDT)
  • AMBER: Ptraj: reading PDB files (Wed Jun 06 2007 - 16:37:31 CDT)
  • AMBER: PMEMD and restart files (Sat May 12 2007 - 13:21:30 CDT)
  • Re: AMBER: using glycam04 parameters (Wed Apr 18 2007 - 11:03:35 CDT)
  • Re: AMBER: using glycam04 parameters (Wed Apr 18 2007 - 08:24:38 CDT)
  • Re: AMBER: Trimannoside Problem (Thu Mar 08 2007 - 08:09:48 CST)
  • Re: AMBER: Charges in TI calculations and leap (Tue Jan 30 2007 - 14:10:54 CST)
  • AMBER: Charges in TI calculations and leap (Tue Jan 30 2007 - 13:35:50 CST)
  • AMBER: vdW parameters for chlorine atom (Wed Jan 17 2007 - 11:19:34 CST)
• Avinash Kumar
  • AMBER: software to extract data from the output file?? (Sat May 26 2007 - 03:49:37 CDT)
• AYTUG TUNCEL
  • AMBER: corrected reaction field energy and PBCAL (Sun Jul 08 2007 - 19:40:53 CDT)
  • AMBER: inconsistency between PBSA and GBSA - help (Sat May 26 2007 - 04:35:36 CDT)
  • AMBER: inconsistency between PBSA and GBSA (Wed May 23 2007 - 12:30:11 CDT)
  • AMBER: inconsistency between PBSA and GBSA (Wed May 23 2007 - 08:26:32 CDT)
  • AMBER: high energy with mm_gbsa igb=5 (Fri May 18 2007 - 01:39:43 CDT)
  • AMBER: high energy with mm_gbsa igb=5 (Thu May 17 2007 - 04:53:07 CDT)
  • AMBER: Missing BELE for MM in 1 (residue 47) (Thu May 10 2007 - 02:32:26 CDT)
  • Re: Re: AMBER: parse radii (Mon Apr 09 2007 - 03:02:59 CDT)
  • AMBER: parse radii (Wed Apr 04 2007 - 04:10:10 CDT)
  • AMBER: how to incorporate ismem =1 into mm_pbsa (Mon Mar 05 2007 - 17:32:19 CST)
  • AMBER: mm_pbsa individual contributions of residues (Mon Mar 05 2007 - 17:12:54 CST)
  • Re: Re: AMBER: crd to pdb conversion (Mon Feb 19 2007 - 09:04:58 CST)
  • AMBER: crd to pdb conversion (Mon Feb 19 2007 - 07:27:34 CST)
  • AMBER: how much restraint ? (Mon Jan 22 2007 - 16:09:12 CST)
  • AMBER: mm_pbsa vertex atom mismatch (Tue Jan 16 2007 - 17:10:35 CST)
• backy
  • AMBER: ele vs van der Waals (Thu Nov 29 2007 - 03:14:19 CST)
  • AMBER: Missing BELE for MM in 1 (Mon Nov 19 2007 - 06:19:09 CST)
  • Re: AMBER: problems in adding ACE and NME group (Thu Jun 28 2007 - 01:13:02 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Wed Jun 27 2007 - 01:55:47 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Mon Jun 25 2007 - 08:21:47 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Thu Jun 21 2007 - 00:45:56 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Thu Jun 21 2007 - 00:00:12 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Wed Jun 20 2007 - 23:00:39 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Wed Jun 20 2007 - 22:54:47 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Wed Jun 20 2007 - 08:15:25 CDT)
  • AMBER: problems in adding ACE and NME group (Wed Jun 20 2007 - 04:09:26 CDT)
• bala
  • AMBER: pbsa installation problem (Mon Mar 05 2007 - 06:34:32 CST)
• Balvinder Singh
  • RE: AMBER: Building parallel Amber 9.0 (Wed Aug 15 2007 - 23:02:38 CDT)
  • RE: AMBER: Building parallel Amber 9.0 (Wed Aug 15 2007 - 22:53:44 CDT)
• Barbault Florent
  • Re: AMBER: RESP using antechamber (Sat Dec 22 2007 - 14:13:31 CST)
  • Re: AMBER: Cutoff list exceeds largest sphere in unit cell (Fri Jul 13 2007 - 13:54:36 CDT)
  • Re: AMBER: antechamber (Mon Jul 09 2007 - 09:59:03 CDT)
  • Re: AMBER: "distance" command in ptraj (Sat Jun 02 2007 - 10:28:44 CDT)
  • Re: AMBER: H-bond in ptraj (Fri Jan 05 2007 - 02:20:22 CST)
• Beale, John
  • AMBER: LEaP bond problem (Wed Nov 07 2007 - 06:57:30 CST)
  • AMBER: parallel implementation of Amber 9 (Fri Sep 14 2007 - 07:40:03 CDT)
  • AMBER: Targeted MD (Sat Sep 08 2007 - 17:29:08 CDT)
  • AMBER: antechamber question (Fri Aug 31 2007 - 09:07:56 CDT)
  • AMBER: (Thu Aug 30 2007 - 08:05:11 CDT)
  • AMBER: articles (Fri Aug 24 2007 - 08:02:05 CDT)
  • AMBER: (Mon Aug 20 2007 - 10:41:06 CDT)
  • AMBER: MPI (Fri Aug 17 2007 - 07:00:33 CDT)
  • AMBER: Building parallel Amber 9.0 (Wed Aug 15 2007 - 07:21:56 CDT)
  • AMBER: Force Field Parameters (Thu Aug 02 2007 - 11:46:16 CDT)
  • AMBER: Linux install (Tue Jul 31 2007 - 06:55:34 CDT)
  • AMBER: Dihedral driver (Thu Jun 07 2007 - 15:08:35 CDT)
  • AMBER: Complexes (Tue May 08 2007 - 13:54:34 CDT)
  • AMBER: PDB files (Mon Apr 30 2007 - 11:16:59 CDT)
  • AMBER: Antechamber (Thu Apr 19 2007 - 08:51:03 CDT)
  • AMBER: Antechamber Warning (Wed Apr 18 2007 - 14:39:31 CDT)
  • AMBER: PDBs (Tue Apr 17 2007 - 07:22:42 CDT)
  • AMBER: Charges in antechamber (Thu Apr 05 2007 - 10:46:34 CDT)
  • AMBER: Xleap errors (Mon Apr 02 2007 - 12:20:43 CDT)
  • AMBER: (Mon Mar 05 2007 - 11:51:29 CST)
  • AMBER: (Mon Mar 05 2007 - 11:50:26 CST)
  • RE: AMBER: Disulfide Problem (Thu Mar 01 2007 - 08:45:24 CST)
  • AMBER: Disulfide Problem (Thu Mar 01 2007 - 07:49:22 CST)
  • AMBER: LEaP crashes (Wed Feb 28 2007 - 10:29:16 CST)
  • RE: AMBER: Disulfide Bonds (Wed Feb 28 2007 - 07:37:48 CST)
  • AMBER: Disulfide Bonds (Wed Feb 28 2007 - 06:56:55 CST)
  • AMBER: PTRAJ problem (Mon Feb 26 2007 - 12:26:21 CST)
  • AMBER: LEaP Problem (Wed Feb 21 2007 - 07:11:13 CST)
  • AMBER: oops (Tue Feb 20 2007 - 07:35:19 CST)
  • AMBER: (Tue Feb 20 2007 - 07:02:24 CST)
  • AMBER: problems with bonding disulfide linkages (Mon Feb 19 2007 - 14:39:10 CST)
  • AMBER: carbohydrate-peptide (Mon Feb 19 2007 - 10:09:54 CST)
  • RE: AMBER: Lone Pairs (Tue Feb 13 2007 - 08:33:44 CST)
  • AMBER: Lone Pairs (Mon Feb 12 2007 - 12:52:48 CST)
  • AMBER: Calcium and peptides (Thu Feb 08 2007 - 12:20:30 CST)
  • AMBER: Glycam (Tue Feb 06 2007 - 07:07:22 CST)
• Ben Sattelle
  • Re: AMBER: junk in `Noshake mask` output section (Wed May 30 2007 - 17:05:20 CDT)
  • AMBER: junk in `Noshake mask` output section (Wed May 30 2007 - 16:23:49 CDT)
  • RE: AMBER: restraint value: written but none specified (Fri Apr 20 2007 - 18:05:47 CDT)
  • Re: AMBER: restraint value: written but none specified (Fri Apr 20 2007 - 17:08:55 CDT)
  • Re: AMBER: restraint value: written but none specified (Fri Apr 20 2007 - 16:51:30 CDT)
  • AMBER: restraint value: written but none specified (Fri Apr 20 2007 - 15:42:56 CDT)
  • AMBER: qm/mm ti (Fri Mar 02 2007 - 07:54:53 CST)
• Ben Tan
  • AMBER: Finding x-displacement (Tue May 15 2007 - 04:23:11 CDT)
  • AMBER: use of pucker function in ptraj (Thu May 10 2007 - 06:00:41 CDT)
• Benjamin Juhl
  • Re: AMBER: pmemd: same rst, different result? (Mon Dec 17 2007 - 04:25:04 CST)
  • Re: AMBER: Machine environment to install AMBER 8 (Tue Aug 14 2007 - 05:49:13 CDT)
  • Re: AMBER: Machine environment to install AMBER 8 (Tue Aug 14 2007 - 04:10:16 CDT)
  • Re: AMBER: Machine environment to install AMBER 8 (Tue Aug 14 2007 - 03:28:09 CDT)
  • Re: AMBER: how to combine two molecules (Fri Aug 10 2007 - 04:11:07 CDT)
  • Re: AMBER: Problem while creating input files in antechamber (Tue Jul 31 2007 - 02:08:35 CDT)
  • Re: AMBER: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 09:18:28 CDT)
  • Re: AMBER: Can t open PDB file in xleap (Mon Jul 16 2007 - 05:53:16 CDT)
  • Re: AMBER: program bug? (Thu Jul 12 2007 - 02:17:31 CDT)
  • Re: AMBER: xleap and amber7 (Mon Jul 09 2007 - 02:08:57 CDT)
  • Re: AMBER: amber9: running parallel error (Thu Apr 12 2007 - 03:33:48 CDT)
  • Re: AMBER: Problem while using antechamber (Tue Apr 10 2007 - 02:12:13 CDT)
  • Re: AMBER: hii (Thu Mar 15 2007 - 03:44:18 CST)
• Bertrand P. S. Russell
  • AMBER: (Mon Sep 24 2007 - 04:40:52 CDT)
• Bertrand Russell
  • Re: AMBER: Machine environment to install AMBER 8 (Wed Aug 15 2007 - 01:34:02 CDT)
  • Re: AMBER: Machine environment to install AMBER 8 (Tue Aug 14 2007 - 04:50:07 CDT)
  • Re: AMBER: Machine environment to install AMBER 8 (Tue Aug 14 2007 - 04:21:07 CDT)
  • Re: AMBER: SGI Altix Compilation Problems (Was: Error - must define AMBERHOME environment variable) (Thu Mar 29 2007 - 03:04:00 CST)
  • Re: AMBER: SGI Altix Compilation Problems (Was: Error - must define AMBERHOME environment variable) (Wed Mar 28 2007 - 00:36:17 CST)
  • Re: AMBER: Error - must define AMBERHOME environment variable (Tue Mar 27 2007 - 12:42:57 CST)
  • Re: AMBER: Error - must define AMBERHOME environment variable (Tue Mar 27 2007 - 12:39:28 CST)
  • Re: AMBER: Error - must define AMBERHOME environment variable (Mon Mar 26 2007 - 23:57:31 CST)
  • Re: AMBER: Error - must define AMBERHOME environment variable (Mon Mar 26 2007 - 11:10:12 CST)
  • Re: AMBER: Error - must define AMBERHOME environment variable (Mon Mar 26 2007 - 11:12:57 CST)
  • Re: AMBER: Error - must define AMBERHOME environment variable (Mon Mar 26 2007 - 02:56:06 CST)
  • Re: AMBER: Error - must define AMBERHOME environment variable (Mon Mar 26 2007 - 03:03:56 CST)
  • Re: AMBER: Error - must define AMBERHOME environment variable (Sat Mar 24 2007 - 14:18:55 CST)
  • AMBER: Error - must define AMBERHOME environment variable (Fri Mar 23 2007 - 14:05:47 CST)
  • Re: AMBER: phe-phe molecule (Mon Feb 26 2007 - 02:03:27 CST)
  • Re: AMBER: phe-phe molecule (Mon Feb 26 2007 - 00:08:42 CST)
  • AMBER: getting same box dimension (Sun Feb 25 2007 - 23:27:40 CST)
  • AMBER: Umbrella sampling - Tutorial (Sat Feb 10 2007 - 01:35:31 CST)
  • Re: AMBER: calculating distance between two atoms (Mon Feb 05 2007 - 06:22:16 CST)
  • AMBER: replacement of mutated atoms in protein structure (Mon Feb 05 2007 - 04:42:37 CST)
  • AMBER: calculating distance between two atoms (Fri Feb 02 2007 - 11:49:07 CST)
  • Re: AMBER: Installation help - SGI Altix 350 (Tue Jan 09 2007 - 01:17:54 CST)
• Bill Ross
  • Re: AMBER: PME and counter ions (Thu Dec 20 2007 - 16:29:37 CST)
  • Re: AMBER: PME and counter ions (Thu Dec 20 2007 - 16:25:15 CST)
  • Re: AMBER: PME and counter ions (Wed Dec 19 2007 - 14:14:19 CST)
  • Re: AMBER: PME and counter ions (Tue Dec 18 2007 - 12:36:38 CST)
  • Re: AMBER: running equilibration (Fri Dec 07 2007 - 19:11:02 CST)
  • Re: AMBER: ** No torsion terms for SNI-NI-SNI-CT (Fri Dec 07 2007 - 16:20:49 CST)
  • Re: AMBER: Problem in running CARNAL (Fri Dec 07 2007 - 11:48:15 CST)
  • Re: AMBER: Problem in running CARNAL (Thu Dec 06 2007 - 13:37:07 CST)
  • Re: AMBER: Xleap and Hydrogens (Tue Nov 27 2007 - 11:11:35 CST)
  • Re: AMBER: Puzzle with WAT (Sun Nov 18 2007 - 12:55:15 CST)
  • Re: AMBER: Puzzle with WAT (Sat Nov 17 2007 - 18:00:06 CST)
  • Re: AMBER: Improper torsion terms (Fri Nov 02 2007 - 10:41:00 CST)
  • Re: AMBER: Getting prmtop and inpcrd (Mon Oct 29 2007 - 13:26:16 CST)
  • Re: AMBER: Problems loading pdb file including Mg ions (Wed Oct 24 2007 - 12:21:43 CDT)
  • Re: AMBER: Simulation died due to lack of disk space (Fri Oct 19 2007 - 10:59:31 CDT)
  • RE: AMBER: Simulation died due to lack of disk space (Thu Oct 18 2007 - 14:00:33 CDT)
  • Re: AMBER: amber md movie using Chimera (Wed Sep 05 2007 - 16:38:32 CDT)
  • Re: AMBER: Cygwin error (Thu Aug 09 2007 - 15:42:48 CDT)
  • Re: AMBER: Cygwin error (Wed Aug 08 2007 - 17:29:24 CDT)
  • Re: AMBER: Cygwin error (Wed Aug 08 2007 - 16:43:49 CDT)
  • Re: AMBER: Problem with antechamber (Thu Aug 02 2007 - 15:14:37 CDT)
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Mon Jul 16 2007 - 18:38:26 CDT)
  • Re: SV: AMBER: Atoms in contact to a specific atoms during MD (Mon Jul 16 2007 - 14:49:45 CDT)
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Mon Jul 09 2007 - 13:48:28 CDT)
  • Re: AMBER: Saving (.)prepin file (Mon Jul 02 2007 - 16:05:53 CDT)
  • Re: AMBER: Saving a structuring from trajectory (Fri Jun 15 2007 - 15:43:23 CDT)
  • Re: AMBER: Installing on windows (Mon Jun 11 2007 - 14:14:04 CDT)
  • Re: AMBER: Installing on windows (Mon Jun 11 2007 - 14:01:06 CDT)
  • Re: AMBER: Group declaration question (Wed May 02 2007 - 14:10:23 CDT)
  • Re: AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38 (Fri Apr 27 2007 - 18:07:54 CDT)
  • Re: AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38 (Fri Apr 27 2007 - 15:41:20 CDT)
  • Re: AMBER: choice of alpha carbons vs side chains (Wed Apr 04 2007 - 18:28:34 CDT)
  • Re: AMBER: Can I measure improper torsion by ptarj? (Tue Mar 13 2007 - 11:23:24 CST)
  • Re: AMBER: extracting coordinate from crd file (Sun Feb 11 2007 - 23:13:38 CST)
  • Re: AMBER: radius of gyration (Mon Jan 29 2007 - 13:51:39 CST)
  • RE: AMBER: ADDIONS do not neutralize to ZERO (Sun Jan 28 2007 - 14:41:43 CST)
  • Re: AMBER: radius of gyration (Sun Jan 28 2007 - 14:01:05 CST)
  • Re: AMBER: coordinates ****** (Tue Jan 23 2007 - 15:20:10 CST)
  • Re: AMBER: nuc.in file (Tue Jan 23 2007 - 11:42:44 CST)
  • RE: AMBER: ADDIONS do not neutralize to ZERO (Tue Jan 23 2007 - 11:30:06 CST)
  • Re: AMBER: ADDIONS do not neutralize to ZERO (Mon Jan 22 2007 - 19:58:11 CST)
  • Re: AMBER: calcium parameter for GB (Thu Jan 18 2007 - 12:36:01 CST)
  • Re: AMBER: Drug bound to the protein (Wed Jan 17 2007 - 13:28:15 CST)
  • Re: AMBER: Leap adding 3 extra atoms (Thu Jan 11 2007 - 13:33:14 CST)
  • RE: AMBER: question about the testing of AMBER9 (Mon Jan 08 2007 - 14:05:19 CST)
  • Re: AMBER: improper torsions (Mon Jan 08 2007 - 14:00:06 CST)
  • Re: AMBER: 22 improper torsions in old prep form (Fri Jan 05 2007 - 12:39:23 CST)
  • Re: AMBER: Re:tree name generated by tleap is different from the input PREP parameter file (Tue Jan 02 2007 - 22:26:14 CST)
• Biman Jana
  • AMBER: Bulk water simulation with centre of mass position restrain (Wed Dec 05 2007 - 12:08:56 CST)
  • AMBER: Value of taup for bulk TIP5P water simulation(amber7) (Mon Nov 26 2007 - 13:25:37 CST)
  • AMBER: Pressure Variation for NPT simulation of TIP5P water (fwd) (Sat Nov 24 2007 - 07:22:39 CST)
  • AMBER: Pressure Variation for NPT simulation of TIP5P water (Thu Nov 22 2007 - 08:50:16 CST)
  • Re: AMBER: TIP5P water simulation using AMBER7 (Sun Nov 11 2007 - 08:21:56 CST)
  • AMBER: TIP5P water simulation using AMBER7 (Sat Nov 10 2007 - 08:57:20 CST)
  • AMBER: TIP5P water Simulation (Wed Nov 07 2007 - 11:12:42 CST)
  • AMBER: (no subject) (Wed Nov 07 2007 - 11:09:00 CST)
• Bing Liu
  • Re: AMBER: mm-pbsa, long distance free energy calculation problem (Thu Jan 18 2007 - 15:09:38 CST)
  • AMBER: mm-pbsa, long distance free energy calculation problem (Thu Jan 18 2007 - 11:06:53 CST)
• BJÖRN KARLSSON
  • AMBER: RDF unit cell volume (Thu Aug 30 2007 - 03:14:20 CDT)
  • AMBER: RDF of pure chloroform (Mon Jun 25 2007 - 10:56:19 CDT)
  • AMBER: Rdf question (Sun Jun 10 2007 - 14:51:16 CDT)
  • AMBER: g(r) in mixtures? (Wed Jun 06 2007 - 02:56:05 CDT)
• Bo Baker
  • RE: AMBER: Energy minimization problem (Thu Apr 05 2007 - 05:14:31 CDT)
  • RE: AMBER: Energy minimization problem (Wed Apr 04 2007 - 19:02:42 CDT)
  • AMBER: Energy minimization problem (Tue Apr 03 2007 - 20:24:05 CDT)
• bosco
  • AMBER: phosphorylation (Tue Dec 04 2007 - 19:36:27 CST)
• Boutheina Kerkeni
  • AMBER: Backbone atoms (Sat Dec 08 2007 - 16:42:20 CST)
  • AMBER: running equilibration (Fri Dec 07 2007 - 18:29:59 CST)
  • AMBER: ** No torsion terms for SNI-NI-SNI-CT (Fri Dec 07 2007 - 16:17:07 CST)
  • AMBER: ** No torsion terms for SNI-NI-SNI-CT (Fri Dec 07 2007 - 16:13:19 CST)
  • AMBER: FATAL: Atom .R<CYF 17>.A<N 1> does not have a type. (Wed Dec 05 2007 - 17:28:41 CST)
• Boutheïna Kerkeni
  • Re: AMBER: modifications to force field for Fe4S4 cubane (Wed Nov 28 2007 - 15:31:02 CST)
  • Re: AMBER: modifications to force field for Fe4S4 cubane (Wed Nov 28 2007 - 09:36:38 CST)
  • Re: AMBER: modifications to force field for Fe4S4 cubane (Tue Nov 27 2007 - 09:23:39 CST)
  • AMBER: modifications to force field for Fe4S4 cubane (Tue Nov 27 2007 - 05:26:22 CST)
  • AMBER: connecting a non standard residue to the rest of an enzyme (Fri Nov 23 2007 - 07:43:36 CST)
  • AMBER: modifications to force field for Fe4S4 cubane (Wed Nov 21 2007 - 15:41:45 CST)
• Brent Krueger
  • AMBER: ff99 vs ff99SB for RNA (Thu Jun 14 2007 - 09:05:12 CDT)
• brmeher_at_iitg.ernet.in
  • AMBER: How to calculate S2 from P2 using ptraj ? (Sat Nov 17 2007 - 00:40:31 CST)
  • AMBER: How to calculate S2 from P2 using ptraj ? (Sat Nov 17 2007 - 00:34:11 CST)
  • AMBER: protocols for high pressure simulation (Tue Aug 28 2007 - 10:23:00 CDT)
  • AMBER: conversion of Macromodel substructure format to .frcmod file (Thu Jun 28 2007 - 05:24:24 CDT)
  • AMBER: Antechamber--Boron Parameters (Mon Jun 25 2007 - 05:04:30 CDT)
  • AMBER: TI calculation: charge is not zero in the perturbed state (Sat Mar 03 2007 - 14:32:02 CST)
• Brooke Elizabeth Adams
  • Re: AMBER: frcmod (Mon Jun 18 2007 - 15:02:13 CDT)
  • Re: AMBER: frcmod (Mon Jun 18 2007 - 14:06:34 CDT)
  • Re: AMBER: frcmod (Fri Jun 15 2007 - 14:11:00 CDT)
  • AMBER: frcmod (Tue Jun 12 2007 - 15:38:50 CDT)
• Campbell, Patrick
  • AMBER: New 2 the board (Wed Dec 12 2007 - 15:12:30 CST)
  • AMBER: Would amber work with Linspire 6.0? (Tue Nov 27 2007 - 17:01:02 CST)
• caoch
  • AMBER: How to get sane package (Tue Oct 02 2007 - 05:09:26 CDT)
• caoch_at_cherry.bio.titech.ac.jp
  • AMBER: AMBER citation questions (Thu Jan 04 2007 - 02:59:08 CST)
• Carlos Javier Nuñez Aguero
  • AMBER: equilibration with amber5, production of MD with amber7 (Fri Jan 19 2007 - 14:47:05 CST)
• Carlos P. Sosa
  • Re: AMBER: Blue Gene, compile Amber9? (Fri Apr 06 2007 - 13:55:28 CDT)
• Carlos Simmerling
  • Re: AMBER: MMTSB Toolset (Mon Dec 17 2007 - 06:26:27 CST)
  • Re: AMBER: replica exchange out files continually overwritten (Fri Dec 14 2007 - 15:11:37 CST)
  • Re: AMBER: replica exchange out files continually overwritten (Fri Dec 14 2007 - 12:58:36 CST)
  • Re: AMBER: Re: Calculating Energies with imin=5 (Fri Nov 30 2007 - 06:32:04 CST)
  • Re: AMBER: Extra-term to the Energy function !! (Tue Nov 27 2007 - 05:12:13 CST)
  • Re: AMBER: umbrella sampling (Sun Nov 25 2007 - 13:52:57 CST)
  • Re: AMBER: Hello (Sat Nov 24 2007 - 12:55:46 CST)
  • Re: AMBER: Hello (Fri Nov 23 2007 - 21:01:13 CST)
  • Re: AMBER: RE: FF94 or FF99? (Thu Nov 22 2007 - 18:13:16 CST)
  • Re: AMBER:How to calculate the free energy of a series of conformations (Wed Nov 21 2007 - 17:04:03 CST)
  • Re: AMBER: EXCEEDED MAXLESADJ in sander.LES.MPI (amber9) (Sat Nov 17 2007 - 15:51:09 CST)
  • Re: AMBER: Parallel scaling (Tue Nov 13 2007 - 05:07:53 CST)
  • Re: AMBER: TIP5P water simulation using AMBER7 (Sun Nov 11 2007 - 08:25:50 CST)
  • Re: AMBER: TIP5P water simulation using AMBER7 (Sat Nov 10 2007 - 09:00:36 CST)
  • Re: AMBER: Can a simulation run on AMBER 9 be compared with another from AMBER 8? (Tue Nov 06 2007 - 05:49:13 CST)
  • Re: Re: AMBER: AMBER 9 - Force Field Options - Question (Mon Nov 05 2007 - 11:39:01 CST)
  • Re: AMBER: Getting prmtop and inpcrd (Mon Oct 29 2007 - 09:47:33 CST)
  • Re: AMBER: replica exchange (Sun Oct 28 2007 - 10:38:15 CST)
  • Re: AMBER: HG atoms in CYX residues (Fri Oct 26 2007 - 05:20:05 CDT)
  • Re: AMBER: AMBER 9 - Force Field Options - Question (Thu Oct 18 2007 - 05:06:44 CDT)
  • Re: AMBER: error while Running TMD (Thu Oct 18 2007 - 05:01:07 CDT)
  • Re: AMBER: error while Running TMD (Wed Oct 17 2007 - 13:50:45 CDT)
  • Re: AMBER: AMBER 9 - Force Field Options - Question (Wed Oct 17 2007 - 08:54:51 CDT)
  • Re: AMBER: constant-pH MD with replica exchange (Thu Oct 11 2007 - 13:30:34 CDT)
  • Re: AMBER: ff99SB and the N- and C- charged terminal residues (Wed Oct 10 2007 - 12:37:13 CDT)
  • Re: AMBER: neb for path between binding sites (Tue Oct 09 2007 - 16:25:27 CDT)
  • Re: AMBER: request for hardware recommendations (Sat Oct 06 2007 - 12:00:13 CDT)
  • Re: AMBER: multi chain simulations (Thu Oct 04 2007 - 14:43:44 CDT)
  • Re: AMBER: multi chain simulations (Thu Oct 04 2007 - 06:28:46 CDT)
  • Re: AMBER: multi chain simulations (Thu Oct 04 2007 - 05:35:22 CDT)
  • Re: AMBER: 31 integers in the first section of a prmtop file (Wed Oct 03 2007 - 13:54:22 CDT)
  • Re: AMBER: 31 integers in the first section of a prmtop file (Wed Oct 03 2007 - 12:15:14 CDT)
  • Re: AMBER: dihedrals (Tue Oct 02 2007 - 05:13:12 CDT)
  • Re: AMBER: fragment parametrization tutorial? (Sat Sep 29 2007 - 16:48:30 CDT)
  • Re: AMBER: restarting REMD simulations (Thu Sep 27 2007 - 11:48:45 CDT)
  • Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! (Wed Sep 26 2007 - 10:44:29 CDT)
  • Re: AMBER: Minimization and MD input files (Tue Sep 25 2007 - 17:08:20 CDT)
  • Re: AMBER: Minimization and MD input files (Tue Sep 25 2007 - 16:27:49 CDT)
  • Re: AMBER: Minimization and MD input files (Tue Sep 25 2007 - 15:34:14 CDT)
  • Re: AMBER: Minimization and MD input files (Tue Sep 25 2007 - 13:30:17 CDT)
  • Re: AMBER: problem with ptraj (Mon Sep 24 2007 - 19:45:44 CDT)
  • Re: AMBER: about MD outputs (Sun Sep 23 2007 - 07:31:06 CDT)
  • Re: AMBER: about MD outputs (Sun Sep 23 2007 - 07:09:03 CDT)
  • Re: AMBER: TMD and "Current RMSD from reference" (Sun Sep 23 2007 - 06:32:47 CDT)
  • Re: AMBER: TMD and "Current RMSD from reference" (Sat Sep 22 2007 - 17:40:08 CDT)
  • Re: AMBER: about restraining atoms (Sat Sep 22 2007 - 08:32:52 CDT)
  • Re: AMBER: TMD and "Current RMSD from reference" (Sat Sep 22 2007 - 08:27:45 CDT)
  • Re: AMBER: Targetted MD and ptraj analysis (Fri Sep 21 2007 - 07:12:50 CDT)
  • Re: AMBER: Explicit water in implicit enviornment? (Mon Sep 17 2007 - 10:35:58 CDT)
  • Re: AMBER: replica exchange simulation (Mon Sep 17 2007 - 09:04:46 CDT)
  • Re: AMBER: Torsion terms in xleap (Fri Sep 14 2007 - 17:42:52 CDT)
  • Re: AMBER: DNA base planarity restraint (Fri Sep 14 2007 - 14:43:03 CDT)
  • Re: AMBER: xleap question (Fri Sep 14 2007 - 11:32:20 CDT)
  • Re: AMBER: xleap question (Fri Sep 14 2007 - 11:32:20 CDT)
  • Re: AMBER: DNA base planarity restraint (Fri Sep 14 2007 - 11:00:22 CDT)
  • Re: AMBER: Problem with Sander (Thu Sep 13 2007 - 18:38:06 CDT)
  • Re: AMBER: PBradii (Tue Sep 11 2007 - 14:06:32 CDT)
  • Re: AMBER: Harmonic constraints (Mon Sep 10 2007 - 09:14:54 CDT)
  • Re: AMBER: Harmonic constraints (Mon Sep 10 2007 - 09:14:27 CDT)
  • Re: AMBER: Harmonic constraints (Fri Sep 07 2007 - 14:06:35 CDT)
  • Re: AMBER: Harmonic constraints (Fri Sep 07 2007 - 12:22:08 CDT)
  • Re: AMBER: Harmonic constraints (Fri Sep 07 2007 - 10:31:46 CDT)
  • Re: AMBER: chiral surfaces (Wed Sep 05 2007 - 19:21:51 CDT)
  • Re: AMBER: Running mpirun -np 1 on different processors (Tue Sep 04 2007 - 08:47:27 CDT)
  • Re: AMBER: ntt parameter in vacuum (Mon Sep 03 2007 - 08:53:16 CDT)
  • Re: AMBER: Using ntr=1 in xleap (Fri Aug 31 2007 - 16:49:14 CDT)
  • Re: AMBER: Measuring Bond Angle over simulation (Fri Aug 31 2007 - 14:34:13 CDT)
  • Re: AMBER: Confusion about Langevin dymamics (Fri Aug 31 2007 - 08:52:02 CDT)
  • Re: AMBER: Distance restraints between center of mass of two molecules (Wed Aug 15 2007 - 16:17:33 CDT)
  • Re: AMBER: Distance restraints between center of mass of two molecules (Wed Aug 15 2007 - 10:52:27 CDT)
  • Re: AMBER: Distance restraints between center of mass of two molecules (Wed Aug 15 2007 - 09:54:40 CDT)
  • Re: AMBER: torsional restraints in a solvated MD simulation. (Tue Aug 14 2007 - 15:41:52 CDT)
  • Re: AMBER: regarding implicit simulation (Tue Aug 14 2007 - 06:22:24 CDT)
  • Re: AMBER: imin=5 and inptraj (Sat Aug 11 2007 - 16:23:29 CDT)
  • Re: AMBER: How to couple only one residue to the temperature bath? (Fri Aug 10 2007 - 17:43:29 CDT)
  • Re: AMBER: How to couple only one residue to the temperature bath? (Fri Aug 10 2007 - 10:55:02 CDT)
  • Re: AMBER: Implicit solvent simulation is too slow. (Fri Aug 10 2007 - 08:07:50 CDT)
  • Re: AMBER: Problem while carrying out minimisation of drug molecule using sander (Tue Aug 07 2007 - 05:57:53 CDT)
  • Re: AMBER: Integrating the alpha-helix bias correction into ff94 (Mon Aug 06 2007 - 14:42:17 CDT)
  • Re: AMBER: (no subject) (Sat Aug 04 2007 - 05:55:29 CDT)
  • Re: AMBER: Problem with Antechamber and point charges (Fri Aug 03 2007 - 14:55:43 CDT)
  • Re: AMBER: planarity restraints for NA (Thu Aug 02 2007 - 09:17:32 CDT)
  • Re: AMBER: planarity restraints for NA (Thu Aug 02 2007 - 08:17:56 CDT)
  • Re: AMBER: (no subject) (Thu Aug 02 2007 - 07:48:36 CDT)
  • Re: AMBER: neutral terminals (Thu Aug 02 2007 - 07:04:15 CDT)
  • Re: AMBER: Problem with Antechamber and point charges (Wed Aug 01 2007 - 14:52:53 CDT)
  • Re: AMBER: about wrap the trajectory (Fri Jul 27 2007 - 11:10:49 CDT)
  • Re: AMBER: about wrap the trajectory (Fri Jul 27 2007 - 09:44:53 CDT)
  • Re: AMBER: about wrap the trajectory (Fri Jul 27 2007 - 09:23:30 CDT)
  • Re: AMBER: about wrap the trajectory (Fri Jul 27 2007 - 06:29:48 CDT)
  • Re: AMBER: about wrap the trajectory (Thu Jul 26 2007 - 11:28:33 CDT)
  • Re: AMBER: MD simulation error (Wed Jul 25 2007 - 12:41:42 CDT)
  • Re: AMBER: not getting topology and restraint file (Wed Jul 25 2007 - 05:16:02 CDT)
  • Re: AMBER: not getting topology and restraint file (Tue Jul 24 2007 - 09:46:49 CDT)
  • Re: AMBER: DNA denatures during MD simulation (Mon Jul 23 2007 - 14:44:35 CDT)
  • Re: AMBER: regarding distance restraints (Mon Jul 23 2007 - 06:26:27 CDT)
  • Re: AMBER: offending restraint (Sun Jul 22 2007 - 06:32:51 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 09:34:35 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 08:57:13 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 07:34:03 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 06:44:36 CDT)
  • Re: AMBER: secstruct command (Thu Jul 19 2007 - 12:46:30 CDT)
  • Re: AMBER: Error during compilation on a SGI Irix machine (Wed Jul 18 2007 - 11:57:27 CDT)
  • Re: AMBER: potential energy calculation (Mon Jul 16 2007 - 20:34:01 CDT)
  • Re: AMBER: convergence in classical MD (Mon Jul 16 2007 - 06:37:09 CDT)
  • Re: AMBER: MPI script (Fri Jul 13 2007 - 17:15:36 CDT)
  • Re: AMBER: related to new amber force field (Fri Jul 13 2007 - 11:33:12 CDT)
  • Re: AMBER: Multiple residues position (Fri Jul 13 2007 - 11:20:19 CDT)
  • Re: AMBER: program bug? (Thu Jul 12 2007 - 10:32:54 CDT)
  • Re: AMBER: question about iwrap (Thu Jul 12 2007 - 08:28:29 CDT)
  • Re: AMBER: question about iwrap (Thu Jul 12 2007 - 06:34:08 CDT)
  • Re: AMBER: MPI Quiescence problem in REMD (Wed Jul 11 2007 - 12:08:23 CDT)
  • Re: AMBER: MPI Quiescence problem in REMD (Wed Jul 11 2007 - 04:28:56 CDT)
  • Re: AMBER: extract protein energy from MD trajectory (Wed Jul 11 2007 - 03:34:31 CDT)
  • Re: AMBER: extract protein energy from MD trajectory (Tue Jul 10 2007 - 17:08:32 CDT)
  • Re: AMBER: surface area over the trajectory (Tue Jul 10 2007 - 14:09:51 CDT)
  • Re: AMBER: tgtrmsmask and tgtfitmask (Tue Jul 10 2007 - 06:26:08 CDT)
  • Re: AMBER: surface area over the trajectory (Tue Jul 10 2007 - 05:33:44 CDT)
  • Re: AMBER: surface area over the trajectory (Mon Jul 09 2007 - 17:30:54 CDT)
  • Re: AMBER: Problem with running Sander (Sun Jul 08 2007 - 06:28:58 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 11:45:43 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 08:14:20 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 07:35:33 CDT)
  • Re: AMBER: Nudget Elastic Band query (Thu Jul 05 2007 - 14:08:31 CDT)
  • Re: AMBER: Nudget Elastic Band query (Thu Jul 05 2007 - 12:53:53 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 11:45:14 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 11:04:12 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 10:25:42 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 09:36:05 CDT)
  • Re: AMBER: Convergence criteria in replica exchange simulations (Thu Jul 05 2007 - 07:26:26 CDT)
  • Re: AMBER: xleap and amber7 (Thu Jul 05 2007 - 07:23:44 CDT)
  • Re: AMBER: testing amber9 for parallel use (Thu Jul 05 2007 - 07:22:20 CDT)
  • Re: AMBER: Simulated annealing - Nudget Elastic Band (Wed Jul 04 2007 - 05:39:10 CDT)
  • Re: AMBER: About amber7 (Tue Jul 03 2007 - 08:57:14 CDT)
  • Re: AMBER: Sander Error (Fri Jun 29 2007 - 21:04:29 CDT)
  • Re: AMBER: radius of gyration (Fri Jun 29 2007 - 06:54:28 CDT)
  • Re: AMBER: bugfix.all (Wed Jun 27 2007 - 15:52:15 CDT)
  • Re: AMBER: rst overflow for implicit REMD (Tue Jun 26 2007 - 10:35:47 CDT)
  • Re: AMBER: Offending restraints???? (Tue Jun 26 2007 - 10:33:47 CDT)
  • Re: AMBER: Offending restraints???? (Tue Jun 26 2007 - 08:59:24 CDT)
  • Re: AMBER: Simulated Annealing (Tue Jun 26 2007 - 06:16:25 CDT)
  • Re: AMBER: Re: ff02 and ff03 parameters (Mon Jun 25 2007 - 18:28:02 CDT)
  • Re: AMBER: remd/rdc's (Sat Jun 23 2007 - 07:43:21 CDT)
  • Re: AMBER: radius of gyration (Fri Jun 22 2007 - 10:40:27 CDT)
  • Re: AMBER: radius of gyration (Fri Jun 22 2007 - 10:14:19 CDT)
  • Re: AMBER: testing protein stability (Fri Jun 22 2007 - 06:06:16 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Wed Jun 20 2007 - 23:28:30 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Wed Jun 20 2007 - 10:37:45 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Wed Jun 20 2007 - 06:28:46 CDT)
  • Re: AMBER: H bond (Tue Jun 19 2007 - 06:24:27 CDT)
  • Re: AMBER: shell model MD (Mon Jun 18 2007 - 11:53:56 CDT)
  • Re: AMBER: problem with running rem on amber9 (NOT A REMD PROBLEM) (Mon Jun 18 2007 - 10:31:19 CDT)
  • Re: AMBER: problem with running rem on amber9 (Mon Jun 18 2007 - 10:10:37 CDT)
  • Re: AMBER: problem with running rem on amber9 (Mon Jun 18 2007 - 07:46:29 CDT)
  • Re: AMBER: implementation of GB model in AMBER (Sun Jun 17 2007 - 07:58:11 CDT)
  • Re: AMBER: performance with implicit solvent (Fri Jun 15 2007 - 15:17:28 CDT)
  • Re: AMBER: ff99 vs ff99SB for RNA (Thu Jun 14 2007 - 11:03:03 CDT)
  • Re: AMBER: ff99 vs ff99SB for RNA (Thu Jun 14 2007 - 09:57:02 CDT)
  • Re: AMBER: NMR vs. X-ray structures (Tue Jun 12 2007 - 05:57:12 CDT)
  • Re: AMBER: Installing on windows (Sun Jun 10 2007 - 18:54:04 CDT)
  • Re: AMBER: problem installing amber7 (Sun Jun 10 2007 - 10:23:10 CDT)
  • Re: AMBER: (Fri Jun 08 2007 - 13:47:43 CDT)
  • Re: AMBER: Potential of mean force. (Fri Jun 08 2007 - 07:08:06 CDT)
  • Re: AMBER: extracting starting structures from equilibration trajectory (Thu Jun 07 2007 - 14:41:36 CDT)
  • Re: AMBER: problem with starting REM on amber9 (Tue Jun 05 2007 - 08:42:29 CDT)
  • Re: AMBER: LES problem (Tue Jun 05 2007 - 07:14:15 CDT)
  • Re: AMBER: Problem about prepare the model when running antechamber (Mon Jun 04 2007 - 15:52:23 CDT)
  • Re: AMBER: Installation Question (Mon Jun 04 2007 - 09:16:30 CDT)
  • Re: AMBER: Once again, "distance" command in ptraj (Mon Jun 04 2007 - 09:15:22 CDT)
  • Re: AMBER: "distance" command in ptraj (Sat Jun 02 2007 - 06:56:15 CDT)
  • Re: AMBER: cutoff & speed-up of GBSA (Thu May 31 2007 - 15:30:00 CDT)
  • Re: AMBER: LES (Thu May 31 2007 - 08:35:57 CDT)
  • Re: AMBER: LES (Thu May 31 2007 - 08:17:02 CDT)
  • Re: AMBER: cutoff & speed-up of GBSA (Wed May 30 2007 - 16:59:41 CDT)
  • Re: AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8 (Wed May 30 2007 - 12:50:05 CDT)
  • Re: AMBER: error in running sander (Tue May 29 2007 - 17:06:29 CDT)
  • Re: AMBER: Hydration points (Tue May 29 2007 - 16:34:54 CDT)
  • Re: AMBER: error in running sander (Tue May 29 2007 - 16:33:42 CDT)
  • Re: AMBER: error in running sander (Tue May 29 2007 - 15:47:24 CDT)
  • Re: AMBER: Les analyse (Tue May 29 2007 - 06:16:22 CDT)
  • Re: AMBER: water count (Mon May 28 2007 - 07:20:30 CDT)
  • Re: AMBER: Less error (Fri May 25 2007 - 05:42:48 CDT)
  • Re: AMBER: rfree: Error input file (Thu May 24 2007 - 13:56:51 CDT)
  • Re: AMBER: REMD error (Thu May 24 2007 - 12:23:02 CDT)
  • Re: AMBER: REMD error (Thu May 24 2007 - 10:41:04 CDT)
  • Re: AMBER: REMD error (Tue May 22 2007 - 16:15:43 CDT)
  • Re: AMBER: Simulated Annealing - Start with Poor Structure (Tue May 22 2007 - 16:08:28 CDT)
  • Re: AMBER: REMD error (Mon May 21 2007 - 10:41:53 CDT)
  • Re: Re :Re: AMBER: multiple excecution of sander (Mon May 21 2007 - 09:12:59 CDT)
  • Re: AMBER: deeper problem with the energetics (Mon May 21 2007 - 09:11:58 CDT)
  • Re: AMBER: multiple excecution of sander (Thu May 17 2007 - 11:03:23 CDT)
  • Re: AMBER: deeper problem with the energetics (Thu May 17 2007 - 08:56:43 CDT)
  • Re: AMBER: MM-PBSA calculation with GB dynamic (Wed May 16 2007 - 09:03:01 CDT)
  • Re: AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set" (Wed May 16 2007 - 08:29:35 CDT)
  • Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj (Wed May 16 2007 - 06:11:15 CDT)
  • Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj (Wed May 16 2007 - 06:09:01 CDT)
  • Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj (Tue May 15 2007 - 14:55:54 CDT)
  • Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj (Tue May 15 2007 - 13:11:57 CDT)
  • Re: AMBER: bug in reprocessing with PB? (Thu May 10 2007 - 13:14:08 CDT)
  • Re: AMBER: hybrid remd (Thu May 10 2007 - 08:39:43 CDT)
  • Re: AMBER: hybrid remd (Thu May 10 2007 - 06:20:14 CDT)
  • Re: AMBER: hybrid remd (Wed May 09 2007 - 16:18:05 CDT)
  • Re: AMBER: hybrid remd (Wed May 09 2007 - 15:52:03 CDT)
  • Re: AMBER: PMF define dehedral angel and distance restrainst for center of mass of domains. (Tue May 08 2007 - 06:11:42 CDT)
  • Re: AMBER: Keq computations (Mon May 07 2007 - 17:43:53 CDT)
  • Re: AMBER:a question about RMSD (Tue Apr 24 2007 - 08:06:40 CDT)
  • Re: AMBER: amber equation of ff99 (Tue Apr 24 2007 - 11:18:57 CDT)
  • Re: AMBER: problem regarding implicit simulation (Tue Apr 24 2007 - 06:25:31 CDT)
  • Re: AMBER: problem regarding implicit simulation (Mon Apr 23 2007 - 06:30:34 CDT)
  • Re: AMBER: Prblm rgrdng Simulated Annealing (Wed Apr 11 2007 - 06:39:30 CDT)
  • Re: AMBER: Prblm rgrdng Simulated Annealing (Wed Apr 11 2007 - 06:23:43 CDT)
  • Re: AMBER: sander (AMBER 9) and -y flag -- not working? (Tue Apr 10 2007 - 14:10:41 CDT)
  • Re: AMBER: Constant volume simulations (Tue Apr 10 2007 - 10:35:14 CDT)
  • Re: AMBER: RE: dihedral term charge dependence (Mon Apr 02 2007 - 11:14:15 CDT)
  • Re: AMBER: phe-phe simulation (Tue Mar 27 2007 - 08:23:15 CST)
  • Re: AMBER: Parameter file for Dipeptide (Tue Mar 27 2007 - 08:20:55 CST)
  • Re: AMBER: restraint in minimization (Mon Mar 26 2007 - 06:19:13 CST)
  • Re: AMBER: phe-phe simulation (Mon Mar 26 2007 - 06:20:52 CST)
  • Re: AMBER: ntt=1 or ntt= 3? (Thu Mar 22 2007 - 15:47:26 CST)
  • Re: AMBER: ntt=1 or ntt= 3? (Thu Mar 22 2007 - 15:30:05 CST)
  • Re: AMBER: restraint in minimization (Thu Mar 22 2007 - 05:14:22 CST)
  • Re: AMBER: ntt=1 or ntt= 3? (Wed Mar 21 2007 - 11:40:20 CST)
  • Re: AMBER: How to reimage the trajectories of LES calculations? (Wed Mar 21 2007 - 11:04:03 CST)
  • Re: AMBER: MMPBSA with water molecule in active site (Sun Mar 18 2007 - 12:07:14 CST)
  • Re: AMBER: MMPBSA with water molecule in active site (Sun Mar 18 2007 - 11:43:44 CST)
  • Re: AMBER: targeted MD problem (Sat Mar 17 2007 - 06:27:28 CST)
  • Re: AMBER: hi (Fri Mar 16 2007 - 05:14:15 CST)
  • Re: AMBER: solvate shell (Thu Mar 15 2007 - 10:36:52 CST)
  • Re: AMBER: Problem related simulation of dimer (Thu Mar 15 2007 - 05:38:57 CST)
  • Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) (Wed Mar 14 2007 - 19:47:23 CST)
  • Re: AMBER: torsion angle (Wed Mar 14 2007 - 06:27:02 CST)
  • Re: AMBER: hi.. (Tue Mar 13 2007 - 06:20:40 CST)
  • Re: AMBER: hi.. (Tue Mar 13 2007 - 06:08:47 CST)
  • Re: AMBER: The parallel test fails while sander.MPI seems to be installed correctly (Mon Mar 12 2007 - 05:51:38 CST)
  • Re: AMBER: addles (Mon Mar 12 2007 - 05:28:20 CST)
  • Re: AMBER: rmsd calculation in ptraj (Sat Mar 10 2007 - 08:26:34 CST)
  • Re: AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat? (Fri Mar 09 2007 - 06:07:48 CST)
  • Re: AMBER: Amber 9, sander imin = 5, -y flag (Wed Mar 07 2007 - 13:15:22 CST)
  • Re: AMBER: psi , phi angles (Mon Mar 05 2007 - 12:56:46 CST)
  • Re: AMBER: psi , phi angles (Mon Mar 05 2007 - 11:39:40 CST)
  • Re: AMBER: psi , phi angles (Mon Mar 05 2007 - 06:08:27 CST)
  • Re: AMBER: coordinate changes using ptraj (Sun Mar 04 2007 - 08:19:33 CST)
  • Re: AMBER: coordinate changes using ptraj (Sat Mar 03 2007 - 18:44:00 CST)
  • Re: AMBER: calculate RMSD of only chain C (Sat Mar 03 2007 - 08:51:34 CST)
  • Re: AMBER: reproducibility between software (Fri Mar 02 2007 - 10:43:04 CST)
  • Re: AMBER: restraints during MD (Fri Mar 02 2007 - 10:27:50 CST)
  • Re: AMBER: Restart Files (Fri Mar 02 2007 - 09:32:46 CST)
  • Re: AMBER: Disulfide Problem (Fri Mar 02 2007 - 08:54:42 CST)
  • Re: AMBER: solvent accessible surface area (SASA) (Fri Mar 02 2007 - 06:14:20 CST)
  • Re: AMBER: solvent accessible surface area (SASA) (Thu Mar 01 2007 - 16:42:31 CST)
  • Re: AMBER: solvent accessible surface area (SASA) (Thu Mar 01 2007 - 10:07:51 CST)
  • Re: AMBER: Disulfide Problem (Thu Mar 01 2007 - 08:15:22 CST)
  • Re: AMBER: solvent accessible surface area (SASA) (Thu Mar 01 2007 - 06:10:55 CST)
  • Re: AMBER: solvent accessible surface area (SASA) (Wed Feb 28 2007 - 16:50:20 CST)
  • Re: AMBER: abnormal high temperature during NPT ensembles MD (Tue Feb 27 2007 - 20:36:01 CST)
  • Re: AMBER: Error in running Replica Exchange MD with amber9 (Sat Feb 24 2007 - 14:27:01 CST)
  • Re: AMBER: Error in running Replica Exchange MD with amber9 (Fri Feb 23 2007 - 09:16:59 CST)
  • Re: AMBER: Sander slower on 16 processors than 8 (Thu Feb 22 2007 - 15:19:18 CST)
  • Re: AMBER: Error in running replica exchange MD (Tue Feb 20 2007 - 08:26:24 CST)
  • Re: AMBER: Error in running replica exchange MD (Tue Feb 20 2007 - 08:17:56 CST)
  • Re: AMBER: problems with bonding disulfide linkages (Mon Feb 19 2007 - 14:45:28 CST)
  • Re: AMBER: MDGRAPE and AMBER (Mon Feb 19 2007 - 08:23:58 CST)
  • Re: AMBER: REMD error on first exchange (Mon Feb 19 2007 - 08:21:16 CST)
  • Re: AMBER: question about ADDLES module (Fri Feb 16 2007 - 19:48:27 CST)
  • Re: AMBER: Torsion Restraint on Glycosidic Bond (Fri Feb 16 2007 - 15:32:44 CST)
  • Re: AMBER: How to modify the velocity of a water molecule? (Thu Feb 15 2007 - 20:58:54 CST)
  • Re: AMBER: Simulating a section of a molecule (Thu Feb 15 2007 - 12:06:50 CST)
  • Re: AMBER: Best Force field for protein, DNA, and organic compounds? (Wed Feb 14 2007 - 08:08:17 CST)
  • Re: AMBER: Best Force field for protein, DNA, and organic compounds? (Wed Feb 14 2007 - 06:28:05 CST)
  • Re: AMBER: How precise is a MD simulation? Which strcutures should be reported? (Wed Feb 14 2007 - 06:25:02 CST)
  • Re: AMBER: Help: 1 ns for implicit solvent (GB) calculations, enough? (Wed Feb 14 2007 - 06:26:31 CST)
  • Re: AMBER: antechamber for topology file (Wed Feb 07 2007 - 06:32:52 CST)
  • Re: AMBER: problem in xleap (Tue Feb 06 2007 - 17:46:29 CST)
  • Re: AMBER: force fields (Tue Feb 06 2007 - 06:50:42 CST)
  • Re: AMBER: equilibration in explicit solvent (Mon Feb 05 2007 - 12:35:30 CST)
  • Re: AMBER: calculating distance between two atoms (Mon Feb 05 2007 - 06:55:19 CST)
  • Re: AMBER: force fields (Mon Feb 05 2007 - 06:49:29 CST)
  • Re: AMBER: angle command in Ptraj (Sat Feb 03 2007 - 07:17:26 CST)
  • Re: AMBER: calculating distance between two atoms (Fri Feb 02 2007 - 15:42:41 CST)
  • Re: AMBER: nonpolar solvation energy (Wed Jan 31 2007 - 13:54:14 CST)
  • Re: AMBER: Gas-phase energies (and more) (Sun Jan 28 2007 - 12:48:13 CST)
  • Re: AMBER: error when compiling Moilview (Thu Jan 25 2007 - 11:34:26 CST)
  • Re: AMBER: error when compiling Moilview (Thu Jan 25 2007 - 06:24:53 CST)
  • Re: AMBER: Molecular dynamic issues (Tue Jan 23 2007 - 08:54:24 CST)
  • Re: AMBER: issues with restrt file (Thu Jan 18 2007 - 12:30:01 CST)
  • Re: AMBER: issues with restrt file (Thu Jan 18 2007 - 12:02:48 CST)
  • Re: AMBER: issues with restrt file (Thu Jan 18 2007 - 11:07:35 CST)
  • Re: AMBER: error when using sander.LES: exceeded MAXLES (Thu Jan 18 2007 - 11:03:08 CST)
  • Re: AMBER: sanger (Thu Jan 18 2007 - 08:09:31 CST)
  • Re: AMBER: Simulations with GB models (Thu Jan 11 2007 - 12:28:16 CST)
  • Re: AMBER: explicit implicit solvent (Wed Jan 10 2007 - 08:53:53 CST)
  • Re: AMBER: Simulation of a charged system (Fri Jan 05 2007 - 17:41:02 CST)
  • Re: AMBER: The unperturbed charge of the unit: -20.999999 is not zero. (Thu Jan 04 2007 - 13:31:29 CST)
  • Re: AMBER: AMBER citation questions (Thu Jan 04 2007 - 05:36:28 CST)
• Carra, Claudio (JSC-SK)[USRA]
  • AMBER: unres (Mon Jun 18 2007 - 15:55:20 CDT)
• Catein Catherine
  • RE: AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ? (Sun Nov 04 2007 - 23:20:48 CST)
  • AMBER: Question about ptraj matrix correl command (Wed Oct 31 2007 - 01:18:55 CST)
  • AMBER: How to calculate the time-dependent transmission coefficient for rate constant esimation from PMF ca (Fri Oct 26 2007 - 02:28:57 CDT)
  • AMBER: Average absolute value of cross velocity (Rate constant from PMF) (Fri Oct 26 2007 - 02:26:58 CDT)
  • RE: AMBER: Polarizable Force Field: Ligand Parameterization et al. (Fri Oct 26 2007 - 02:17:16 CDT)
  • AMBER: An enquiry about "Dynamics of ligand escape from the heme pocket of myoglobin (JACS, 1988, 110, 7690 (Wed Oct 24 2007 - 07:04:42 CDT)
  • AMBER: How to intergrate the area under a curve. (Mon Oct 22 2007 - 01:34:16 CDT)
  • RE: AMBER: Targetted MD and ptraj analysis (Thu Sep 20 2007 - 21:11:30 CDT)
  • AMBER: GBSA or PBSA: GPB or GGB are +ve or -ve? (Tue Sep 18 2007 - 02:46:06 CDT)
  • AMBER: Potential of mean force: how to extract the min structure? (Tue Sep 18 2007 - 02:39:12 CDT)
  • RE: AMBER: decomposition energy (Wed Sep 05 2007 - 05:42:42 CDT)
  • AMBER: GBSA: NMODE ERROR (Wed Sep 05 2007 - 05:49:32 CDT)
  • AMBER: PMF calculation - minimum conformer (Wed Sep 05 2007 - 05:48:04 CDT)
  • AMBER: (Tue Sep 04 2007 - 00:56:20 CDT)
  • AMBER: spring constant for restraint (Thu Jun 14 2007 - 04:29:17 CDT)
  • AMBER: (no subject) (Thu Jun 14 2007 - 00:54:28 CDT)
  • AMBER: Input files for the Potential of mean force. (Sun Jun 10 2007 - 21:43:12 CDT)
  • AMBER: Potential of mean force. (Fri Jun 08 2007 - 07:01:42 CDT)
  • AMBER: Should we just vary one parameter at a time only for PMF calculations? (Thu Jun 07 2007 - 10:18:51 CDT)
  • AMBER: How to fix two angle but do umberlla sampling for distance? (Thu Jun 07 2007 - 10:14:30 CDT)
  • AMBER: (no subject) (Wed May 30 2007 - 10:16:19 CDT)
  • AMBER: Umbrella Sampling for the twist angle of a DNA base pairs (Wed May 30 2007 - 10:11:36 CDT)
  • AMBER: Umbrella Sampling for the twist angle of a DNA base pairs (Wed May 30 2007 - 03:33:18 CDT)
  • AMBER: Antechamber (Sun May 27 2007 - 19:45:42 CDT)
  • Re: AMBER: hbond ptraj pls help. (Wed May 23 2007 - 05:17:27 CDT)
  • AMBER: MM/GBSA error message (Wed May 23 2007 - 00:09:51 CDT)
  • AMBER: (no subject) (Wed May 23 2007 - 00:00:36 CDT)
  • AMBER: hbond ptraj pls help. (Tue May 22 2007 - 23:56:50 CDT)
  • Re: AMBER: hbond ptraj (Thu May 17 2007 - 01:33:31 CDT)
  • AMBER: hbond ptraj (Wed May 16 2007 - 22:39:02 CDT)
  • AMBER: PMF: WHAM result (Fri May 11 2007 - 22:28:30 CDT)
  • AMBER: PMF along 1D axis or every axis (Fri May 11 2007 - 22:05:57 CDT)
  • AMBER: PMF for DG calculation. (Fri May 11 2007 - 21:45:30 CDT)
  • AMBER: distance.restraint for two groups of atoms (center of mass) (Fri May 11 2007 - 21:30:36 CDT)
  • AMBER: umbrella sampling: distance restraint (Thu May 10 2007 - 05:25:46 CDT)
  • AMBER: PMF define dehedral angel and distance restrainst for center of mass of domains. (Tue May 08 2007 - 01:28:14 CDT)
  • Re: AMBER: Rate of Dissociation (Fri May 04 2007 - 21:10:02 CDT)
  • Re: AMBER: Potential of mean force, how to calculate rate of dissociation? (Fri May 04 2007 - 20:55:26 CDT)
  • AMBER: Rate of Dissociation (Fri May 04 2007 - 04:37:46 CDT)
  • AMBER: Tutorial 3: MM-PBSA.....implicit solvent for MD calculations? (Fri May 04 2007 - 03:13:44 CDT)
  • Re: AMBER: Potential of mean force, how to calculate rate of dissociation? (Thu May 03 2007 - 21:13:55 CDT)
  • AMBER: Potential of mean force, how to calculate rate of dissociation? (Thu May 03 2007 - 04:46:27 CDT)
  • Re: AMBER: How precise is a MD simulation? Which strcutures should be reported? (Tue Feb 13 2007 - 22:28:09 CST)
  • AMBER: Help: 1 ns for implicit solvent (GB) calculations, enough? (Tue Feb 13 2007 - 22:18:23 CST)
  • AMBER: Best Force field for protein, DNA, and organic compounds? (Tue Feb 13 2007 - 22:13:31 CST)
  • RE: AMBER: atomicfluct (Tue Feb 13 2007 - 21:36:35 CST)
  • AMBER: atomicfluct (Sun Feb 11 2007 - 23:45:40 CST)
  • Re: AMBER: DNA structure analysis (Wed Jan 17 2007 - 10:23:08 CST)
  • Re: AMBER: DNA structure analysis (Wed Jan 17 2007 - 10:24:16 CST)
  • AMBER: DNA structure analysis (Tue Jan 16 2007 - 21:12:42 CST)
• Cen Gao
  • AMBER: umbrella sampling dihedral restraint question (Thu Jun 14 2007 - 15:33:51 CDT)
• Cenk Andac
  • Re: AMBER: Force field for RNA with U-turn motif (Wed Aug 22 2007 - 13:31:04 CDT)
  • Re: AMBER: Force field for RNA with U-turn motif (Wed Aug 22 2007 - 11:08:29 CDT)
  • AMBER: Force field for RNA with U-turn motif (Tue Aug 21 2007 - 08:52:48 CDT)
  • Re: AMBER: question about formatted mdrcrd files... (Sun Jul 22 2007 - 20:37:43 CDT)
  • Re: AMBER: question about formatted mdrcrd files... (Sun Jul 22 2007 - 19:51:02 CDT)
  • AMBER: question about formatted mdrcrd files... (Sun Jul 22 2007 - 11:47:45 CDT)
  • AMBER: Question about NAB (Nucleic Acid Builder) (Wed Jul 11 2007 - 03:30:18 CDT)
  • AMBER: error due to exceeding left-hand side digital numbers in restart output (Mon Jun 18 2007 - 03:09:36 CDT)
  • Re: AMBER: Nucleic acid analyse : base pair parameters, backbone torsions... (Mon Jun 04 2007 - 17:00:25 CDT)
  • Re: AMBER: Hydration points (Wed May 30 2007 - 16:23:33 CDT)
  • AMBER: Hydration points (Tue May 29 2007 - 16:31:24 CDT)
  • Re: AMBER: Antechamber (Mon May 28 2007 - 01:56:57 CDT)
  • AMBER: Question about determination of hydration points in binding sites (Sun May 27 2007 - 03:51:27 CDT)
  • RE: AMBER: mm-pbsa error with nm = 1 (Wed May 02 2007 - 07:55:55 CDT)
  • RE: AMBER: mm-pbsa error with nm = 1 (Wed May 02 2007 - 05:50:47 CDT)
  • Re: AMBER: mm-pbsa error with nm = 1 (Tue May 01 2007 - 18:58:17 CDT)
  • Re: AMBER: Request for addition of a useful command in ptraj module of AMBER #2 (Mon Apr 23 2007 - 17:35:36 CDT)
  • AMBER: Request for addition of a useful command in ptraj module of AMBER #2 (Tue Apr 17 2007 - 12:24:37 CDT)
  • AMBER: Request for addition of a useful command in ptraj module of AMBER (Tue Apr 17 2007 - 12:18:30 CDT)
  • Re: AMBER: Question about MMPBSA v9 (Wed Apr 11 2007 - 05:38:12 CDT)
  • AMBER: Question about MMPBSA v9 (Mon Apr 09 2007 - 05:54:39 CDT)
  • Re: AMBER: water density (Fri Mar 23 2007 - 17:13:16 CST)
  • Re: AMBER: Essential ions and water molecules in MMPBSA computations (Mon Mar 19 2007 - 07:30:00 CST)
  • Re: AMBER: Essential ions and water molecules in MMPBSA computations (Mon Mar 19 2007 - 07:16:42 CST)
  • Re: AMBER: Essential ions and water molecules in MMPBSA computations (Mon Mar 12 2007 - 08:03:03 CST)
  • AMBER: Essential ions and water molecules in MMPBSA computations (Mon Mar 12 2007 - 03:13:56 CST)
  • AMBER: Question about translational and rotational degree of freedom in MM-PBSA v9 computations (Sun Mar 04 2007 - 06:06:22 CST)
  • Re: AMBER: Compiling Amber 8 on SuSE 10.2 (Wed Feb 07 2007 - 14:02:17 CST)
  • Re: AMBER: organic solvent : hexan octan (Wed Jan 24 2007 - 13:37:12 CST)
  • Re: AMBER: organic solvent : hexan octan (Wed Jan 24 2007 - 12:18:19 CST)
  • AMBER: Problem with installation of the leap module of AMBER9 on Linux Suse 10.2 (Tue Jan 23 2007 - 06:03:37 CST)
• cgji
  • Re: Re: AMBER: AMBER 9 - Force Field Options - Question (Mon Nov 05 2007 - 11:19:58 CST)
  • AMBER: How can i calculate generalized order parameters using ptraj. (Sun Oct 28 2007 - 08:59:37 CST)
  • Re: Re: AMBER: anal calculatons (Tue Oct 16 2007 - 00:48:09 CDT)
  • Re: AMBER: lipid bilayer (Thu Oct 11 2007 - 09:38:45 CDT)
  • AMBER: Statistical uncertainty estimation in Thermodynamic integration calculation.. (Mon Sep 24 2007 - 08:13:36 CDT)
• Chengwen Chen
  • AMBER: a problem of surface area calulated by MM/PBSA (Mon Apr 30 2007 - 02:34:38 CDT)
  • Re: AMBER: amber equation of ff99 (Tue Apr 24 2007 - 21:19:15 CDT)
  • AMBER: amber equation of ff99 (Tue Apr 24 2007 - 11:13:54 CDT)
  • AMBER: about define improper torsion in .frcmod file (Wed Apr 04 2007 - 04:02:57 CDT)
  • Re: AMBER: Can I measure improper torsion by ptarj? (Mon Mar 12 2007 - 22:18:24 CST)
  • AMBER: Can I measure improper torsion by ptarj? (Mon Mar 12 2007 - 10:21:55 CST)
  • Re: AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat? (Sat Mar 10 2007 - 01:37:06 CST)
  • AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat? (Fri Mar 09 2007 - 02:04:00 CST)
  • AMBER: question about distance restraint on terminal WC of DNA duplex (AMBER9) (Fri Feb 09 2007 - 02:25:00 CST)
  • Re: AMBER: some questions about minimization and MD of DNA duplex with sander (Mon Feb 05 2007 - 23:43:29 CST)
  • Re: AMBER: some questions about minimization and MD of DNA duplex with sander (Thu Feb 01 2007 - 23:40:11 CST)
  • AMBER: some questions about minimization and MD of DNA duplex with sander (Wed Jan 31 2007 - 01:44:13 CST)
  • AMBER: deformation of DNA duplex after MD simulation (AMBER9) (Sat Jan 20 2007 - 22:28:59 CST)
  • Re: AMBER: The convergence criteria for the energy minimization of the DNA molecule (dodecmer duplux) (Sat Jan 20 2007 - 21:55:46 CST)
  • AMBER: The convergence criteria for the energy minimization of the DNA molecule (dodecmer duplux) (Fri Jan 19 2007 - 03:37:53 CST)
  • Re: AMBER: AMBER complile problem (Mon Jan 01 2007 - 21:19:08 CST)
• Chng Choon-Peng
  • Re: AMBER: heical content in simulations (Tue Aug 07 2007 - 03:19:26 CDT)
• Chris Moth
  • Re: AMBER: a question of ptraj (Mon Dec 31 2007 - 14:38:21 CST)
  • AMBER: PME and counter ions (Wed Dec 19 2007 - 18:21:46 CST)
  • Re: AMBER: I need some help in PTRAJ (Mon Dec 03 2007 - 19:29:21 CST)
  • Re: AMBER: Re: Calculating Energies with imin=5 (Fri Nov 30 2007 - 11:49:46 CST)
  • Re: AMBER: Re: Calculating Energies with imin=5 (Fri Nov 30 2007 - 08:11:40 CST)
  • Re: AMBER: invalid digit '*' in the input file (Mon Nov 12 2007 - 08:40:26 CST)
  • Re: AMBER: Add hydrogen and charge calculation (Mon Aug 27 2007 - 15:33:25 CDT)
  • AMBER: NETCDF (Fri Aug 24 2007 - 08:03:37 CDT)
  • Re: AMBER: NETCDF (Fri Aug 24 2007 - 07:58:34 CDT)
  • Re: AMBER: How to perform MD simulation in NVT ensemble? (Thu Aug 23 2007 - 12:07:30 CDT)
  • Re: AMBER: imin=5 and inptraj (Sat Aug 11 2007 - 16:37:11 CDT)
  • Re: AMBER: PCA with ptraj (Sun Jul 29 2007 - 07:27:32 CDT)
  • Re: AMBER: hbond ptraj (Thu May 17 2007 - 07:14:31 CDT)
  • Re: AMBER: restraint value: written but none specified (Fri Apr 20 2007 - 16:16:52 CDT)
  • AMBER: ptraj and quasi harmonic analysis (Thu Apr 19 2007 - 14:58:52 CDT)
  • Re: AMBER: signal SIGSEGV(11) (Wed Apr 18 2007 - 15:22:58 CDT)
  • Re: AMBER: sander (AMBER 9) and -y flag -- not working? (Tue Apr 10 2007 - 13:36:22 CDT)
  • AMBER: SANDER PMEMD ntpr ntwx discrepancy (?bug? report) (Mon Apr 09 2007 - 12:32:35 CDT)
  • AMBER: SANDER PMEMD ntpr ntwx discrepancy (?bug? report) (Fri Apr 06 2007 - 16:07:17 CDT)
  • AMBER: netcdf support needed (Amber 9, sander imin = 5, -y flag) (Fri Apr 06 2007 - 13:50:29 CDT)
  • AMBER: units of mwcovar matrix befor conversion (Thu Feb 22 2007 - 17:01:57 CST)
  • Re: AMBER: Fwd: help me out... (Mon Feb 12 2007 - 09:08:24 CST)
  • AMBER: workaround for ibm xlf90 powerpc FORTRAN compiler: -q64 and -O3 yield Run.dhfr.min failure (Thu Feb 01 2007 - 12:33:33 CST)
  • Re: AMBER: ADDIONS do not neutralize to ZERO (Mon Jan 29 2007 - 15:30:20 CST)
  • Re: AMBER: amber 9 (Thu Jan 11 2007 - 13:43:27 CST)
  • AMBER: CYX residue missing from Amber 9 ff03ua (?) (Thu Jan 11 2007 - 13:32:04 CST)
• Chris-Kriton Skylaris
  • AMBER: AMBER question: Combining Gaff and ff99 forcefields for a single molecule (Fri Feb 23 2007 - 03:54:00 CST)
• Christophe Guilbert
  • Re: AMBER: Would amber work with Linspire 6.0? (Tue Nov 27 2007 - 21:35:35 CST)
• Christopher Gaughan
  • AMBER: mm_pbsa continue run (Sun Dec 02 2007 - 12:46:42 CST)
  • AMBER: restrained md and mm pbsa (Thu Aug 02 2007 - 09:15:17 CDT)
  • AMBER: protonate (Wed May 16 2007 - 10:56:37 CDT)
  • AMBER: Atoms closer to 2 angstroms to each other (Mon May 07 2007 - 09:38:06 CDT)
  • Re: AMBER: Constant volume simulations (Tue Apr 10 2007 - 12:12:14 CDT)
  • Re: AMBER: Constant volume simulations (Tue Apr 10 2007 - 10:50:39 CDT)
  • Re: AMBER: Constant volume simulations (Tue Apr 10 2007 - 10:31:58 CDT)
  • AMBER: Constant volume simulations (Mon Apr 09 2007 - 13:59:26 CDT)
  • AMBER: choice of alpha carbons vs side chains (Wed Apr 04 2007 - 17:34:31 CDT)
  • AMBER: Replica Exchange (Tue Feb 13 2007 - 15:20:08 CST)
• Christopher Jones
  • RE: AMBER: amber on AMD opteron-250 (Tue Dec 11 2007 - 16:08:31 CST)
  • AMBER: amber9 parallel compile problem (Wed Oct 31 2007 - 11:09:32 CST)
• Chrystal Bruce
  • AMBER: Installation Question (Mon Jun 04 2007 - 09:53:46 CDT)
• Chupakhin Vladimir
  • Re: AMBER: xleap (Tue Jan 30 2007 - 04:55:40 CST)
  • Re: AMBER: Molecular dynamic issues (Tue Jan 23 2007 - 08:50:56 CST)
  • Re: AMBER: sanger (Thu Jan 18 2007 - 08:05:01 CST)
• Claire Zerafa
  • AMBER: hbond analysis output (Wed Oct 24 2007 - 14:21:02 CDT)
• clarkzhy
  • To Mr. Ross Walker Re: RE: AMBER: How to add semi-experience parameter in divcon? (Thu Jun 21 2007 - 20:19:23 CDT)
  • AMBER: How to add semi-experience parameter in divcon? (Tue Jun 19 2007 - 09:23:04 CDT)
• Colby C
  • AMBER: Gaff Charge (Mon Jul 16 2007 - 22:39:15 CDT)
  • Re: AMBER: Sander Error (Mon Jul 09 2007 - 10:39:50 CDT)
  • Re: AMBER: Sander Error (Tue Jul 03 2007 - 13:21:18 CDT)
  • Re: AMBER: Sander Error (Fri Jun 29 2007 - 16:25:35 CDT)
  • AMBER: Sander Error (Fri Jun 29 2007 - 09:47:05 CDT)
  • Re: AMBER: 5 Ligands and 1 Protein (Thu Jun 21 2007 - 16:45:46 CDT)
  • Re: AMBER: 5 Ligands and 1 Protein (Wed Jun 20 2007 - 21:01:40 CDT)
  • Re: AMBER: 5 Ligands and 1 Protein (Wed Jun 20 2007 - 19:10:22 CDT)
  • AMBER: 5 Ligands and 1 Protein (Wed Jun 20 2007 - 13:07:33 CDT)
  • Re: AMBER: xleap on cygwin (Tue Jun 12 2007 - 19:42:52 CDT)
  • Re: AMBER: xleap on cygwin (Tue Jun 12 2007 - 11:34:21 CDT)
  • AMBER: xleap on cygwin (Mon Jun 11 2007 - 20:59:17 CDT)
  • Re: AMBER: Installing on windows (Mon Jun 11 2007 - 12:14:33 CDT)
  • Re: AMBER: Installing on windows (Mon Jun 11 2007 - 10:17:07 CDT)
  • Re: AMBER: Installing on windows (Mon Jun 11 2007 - 09:42:40 CDT)
  • Re: AMBER: Installing on windows (Mon Jun 11 2007 - 07:56:39 CDT)
  • Re: AMBER: Installing on windows (Sun Jun 10 2007 - 22:34:58 CDT)
  • Re: AMBER: Installing on windows (Sun Jun 10 2007 - 20:48:30 CDT)
  • AMBER: Installing on windows (Sun Jun 10 2007 - 18:42:25 CDT)
• Cooper, Matthew
  • RE: AMBER: thermodynamic integration (Fri Nov 09 2007 - 08:32:52 CST)
  • RE: AMBER: thermodynamic integration (Fri Nov 09 2007 - 08:03:32 CST)
  • AMBER: thermodynamic integration (Thu Nov 08 2007 - 15:14:25 CST)
• Craig Gough
  • AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8 (Fri Feb 23 2007 - 02:47:36 CST)
  • AMBER: MDGRAPE and AMBER (Mon Feb 19 2007 - 02:34:43 CST)
• cristian
  • AMBER: mmpbsa decomposition error (Fri Jun 08 2007 - 10:34:21 CDT)
  • Re: AMBER: rms in nmode (Fri Jun 01 2007 - 02:59:18 CDT)
• cristian obiol
  • AMBER: Group declaration question (Wed May 02 2007 - 04:28:19 CDT)
• crowfoot_at_unr.nevada.edu
  • AMBER: Multiple Bonds to one Atom (Thu Apr 12 2007 - 15:41:36 CDT)
• Cyril Bauvais
  • AMBER: problem decomposing energies (MMPBSA) (Tue Mar 20 2007 - 05:15:29 CST)
  • AMBER: problem decomposing energies (MMPBSA) (Thu Mar 15 2007 - 03:27:57 CST)
• D.Usharani
  • Re: AMBER: Reg restraint value obtained during umbrella sampling (Fri Jun 08 2007 - 01:01:46 CDT)
  • AMBER: Reg COM restraint to DNA (Wed Jun 06 2007 - 04:56:00 CDT)
  • Re: AMBER: Reg restraint value obtained during umbrella sampling (Sat Jun 02 2007 - 06:07:43 CDT)
  • Re: AMBER: Reg restraint value obtained during umbrella sampling (Fri Jun 01 2007 - 12:12:23 CDT)
  • Re: AMBER: Reg restraint value obtained during umbrella sampling (Thu May 31 2007 - 13:28:50 CDT)
  • AMBER: Reg restraint value obtained during umbrella sampling (Thu May 31 2007 - 12:22:21 CDT)
• Dan Kidger
  • AMBER: bug in nonbond_list.f (nee ew_setup.f) (Mon Jul 02 2007 - 04:42:58 CDT)
• Daniel Oehme
  • AMBER: QM/MM NPT Simulation (Thu Apr 19 2007 - 23:46:14 CDT)
  • AMBER: REMD error on first exchange (Sun Feb 18 2007 - 20:31:57 CST)
• Dave, Sonya
  • RE: AMBER: Simulating a section of a molecule (Thu Feb 15 2007 - 17:10:06 CST)
  • AMBER: Simulating a section of a molecule (Thu Feb 15 2007 - 10:59:53 CST)
  • RE: AMBER: How precise is a MD simulation? (Wed Feb 14 2007 - 12:35:16 CST)
  • RE: AMBER: How precise is a MD simulation? (Tue Feb 13 2007 - 14:01:23 CST)
  • AMBER: How precise is a MD simulation? (Mon Feb 12 2007 - 18:00:07 CST)
  • RE: AMBER: simulating part of a molecule with homology modeling (Mon Feb 12 2007 - 10:50:36 CST)
  • AMBER: simulating part of a molecule with homology modeling (Sat Feb 10 2007 - 18:00:11 CST)
• David A. Case
  • Re: AMBER: RESP charge fitting using antechamber (Sat Dec 29 2007 - 20:05:25 CST)
  • Re: AMBER: An enquiry about "Dynamics of ligand escape from the heme pocket of myoglobin (JACS, 1988, 110, 7690 (Wed Dec 26 2007 - 11:52:20 CST)
  • Re: AMBER: installation of amber9 on suse linux 10.3 (Mon Dec 24 2007 - 00:03:38 CST)
  • Re: AMBER: PME and counter ions (Wed Dec 19 2007 - 20:41:30 CST)
  • Re: AMBER: PME and counter ions (Wed Dec 19 2007 - 19:01:00 CST)
  • Re: AMBER: PME and counter ions (Wed Dec 19 2007 - 14:01:55 CST)
  • Re: AMBER: amber9/mmtsb (Wed Dec 19 2007 - 10:19:47 CST)
  • Re: AMBER: amber9/mmtsb (Tue Dec 18 2007 - 09:59:11 CST)
  • Re: AMBER: pmemd: same rst, different result? (Tue Dec 18 2007 - 09:46:56 CST)
  • Re: AMBER: xleap loading files (Sat Dec 15 2007 - 00:26:13 CST)
  • Re: AMBER: nmode ntrun=2 (Fri Dec 14 2007 - 12:27:44 CST)
  • Re: AMBER: replica exchange out files continually overwritten (Fri Dec 14 2007 - 11:17:09 CST)
  • Re: AMBER: Troubling with installing Amber8 (Fri Dec 14 2007 - 10:39:58 CST)
  • Re: AMBER: New 2 the board (Wed Dec 12 2007 - 18:03:46 CST)
  • Re: AMBER: tleap crashing (Tue Dec 11 2007 - 17:04:25 CST)
  • Re: AMBER: TI Approach - mass perturbation (Tue Dec 11 2007 - 01:13:08 CST)
  • Re: AMBER: Troubling with installing Amber8 (Sun Dec 09 2007 - 11:18:29 CST)
  • Re: AMBER: Re: Amber_ifort_x86_64 test error (Sun Dec 09 2007 - 11:13:00 CST)
  • Re: AMBER: some input problem (Sun Dec 09 2007 - 11:09:51 CST)
  • Re: AMBER: website problems (Sun Dec 09 2007 - 11:03:47 CST)
  • Re: AMBER: Backbone atoms (Sat Dec 08 2007 - 16:58:30 CST)
  • Re: AMBER: Continuing an amber 8 simulation with amber 9 (Sat Dec 08 2007 - 12:40:09 CST)
  • Re: AMBER: ** No torsion terms for SNI-NI-SNI-CT (Fri Dec 07 2007 - 19:24:30 CST)
  • Re: AMBER: Troubles installing amber (Fri Dec 07 2007 - 16:15:36 CST)
  • Re: AMBER: Surface (Thu Dec 06 2007 - 15:34:04 CST)
  • Re: AMBER: correlation time (Thu Dec 06 2007 - 11:09:07 CST)
  • Re: AMBER: nmode ntrun=2 (Thu Dec 06 2007 - 11:06:01 CST)
  • Re: AMBER: How to apply psuedo-bonds for restraints (Thu Dec 06 2007 - 10:56:59 CST)
  • Re: AMBER: How to apply psuedo-bonds for restraints (Wed Dec 05 2007 - 20:16:43 CST)
  • Re: Fwd: Re: AMBER: leap restrainTorsion (Wed Dec 05 2007 - 20:15:36 CST)
  • Re: AMBER: FATAL: Atom .R<CYF 17>.A<N 1> does not have a type. (Wed Dec 05 2007 - 18:41:32 CST)
  • Re: AMBER: THF parameters (Wed Dec 05 2007 - 11:56:18 CST)
  • Re: AMBER: nmode ntrun=2 (Wed Dec 05 2007 - 11:58:34 CST)
  • Re: AMBER: leap restrainTorsion (Wed Dec 05 2007 - 10:50:12 CST)
  • Re: AMBER: POPS Lipid Bilayer: Full Parameter/Topology File (Tue Dec 04 2007 - 19:11:53 CST)
  • Re: AMBER: modifications to force field for Fe4S4 cubane (Tue Dec 04 2007 - 12:57:39 CST)
  • Re: AMBER: correlation time (Tue Dec 04 2007 - 12:40:20 CST)
  • Re: AMBER: Free energy for part of the system (Tue Dec 04 2007 - 12:37:16 CST)
  • Re: AMBER: Free energy for part of the system (Mon Dec 03 2007 - 20:35:50 CST)
  • Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault (Mon Dec 03 2007 - 11:08:48 CST)
  • Re: AMBER: leaprc.ff02polEP.r1into xleap (Thu Nov 29 2007 - 09:40:04 CST)
  • Re: AMBER: Weird restart file with ioutfm=0, iwrap=1 and ntwprt >0 (Wed Nov 28 2007 - 13:27:52 CST)
  • Re: AMBER: leaprc.ff02polEP.r1into xleap (Wed Nov 28 2007 - 12:58:30 CST)
  • Re: AMBER: addles (Wed Nov 28 2007 - 11:46:57 CST)
  • Re: AMBER: (no subject) (Wed Nov 28 2007 - 11:09:04 CST)
  • Re: AMBER: bondi radii problems (Wed Nov 28 2007 - 10:32:21 CST)
  • Re: AMBER: Polarizable potential (Wed Nov 28 2007 - 10:19:06 CST)
  • Re: AMBER: modifications to force field for Fe4S4 cubane (Tue Nov 27 2007 - 15:10:40 CST)
  • Re: AMBER: question about ntx=5 (Tue Nov 27 2007 - 10:49:33 CST)
  • Re: AMBER: Xleap and Hydrogens (Tue Nov 27 2007 - 10:40:05 CST)
  • Re: AMBER: Polarizable potentials (Mon Nov 26 2007 - 20:23:05 CST)
  • Re: AMBER: Restrained MD (amber9) (Mon Nov 26 2007 - 17:49:43 CST)
  • Re: AMBER: question about ntx=5 (Sun Nov 25 2007 - 18:27:30 CST)
  • Re: AMBER: Hello (Sun Nov 25 2007 - 00:14:23 CST)
  • Re: AMBER: Pressure Variation for NPT simulation of TIP5P water (fwd) (Sat Nov 24 2007 - 11:36:44 CST)
  • AMBER: antechamber problem (Fri Nov 23 2007 - 20:40:21 CST)
  • Re: AMBER: frcmod file and NONB for dummy atoms (Fri Nov 23 2007 - 12:58:46 CST)
  • Re: AMBER: RE: FF94 or FF99? (Fri Nov 23 2007 - 12:51:18 CST)
  • Re: AMBER: connecting a non standard residue to the rest of an enzyme (Fri Nov 23 2007 - 12:39:13 CST)
  • Re: AMBER: About TER records (Fri Nov 23 2007 - 12:35:46 CST)
  • Re: AMBER: Pressure Variation for NPT simulation of TIP5P water (Thu Nov 22 2007 - 11:34:34 CST)
  • Re: AMBER: Problem with LEaP generating topology and coord files after double bond creation (Wed Nov 21 2007 - 19:08:08 CST)
  • Re: AMBER: modifications to force field for Fe4S4 cubane (Wed Nov 21 2007 - 16:30:30 CST)
  • Re: AMBER:How to calculate the free energy of a series of conformations (Wed Nov 21 2007 - 13:42:09 CST)
  • Re: AMBER: Implicit/Explicit solvation (Wed Nov 21 2007 - 10:46:19 CST)
  • Re: AMBER: newby question on converting xyz format to pdb format after energy minimization (Tue Nov 20 2007 - 15:33:08 CST)
  • Re: AMBER: How to calculate S2 from P2 using ptraj ? (Mon Nov 19 2007 - 12:04:48 CST)
  • Re: AMBER: Fwd: [chirality.c] Atom did not match (Sat Nov 17 2007 - 10:53:01 CST)
  • Re: AMBER: Fwd: [chirality.c] Atom did not match (Fri Nov 16 2007 - 18:03:33 CST)
  • Re: AMBER: &shf setup (Fri Nov 16 2007 - 17:59:19 CST)
  • Re: AMBER: chem shift format (Fri Nov 16 2007 - 18:00:27 CST)
  • Re: AMBER: antechamber --> sander problem (Fri Nov 16 2007 - 15:17:50 CST)
  • Re: AMBER: xleap heme iron coordination error (Fri Nov 16 2007 - 13:47:53 CST)
  • Re: [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] (Fri Nov 16 2007 - 00:12:45 CST)
  • Re: AMBER: Understading of mdcrd file and pdb file.. (Fri Nov 16 2007 - 00:23:30 CST)
  • Re: AMBER: amber9 leap installation error on sgi_altix (Tue Nov 13 2007 - 17:27:55 CST)
  • Re: AMBER: Problem with xLeap (Tue Nov 13 2007 - 11:55:24 CST)
  • Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine (Tue Nov 13 2007 - 10:28:52 CST)
  • Re: AMBER: Problem with xLeap (Tue Nov 13 2007 - 10:08:24 CST)
  • Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine (Tue Nov 13 2007 - 09:54:38 CST)
  • Re: AMBER: TIP5P water simulation using AMBER7 (Sun Nov 11 2007 - 16:04:08 CST)
  • Re: AMBER: thermodynamic integration (Fri Nov 09 2007 - 12:27:48 CST)
  • Re: AMBER: How can i calculate generalized order parameters using ptraj. (Thu Nov 08 2007 - 20:23:34 CST)
  • Re: AMBER: divcon (Thu Nov 08 2007 - 20:06:55 CST)
  • Re: AMBER: xleap patch for xorg-7.3 ?? (Thu Nov 08 2007 - 20:03:39 CST)
  • Re: AMBER: thermodynamic integration (Thu Nov 08 2007 - 19:49:49 CST)
  • Re: AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels) (Thu Nov 08 2007 - 14:16:57 CST)
  • Re: AMBER: make test.parallel (Thu Nov 08 2007 - 09:58:39 CST)
  • Re: AMBER: (no subject) (Wed Nov 07 2007 - 11:11:43 CST)
  • Re: AMBER: LEaP bond problem (Wed Nov 07 2007 - 10:39:49 CST)
  • Re: AMBER: Question (Tue Nov 06 2007 - 23:18:33 CST)
  • Re: AMBER: Energy minimization problem of -SO3H group (Tue Nov 06 2007 - 23:12:08 CST)
  • Re: AMBER: Minimum energy tolerance gradient setting for minimization (Tue Nov 06 2007 - 10:03:18 CST)
  • Re: AMBER: ptraj frames maximum (Mon Nov 05 2007 - 10:37:11 CST)
  • Re: AMBER: ptraj frames maximum (Mon Nov 05 2007 - 09:34:20 CST)
  • Re: AMBER: dihedral angles (Wed Oct 31 2007 - 22:09:24 CST)
  • Re: AMBER: How to get sane package (Wed Oct 31 2007 - 22:09:08 CST)
  • Re: AMBER: gibbs problems (Wed Oct 31 2007 - 22:09:35 CST)
  • Re: AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels) (Wed Oct 31 2007 - 15:52:18 CST)
  • Re: AMBER: &dipole input and some questions on using polarizable force fields (Wed Oct 31 2007 - 08:38:34 CST)
  • Re: AMBER: &dipole input and some questions on using polarizable force fields (Tue Oct 30 2007 - 09:58:20 CST)
  • Re: AMBER: &dipole input and some questions on using polarizable force fields (Tue Oct 30 2007 - 07:42:44 CST)
  • Re: AMBER: mdfil: Error unknown flag: -p4pg (Mon Oct 29 2007 - 20:46:01 CST)
  • Re: AMBER: problems compiling amber on mac OSX (Fri Oct 26 2007 - 10:48:35 CDT)
  • Re: AMBER: segmentation fault occured doing MD (Fri Oct 26 2007 - 10:32:07 CDT)
  • Re: AMBER: HG atoms in CYX residues (Fri Oct 26 2007 - 10:28:36 CDT)
  • Re: AMBER: Average absolute value of cross velocity (Rate constant from PMF) (Fri Oct 26 2007 - 10:22:40 CDT)
  • Re: AMBER: prepin file format description; pointers on parameterization (Wed Oct 24 2007 - 19:27:39 CDT)
  • Re: AMBER: Thermodynamic Integration with Explicit Solvent (Tue Oct 09 2007 - 21:36:38 CDT)
  • Re: AMBER: Heat capacity, diffusivity way off in this simulation of SPC/E water? (Tue Oct 09 2007 - 09:09:02 CDT)
  • Re: AMBER: entropy with ptraj (Mon Oct 08 2007 - 08:47:57 CDT)
  • Re: AMBER: Problems with cpin file (Tue Oct 02 2007 - 10:16:45 CDT)
  • Re: AMBER: regarding non bonded energy caculations (Mon Oct 01 2007 - 09:46:00 CDT)
  • Re: AMBER: fragment parametrization tutorial? (Sun Sep 30 2007 - 00:04:16 CDT)
  • Re: AMBER: follow-up (Fri Sep 28 2007 - 15:11:32 CDT)
  • Re: AMBER: implicit minimization (Fri Sep 28 2007 - 10:17:16 CDT)
  • Re: AMBER: step-by-ste weight changes of dwt -- patch? (Thu Sep 27 2007 - 14:04:20 CDT)
  • Re: AMBER: needing more detailed knowledge of tautp than the manual (Thu Sep 27 2007 - 10:49:37 CDT)
  • Re: AMBER: force field question (Thu Sep 27 2007 - 10:45:38 CDT)
  • Re: AMBER: Solvation Issues (Wed Sep 26 2007 - 18:16:58 CDT)
  • Re: AMBER: NMR refinement (Wed Sep 26 2007 - 17:03:01 CDT)
  • Re: AMBER: Minimization and MD input files (Tue Sep 25 2007 - 14:27:37 CDT)
  • Re: AMBER: total energy in sander and nmode (Tue Sep 25 2007 - 09:56:49 CDT)
  • Re: AMBER: energy calculation (Tue Sep 25 2007 - 09:51:40 CDT)
  • Re: AMBER: (Sun Sep 23 2007 - 20:31:19 CDT)
  • Re: AMBER: Solvation net forces (Tue Sep 18 2007 - 19:14:55 CDT)
  • Re: AMBER: Torsion terms in xleap (Mon Sep 17 2007 - 21:35:24 CDT)
  • Re: AMBER: Problem with Getting SHAKE to work (Mon Sep 17 2007 - 11:38:26 CDT)
  • Re: AMBER: Problem with Getting SHAKE to work (Sun Sep 16 2007 - 00:05:55 CDT)
  • Re: AMBER: Can I set harmonic constraints in SMD simulations ? (Sat Sep 15 2007 - 11:59:33 CDT)
  • Re: AMBER: Problem encountered during thermodynamic integration (Sat Sep 15 2007 - 12:02:39 CDT)
  • Re: AMBER: AMBER sander (Fri Sep 14 2007 - 19:50:47 CDT)
  • Re: AMBER: Torsion terms in xleap (Fri Sep 14 2007 - 19:44:17 CDT)
  • Re: AMBER: for makeDIST_RST (Fri Sep 14 2007 - 10:10:28 CDT)
  • Re: AMBER: parallel implementation of Amber 9 (Fri Sep 14 2007 - 10:04:16 CDT)
  • Re: AMBER: FF02: sander problem with irstdip=1 (Fri Sep 14 2007 - 09:59:26 CDT)
  • Re: AMBER: TIP5P questions (Thu Sep 13 2007 - 19:17:12 CDT)
  • Re: AMBER: Problems with Carbohydrate Non-standard Residue (Wed Sep 12 2007 - 09:47:48 CDT)
  • Re: AMBER: Missplaced TERs (Mon Sep 10 2007 - 17:46:57 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Thu Sep 06 2007 - 23:38:27 CDT)
  • Re: AMBER: amber md movie using Chimera (Wed Sep 05 2007 - 13:12:27 CDT)
  • Re: AMBER: installing LMOD error (Wed Sep 05 2007 - 00:35:24 CDT)
  • Re: AMBER: Problem compiling AMBER 9 on ppc64 (Tue Sep 04 2007 - 15:56:06 CDT)
  • Re: AMBER: installing LMOD error (Tue Sep 04 2007 - 10:01:06 CDT)
  • Re: AMBER: ntt parameter in vacuum (Mon Sep 03 2007 - 10:51:53 CDT)
  • Re: AMBER: modified leaprc for glycoproteins (Fri Aug 31 2007 - 16:42:03 CDT)
  • Re: AMBER: Using ntr=1 in xleap (Fri Aug 31 2007 - 17:52:13 CDT)
  • Re: AMBER: Connecting two ethanes in LEaP (Fri Aug 31 2007 - 11:18:18 CDT)
  • Re: AMBER: Confusion about Langevin dymamics (Fri Aug 31 2007 - 09:53:47 CDT)
  • Re: AMBER: bad atom type:F (Thu Aug 30 2007 - 10:35:00 CDT)
  • Re: AMBER: protocols for high pressure simulation (Tue Aug 28 2007 - 10:41:58 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Mon Aug 27 2007 - 17:29:49 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Mon Aug 27 2007 - 10:58:20 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Thu Aug 23 2007 - 19:28:29 CDT)
  • Re: AMBER: Regarding free energy calculation and covalent bond (Thu Aug 23 2007 - 11:52:17 CDT)
  • Re: AMBER: How to use AMBER Parameter Database ? (Thu Aug 23 2007 - 11:53:55 CDT)
  • Re: AMBER: Ca(2+) parameter (Thu Aug 23 2007 - 10:04:01 CDT)
  • Re: AMBER: xLeap "Could not find type" error (Wed Aug 22 2007 - 10:45:02 CDT)
  • Re: AMBER: xLeap "Could not find type" error (Wed Aug 22 2007 - 10:15:25 CDT)
  • Re: AMBER: xLeap "Could not find type" error (Tue Aug 21 2007 - 19:40:09 CDT)
  • Re: AMBER: (Mon Aug 20 2007 - 19:31:21 CDT)
  • Re: AMBER: charges in PBSA calculation (Sun Aug 19 2007 - 19:57:14 CDT)
  • AMBER: question about a 20 kDa protein (Sat Aug 18 2007 - 11:07:09 CDT)
  • Re: AMBER: Thermodynamic Integration for a CHARGED molecule (Fri Aug 17 2007 - 10:46:38 CDT)
  • Re: AMBER: What is the best computer for running AMBER simulations? (Thu Aug 16 2007 - 18:42:54 CDT)
  • Re: AMBER: Missplaced TERs (Thu Aug 16 2007 - 13:53:10 CDT)
  • Re: AMBER: EXTRA_PTS: frtype 2 Should not be here (Thu Aug 16 2007 - 11:33:52 CDT)
  • Re: AMBER: antechamber, how does it work (Thu Aug 16 2007 - 10:40:16 CDT)
  • Re: AMBER: Normal Mode Analysis (Wed Aug 15 2007 - 17:56:46 CDT)
  • Re: AMBER: EXTRA_PTS: frtype 2 Should not be here (Wed Aug 15 2007 - 12:34:49 CDT)
  • Re: AMBER: antechamber, how does it work (Wed Aug 15 2007 - 12:07:22 CDT)
  • Re: AMBER: torsional restraints in a solvated MD simulation. (Tue Aug 14 2007 - 15:50:31 CDT)
  • Re: AMBER: (Tue Aug 14 2007 - 10:27:48 CDT)
  • Re: AMBER: How to carry out drug-dna complex simulations (Tue Aug 14 2007 - 10:18:47 CDT)
  • Re: AMBER: Using TLEAP to set up MD in the crystal lattice space? (Mon Aug 13 2007 - 20:26:24 CDT)
  • Re: AMBER: setbox command error (Mon Aug 13 2007 - 15:38:30 CDT)
  • Re: AMBER: how to combine two molecules (Mon Aug 13 2007 - 11:43:57 CDT)
  • Re: AMBER: hybridization in Amber, pertaining to resonant structures, ions (Sat Aug 11 2007 - 15:35:15 CDT)
  • Re: AMBER: NVE energy and temperature drift (Sat Aug 11 2007 - 15:28:30 CDT)
  • Re: AMBER: Citation for Langevin thermostat? (Sat Aug 11 2007 - 14:47:59 CDT)
  • Re: AMBER: Binary file curiosities (Mon Aug 06 2007 - 10:03:07 CDT)
  • Re: AMBER: Problem while carrying out minimisation of drug molecule using sander (Mon Aug 06 2007 - 09:35:25 CDT)
  • Re: AMBER: nucleic acid electrostatic energy (Sat Aug 04 2007 - 10:28:36 CDT)
  • Re: AMBER: Binary file curiosities (Fri Aug 03 2007 - 18:21:25 CDT)
  • Re: AMBER: Antechamber formal charges with Gasteiger method (Fri Aug 03 2007 - 15:17:11 CDT)
  • Re: AMBER: bug in nonbond_list.f (nee ew_setup.f) (Fri Aug 03 2007 - 10:14:27 CDT)
  • Re: AMBER: unable to save prmtop/inpcrd for chcl3box (Fri Aug 03 2007 - 09:58:03 CDT)
  • Re: AMBER: Information about Amber 9 (Fri Aug 03 2007 - 09:53:22 CDT)
  • Re: AMBER: Problem generating .prepin file in Antechamber (Thu Aug 02 2007 - 15:53:03 CDT)
  • Re: AMBER: edit.out amber version 9 (Thu Aug 02 2007 - 14:00:22 CDT)
  • Re: AMBER: Problem with antechamber (Thu Aug 02 2007 - 10:07:30 CDT)
  • Re: AMBER: bugfix for impropers in parmchk (Thu Aug 02 2007 - 00:04:20 CDT)
  • Re: AMBER: problem compiling Amber9 on 64-machine (Wed Aug 01 2007 - 11:43:21 CDT)
  • Re: AMBER: problem compiling Amber9 on 64-machine (Wed Aug 01 2007 - 11:36:37 CDT)
  • Re: AMBER: problem compiling Amber9 on 64-machine (Wed Aug 01 2007 - 09:50:30 CDT)
  • Re: AMBER: Linux install (Tue Jul 31 2007 - 10:35:37 CDT)
  • Re: AMBER: errors in SHIFTS execution (Mon Jul 30 2007 - 10:37:26 CDT)
  • Re: AMBER: errors in SHIFTS execution (Sun Jul 29 2007 - 10:44:05 CDT)
  • Re: AMBER: FLAG LENNARD_JONES_ACOEF NAN (Fri Jul 27 2007 - 10:19:49 CDT)
  • Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 17:48:55 CDT)
  • Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 16:32:32 CDT)
  • Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 14:56:24 CDT)
  • Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 12:36:43 CDT)
  • Re: AMBER: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 11:09:18 CDT)
  • Re: AMBER: MD simulation error (Tue Jul 24 2007 - 19:55:09 CDT)
  • Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap (Tue Jul 24 2007 - 10:20:30 CDT)
  • Re: AMBER: Bug report: a bug of xleap associated with NumLock (Tue Jul 24 2007 - 10:16:07 CDT)
  • Re: AMBER: regarding distance restraints (Mon Jul 23 2007 - 09:56:03 CDT)
  • Re: AMBER: using amber to minimize structure obatined from cyana (Mon Jul 23 2007 - 09:52:00 CDT)
  • Re: AMBER: parallel compilation (Mon Jul 23 2007 - 09:55:02 CDT)
  • Re: AMBER: question about formatted mdrcrd files... (Sun Jul 22 2007 - 18:30:06 CDT)
  • Re: AMBER: offending restraint (Sat Jul 21 2007 - 20:35:51 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 11:16:46 CDT)
  • Re: AMBER: DNA RNA recognition problem (Thu Jul 19 2007 - 10:01:17 CDT)
  • Re: AMBER: Error during compilation on a SGI Irix machine (Wed Jul 18 2007 - 23:34:18 CDT)
  • Re: AMBER: General AMBER questions (Wed Jul 18 2007 - 18:12:34 CDT)
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Tue Jul 17 2007 - 18:15:59 CDT)
  • Re: AMBER: potential energy calculation (Tue Jul 17 2007 - 18:08:54 CDT)
  • Re: AMBER: Known residue, unknown error in teLeap (Tue Jul 17 2007 - 11:49:41 CDT)
  • Re: AMBER: Non-standard amino acid residue (Tue Jul 17 2007 - 09:53:46 CDT)
  • Re: AMBER: Gaff Charge (Tue Jul 17 2007 - 00:18:17 CDT)
  • Re: AMBER: Problems simulating a big system (Mon Jul 16 2007 - 20:44:09 CDT)
  • Re: AMBER: Known residue, unknown error in teLeap (Mon Jul 16 2007 - 20:32:16 CDT)
  • Re: AMBER: refc error (Mon Jul 16 2007 - 19:25:20 CDT)
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Mon Jul 16 2007 - 19:13:45 CDT)
  • Re: AMBER: help with phosphotyrosine (Mon Jul 16 2007 - 13:11:51 CDT)
  • Re: AMBER: Non bond list overflow (Sun Jul 15 2007 - 18:50:11 CDT)
  • Re: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help (Thu Jul 12 2007 - 18:03:45 CDT)
  • Re: AMBER: Amber9 analyze timecorr manual ambigous (Thu Jul 12 2007 - 17:58:30 CDT)
  • Re: AMBER: Amber9 analyze timecorr manual ambigous (Thu Jul 12 2007 - 14:55:15 CDT)
  • Re: AMBER: program bug? (Thu Jul 12 2007 - 10:22:35 CDT)
  • Re: AMBER: Question about NAB (Nucleic Acid Builder) (Wed Jul 11 2007 - 18:23:05 CDT)
  • Re: AMBER: question about iwrap (Wed Jul 11 2007 - 18:24:11 CDT)
  • Re: AMBER: Problem with running Sander (Tue Jul 10 2007 - 18:17:56 CDT)
  • Re: AMBER: Could not find cntrl namelist (Tue Jul 10 2007 - 18:04:15 CDT)
  • Re: AMBER: Problem with running Sander (Tue Jul 10 2007 - 17:39:31 CDT)
  • Re: AMBER: Could not find cntrl namelist (Tue Jul 10 2007 - 12:52:10 CDT)
  • Re: AMBER: Saving (.)prepin file (Tue Jul 10 2007 - 12:45:58 CDT)
  • Re: AMBER: tgtrmsmask and tgtfitmask (Tue Jul 10 2007 - 11:01:27 CDT)
  • Re: AMBER: ????pig5678?????? (Tue Jul 10 2007 - 10:14:45 CDT)
  • Re: AMBER: TIP4P MD simulations (Mon Jul 09 2007 - 13:31:15 CDT)
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Mon Jul 09 2007 - 09:58:51 CDT)
  • Re: AMBER: program bug? (Mon Jul 09 2007 - 09:48:35 CDT)
  • Re: AMBER: antechamber (Mon Jul 09 2007 - 09:41:23 CDT)
  • Re: AMBER: Problem with running Sander (Sat Jul 07 2007 - 23:59:05 CDT)
  • Re: AMBER: antechamber: mopac charges (Thu Jul 05 2007 - 15:24:09 CDT)
  • Re: AMBER: antechamber: mopac charges (Wed Jul 04 2007 - 18:27:02 CDT)
  • Re: AMBER: Problem with leaprc (Wed Jul 04 2007 - 15:31:29 CDT)
  • Re: AMBER: Fwd: antechamber save prmtop inpcrd (Wed Jul 04 2007 - 15:15:21 CDT)
  • Re: AMBER: Problem with leaprc (Wed Jul 04 2007 - 11:15:39 CDT)
  • Re: AMBER: Fwd: antechamber save prmtop inpcrd (Wed Jul 04 2007 - 10:53:04 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Tue Jul 03 2007 - 01:34:13 CDT)
  • Re: AMBER: Slow Processor Loads when Using PMEMD (Mon Jul 02 2007 - 20:24:09 CDT)
  • Re: AMBER: convergence criterion not reached (Mon Jul 02 2007 - 20:14:53 CDT)
  • Re: AMBER: Saving (.)prepin file (Mon Jul 02 2007 - 15:56:57 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Mon Jul 02 2007 - 15:20:27 CDT)
  • Re: AMBER: Problem with leaprc (Mon Jul 02 2007 - 09:44:59 CDT)
  • Re: AMBER: amber7 and xleap (Sat Jun 30 2007 - 19:57:13 CDT)
  • Re: AMBER: Problem with leaprc (Sat Jun 30 2007 - 10:32:03 CDT)
  • Re: Fwd: Re: AMBER: make test serial (Sat Jun 30 2007 - 10:28:01 CDT)
  • Re: AMBER: make serial failure for xleap (Fri Jun 29 2007 - 18:28:36 CDT)
  • Re: AMBER: Serial "make" failure with xleap (Fri Jun 29 2007 - 13:16:54 CDT)
  • Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH (Fri Jun 29 2007 - 11:05:09 CDT)
  • Re: AMBER: Problem with leaprc (Fri Jun 29 2007 - 10:47:51 CDT)
  • Re: Re: AMBER: $AMBERHOME on PATH (Thu Jun 28 2007 - 13:37:58 CDT)
  • Re: AMBER: configure question (Thu Jun 28 2007 - 11:26:34 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Thu Jun 28 2007 - 11:04:52 CDT)
  • Re: RE: Re: AMBER: $AMBERHOME on PATH (Thu Jun 28 2007 - 11:00:55 CDT)
  • Re: AMBER: remd/rdc's (Thu Jun 28 2007 - 10:37:44 CDT)
  • Re: AMBER: bugfix.all (Wed Jun 27 2007 - 15:55:52 CDT)
  • Re: Fwd: Re: AMBER: $AMBERHOME on PATH & compilations (Wed Jun 27 2007 - 12:06:38 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Wed Jun 27 2007 - 11:19:51 CDT)
  • Re: AMBER: "FATAL: Atom xxx does not have a type." (Tue Jun 26 2007 - 17:20:21 CDT)
  • Re: AMBER: Unexpected Failure in XLeap (Tue Jun 26 2007 - 15:47:30 CDT)
  • Re: AMBER: $AMBERHOME on PATH (Tue Jun 26 2007 - 13:01:02 CDT)
  • Re: AMBER: Offending restraints???? (Tue Jun 26 2007 - 11:37:21 CDT)
  • Re: AMBER: rst overflow for implicit REMD (Tue Jun 26 2007 - 10:28:28 CDT)
  • Re: AMBER: Offending restraints???? (Tue Jun 26 2007 - 10:27:18 CDT)
  • Re: AMBER: set up system solution with 3 different components, each with multiple copies (Tue Jun 26 2007 - 10:08:50 CDT)
  • Re: AMBER: Antechamber--Boron Parameters (Mon Jun 25 2007 - 20:08:48 CDT)
  • Re: AMBER: PMF calculation (Mon Jun 25 2007 - 19:47:25 CDT)
  • Re: AMBER: prepin for metal centre (Mon Jun 25 2007 - 19:43:26 CDT)
  • Re: AMBER: Simulated Annealing (Mon Jun 25 2007 - 19:34:38 CDT)
  • Re: AMBER: remd/rdc's (Sat Jun 23 2007 - 12:44:17 CDT)
  • Re: AMBER: 5 Ligands and 1 Protein (Fri Jun 22 2007 - 10:05:28 CDT)
  • Re: AMBER: sander core dumped during minimization (Thu Jun 21 2007 - 00:16:11 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Thu Jun 21 2007 - 00:10:43 CDT)
  • Re: AMBER: 5 Ligands and 1 Protein (Thu Jun 21 2007 - 00:02:20 CDT)
  • Re: AMBER: 5 Ligands and 1 Protein (Wed Jun 20 2007 - 19:16:27 CDT)
  • Re: AMBER: 5 Ligands and 1 Protein (Wed Jun 20 2007 - 18:46:23 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Wed Jun 20 2007 - 10:41:43 CDT)
  • Re: AMBER: frcmod (Mon Jun 18 2007 - 14:37:52 CDT)
  • Re: AMBER: problem with running rem on amber9 (Mon Jun 18 2007 - 13:22:01 CDT)
  • Re: AMBER: error due to exceeding left-hand side digital numbers in restart output (Mon Jun 18 2007 - 13:06:16 CDT)
  • Re: AMBER: Amber Installation Error (Mon Jun 18 2007 - 12:52:05 CDT)
  • Re: AMBER: isolated NTP (Mon Jun 18 2007 - 10:39:06 CDT)
  • Re: AMBER: umbrella sampling dihedral restraint question (Mon Jun 18 2007 - 00:46:16 CDT)
  • Re: AMBER: isolated NTP (Mon Jun 18 2007 - 00:40:29 CDT)
  • Re: AMBER: MMPBSA-nmode .top question (Mon Jun 18 2007 - 00:35:39 CDT)
  • Re: AMBER: Energy outputs in TI Approach (Sat Jun 16 2007 - 10:19:23 CDT)
  • Re: AMBER: distance scan (Sat Jun 16 2007 - 10:21:05 CDT)
  • Re: AMBER: frcmod (Fri Jun 15 2007 - 16:43:48 CDT)
  • Re: AMBER: PDB problems (Fri Jun 15 2007 - 15:24:44 CDT)
  • Re: AMBER: performance with implicit solvent (Fri Jun 15 2007 - 15:18:31 CDT)
  • Re: AMBER: Amber Installation Error (Fri Jun 15 2007 - 13:56:29 CDT)
  • Re: AMBER: Hbonds (Fri Jun 15 2007 - 13:06:26 CDT)
  • Re: AMBER: Hbonds (Wed Jun 13 2007 - 15:50:11 CDT)
  • Re: AMBER: problems using TIP4PBOX (Wed Jun 13 2007 - 07:26:11 CDT)
  • Re: AMBER: frcmod (Tue Jun 12 2007 - 16:34:35 CDT)
  • Re: AMBER: problem in installing amber9 (Tue Jun 12 2007 - 16:29:14 CDT)
  • Re: AMBER: dihedral parameters (Tue Jun 12 2007 - 14:35:57 CDT)
  • Re: AMBER: (Tue Jun 12 2007 - 14:29:06 CDT)
  • Re: AMBER: Installing on windows (Sun Jun 10 2007 - 23:25:28 CDT)
  • Re: AMBER: problem installing amber7 (Sun Jun 10 2007 - 21:59:17 CDT)
  • Re: AMBER: Trouble on wiki about GAFF (Fri Jun 08 2007 - 11:11:17 CDT)
  • Re: AMBER: Should we just vary one parameter at a time only for PMF calculations? (Fri Jun 08 2007 - 10:55:12 CDT)
  • Re: AMBER: Trouble on wiki about GAFF (Thu Jun 07 2007 - 22:31:12 CDT)
  • Re: AMBER: Restraining valence angles (Wed Jun 06 2007 - 09:49:08 CDT)
  • Re: AMBER: pdb flie format (Sun Jun 03 2007 - 22:04:58 CDT)
  • Re: AMBER: dihedral simulation (Sun Jun 03 2007 - 22:06:26 CDT)
  • Re: AMBER: Reg restraint value obtained during umbrella sampling (Sat Jun 02 2007 - 15:07:47 CDT)
  • Re: AMBER: Reg restraint value obtained during umbrella sampling (Fri Jun 01 2007 - 20:19:35 CDT)
  • Re: AMBER: problem in installing amber9 (Fri Jun 01 2007 - 20:12:56 CDT)
  • Re: AMBER: BUG? Does TLEAP understand SPC/E water? (Fri Jun 01 2007 - 13:39:42 CDT)
  • Re: AMBER: BUG? Does TLEAP understand SPC/E water? (Fri Jun 01 2007 - 13:37:10 CDT)
  • Re: AMBER: rms in nmode (Fri Jun 01 2007 - 10:50:27 CDT)
  • Re: AMBER: Question about separating bonded force (Fri Jun 01 2007 - 10:42:29 CDT)
  • Re: AMBER: Reg restraint value obtained during umbrella sampling (Thu May 31 2007 - 15:39:39 CDT)
  • Re: AMBER: cutoff & speed-up of GBSA (Thu May 31 2007 - 15:31:42 CDT)
  • Re: AMBER: Reg restraint value obtained during umbrella sampling (Thu May 31 2007 - 14:17:53 CDT)
  • Re: AMBER: electric field calculation (Thu May 31 2007 - 11:44:34 CDT)
  • Re: AMBER: RESTRAINTMASK (Thu May 31 2007 - 10:59:42 CDT)
  • Re: AMBER: electric field calculation (Wed May 30 2007 - 18:14:37 CDT)
  • Re: AMBER: junk in `Noshake mask` output section (Wed May 30 2007 - 16:47:51 CDT)
  • Re: AMBER: divcon missing in Antechamber 1.27 (Tue May 29 2007 - 09:24:20 CDT)
  • Re: AMBER: divcon missing in Antechamber 1.27 (Mon May 28 2007 - 20:33:52 CDT)
  • Re: AMBER: thermodynamic integration (Thu May 24 2007 - 23:14:43 CDT)
  • Re: AMBER: NAB normal mode output (Thu May 24 2007 - 23:17:04 CDT)
  • Re: AMBER: Docking with AMber (Mon May 21 2007 - 23:26:07 CDT)
  • AMBER: Langevin dynamics in NAB (Sun May 20 2007 - 20:39:42 CDT)
  • Re: AMBER: antechamber question (Sun May 20 2007 - 09:44:18 CDT)
  • Re: AMBER: Temperature Drift in MD (NAB) (Sat May 19 2007 - 23:03:24 CDT)
  • Re: AMBER: Temperature Drift in MD (NAB) (Fri May 18 2007 - 18:07:09 CDT)
  • Re: AMBER: AMBER8 compiler with intel 9.1 compiler (Thu May 17 2007 - 20:38:00 CDT)
  • Re: AMBER: AMBER8 compiler with intel 9.1 compiler (Thu May 17 2007 - 20:32:55 CDT)
  • Re: AMBER: NAB Average Structure (Thu May 17 2007 - 16:13:10 CDT)
  • Re: AMBER: NAB Average Structure (Thu May 17 2007 - 11:32:59 CDT)
  • Re: AMBER: AMBER8 compiler with intel 9.1 compiler (Wed May 16 2007 - 16:01:21 CDT)
  • Re: AMBER: work with constant pH on amber8 (Wed May 16 2007 - 13:40:42 CDT)
  • Re: AMBER: protonate (Wed May 16 2007 - 11:33:20 CDT)
  • Re: AMBER: protonate (Wed May 16 2007 - 11:32:37 CDT)
  • Re: AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set" (Wed May 16 2007 - 11:04:57 CDT)
  • Re: AMBER: Heat of Vaporization (Tue May 15 2007 - 15:14:24 CDT)
  • Re: AMBER: Heat of Vaporization (Tue May 15 2007 - 11:51:36 CDT)
  • Re: AMBER: Heat of Vaporization (Tue May 15 2007 - 11:09:27 CDT)
  • Re: AMBER: Energy Spread using GB & Langevin Dynamics (NAB) (Tue May 15 2007 - 11:03:52 CDT)
  • Re: AMBER: Rotations about center of mass of an isolated system (Mon May 14 2007 - 19:06:24 CDT)
  • Re: AMBER: Energy Spread using GB & Langevin Dynamics (NAB) (Mon May 14 2007 - 16:40:50 CDT)
  • Re: AMBER: Rotations about center of mass of an isolated system (Mon May 14 2007 - 16:37:09 CDT)
  • Re: AMBER: Rotations about center of mass of an isolated system (Mon May 14 2007 - 11:19:20 CDT)
  • Re: AMBER: PMF for DG calculation. (Mon May 14 2007 - 10:01:41 CDT)
  • Re: AMBER: missing impropers for nitros? (Sat May 12 2007 - 12:37:27 CDT)
  • Re: AMBER: distance.restraint for two groups of atoms (center of mass) (Sat May 12 2007 - 12:18:59 CDT)
  • Re: AMBER: antechamber (Sat May 12 2007 - 12:13:39 CDT)
  • Re: AMBER: single phospholipid molecule in vacuo (Thu May 10 2007 - 18:51:39 CDT)
  • Re: AMBER: Amber 9 compile on OS X (Thu May 10 2007 - 18:48:49 CDT)
  • Re: AMBER: leap problem (Thu May 10 2007 - 15:51:13 CDT)
  • Re: AMBER: (no subject) (Thu May 10 2007 - 15:37:21 CDT)
  • Re: AMBER: Sander (Amber 9) crash on cortex (Thu May 10 2007 - 14:55:16 CDT)
  • Re: AMBER: bug in reprocessing with PB? (Thu May 10 2007 - 13:24:20 CDT)
  • Re: AMBER: Electrostatic Energy in MD Simulation (GB) (Thu May 10 2007 - 12:45:45 CDT)
  • Re: AMBER: GB Energy Spreads for MD Structures (Mon May 07 2007 - 16:13:41 CDT)
  • Re: AMBER: Atoms closer to 2 angstroms to each other (Mon May 07 2007 - 09:55:30 CDT)
  • Re: AMBER: polarizable water models. (Sun May 06 2007 - 16:31:50 CDT)
  • Re: AMBER: Problem with calcpka.pl and constant pH (Thu May 03 2007 - 12:13:50 CDT)
  • Re: AMBER: command line alternatives for teLeap (Thu May 03 2007 - 09:30:00 CDT)
  • Re: AMBER: PDB files (Mon Apr 30 2007 - 15:00:33 CDT)
  • Re: AMBER: AMBER MINIMIZATION (Mon Apr 30 2007 - 10:24:34 CDT)
  • Re: AMBER: a problem of surface area calulated by MM/PBSA (Mon Apr 30 2007 - 10:20:43 CDT)
  • Re: AMBER: thermodynamic integration (Sat Apr 28 2007 - 16:26:28 CDT)
  • Re: AMBER: Error in protonating (Sat Apr 28 2007 - 16:26:08 CDT)
  • Re: AMBER: Error on compiling AMBER8 (Wed Apr 25 2007 - 13:33:11 CDT)
  • Re: AMBER: Error on compiling AMBER8 (Tue Apr 24 2007 - 22:31:44 CDT)
  • Re: AMBER: prep file new residue (Tue Apr 24 2007 - 14:12:44 CDT)
  • Re: AMBER: Problems with AMBER8 on 32-bit FC6 (Mon Apr 23 2007 - 16:17:09 CDT)
  • Re: AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out" (Sat Apr 21 2007 - 14:04:23 CDT)
  • Re: AMBER: restraint value: written but none specified (Fri Apr 20 2007 - 16:15:05 CDT)
  • Re: AMBER: ptraj and quasi harmonic analysis (Fri Apr 20 2007 - 11:49:26 CDT)
  • Re: AMBER: rigid epoxide substrate (Fri Apr 20 2007 - 10:30:42 CDT)
  • Re: AMBER: ptraj and quasi harmonic analysis (Fri Apr 20 2007 - 10:23:34 CDT)
  • Re: AMBER: AIX 5 test failures: -NaNQ (Thu Apr 19 2007 - 20:13:46 CDT)
  • Re: AMBER: Blue Gene, compile Amber9? (Thu Apr 19 2007 - 16:31:25 CDT)
  • Re: AMBER: regarding frcmod file (Thu Apr 19 2007 - 11:14:03 CDT)
  • Re: AMBER: signal SIGSEGV(11) (Wed Apr 18 2007 - 10:49:24 CDT)
  • Re: AMBER: using glycam04 parameters (Wed Apr 18 2007 - 10:28:27 CDT)
  • Re: AMBER: frcmod file (Wed Apr 18 2007 - 10:22:01 CDT)
  • Re: AMBER: using glycam04 parameters (Tue Apr 17 2007 - 16:37:35 CDT)
  • Re: AMBER: Re: MM-PBSA amber script problem (Tue Apr 17 2007 - 16:35:59 CDT)
  • Re: AMBER: nscm in simulation annealing (Tue Apr 17 2007 - 11:18:02 CDT)
  • Re: AMBER: mdfil.f (Mon Apr 16 2007 - 12:25:02 CDT)
  • Re: AMBER: Problem with PCSHIFT module (Sun Apr 15 2007 - 23:24:01 CDT)
  • Re: AMBER: Amber 8 support of CHARMM ff? (Sat Apr 14 2007 - 14:21:23 CDT)
  • Re: AMBER: polarization and water density (Fri Apr 13 2007 - 14:53:42 CDT)
  • Re: AMBER: nscm in simulation annealing (Fri Apr 13 2007 - 14:48:13 CDT)
  • Re: AMBER: Restraints and free energy (Fri Apr 13 2007 - 12:22:49 CDT)
  • Re: AMBER: nscm in simulation annealing (Fri Apr 13 2007 - 12:22:32 CDT)
  • Re: AMBER: bad atom type errors in GB for halides? (Thu Apr 12 2007 - 19:04:55 CDT)
  • Re: AMBER: nscm in simulation annealing (Thu Apr 12 2007 - 19:05:01 CDT)
  • Re: AMBER: nscm in simulation annealing (Thu Apr 12 2007 - 11:41:03 CDT)
  • Re: AMBER: working with Antechamber (Wed Apr 11 2007 - 14:56:00 CDT)
  • Re: AMBER: Problem with Sander restart file. (Wed Apr 11 2007 - 13:11:40 CDT)
  • Re: AMBER: Question about MMPBSA v9 (Tue Apr 10 2007 - 21:20:58 CDT)
  • Re: AMBER: Problems during compilation and test. (Tue Apr 10 2007 - 20:27:39 CDT)
  • Re: AMBER: Constant volume simulations (Mon Apr 09 2007 - 15:24:09 CDT)
  • Re: AMBER: ptraj:problems with time correlation calculation (comp. with NMR experiments) (Mon Apr 09 2007 - 12:27:59 CDT)
  • Re: AMBER: Fails to load libraries present in /leap/lib/ (Mon Apr 09 2007 - 12:25:41 CDT)
  • Re: AMBER: NTX=7 ?............lastist= ?...........lastrst= ????? (Mon Apr 09 2007 - 12:21:21 CDT)
  • Re: AMBER: supplement ptraj:problems with time correlation calculation (comp. with NMR experiments) (Mon Apr 09 2007 - 09:56:56 CDT)
  • Re: AMBER: PDB file format for AMBER (Sat Apr 07 2007 - 10:56:18 CDT)
  • Re: AMBER: SANDER PMEMD ntpr ntwx discrepancy (?bug? report) (Fri Apr 06 2007 - 17:37:46 CDT)
  • Re: AMBER: Energy minimization problem (Wed Apr 04 2007 - 20:25:26 CDT)
  • Re: AMBER: about define improper torsion in .frcmod file (Wed Apr 04 2007 - 10:25:11 CDT)
  • Re: AMBER: Energy minimization problem (Tue Apr 03 2007 - 20:39:37 CDT)
  • Re: AMBER: nmode (Tue Apr 03 2007 - 11:31:54 CDT)
  • Re: AMBER: nmode (Tue Apr 03 2007 - 10:25:52 CDT)
  • Re: AMBER: phosphorylated residues (Mon Apr 02 2007 - 17:13:37 CDT)
  • Re: AMBER: Xleap errors (Mon Apr 02 2007 - 12:32:47 CDT)
  • Re: AMBER: Error at Equilibration.... (Mon Apr 02 2007 - 10:45:57 CDT)
  • Re: AMBER: Problem with PCSHIFT module (Sat Mar 31 2007 - 22:13:12 CST)
  • Re: AMBER: Some problems during the testing of Amber. (Sat Mar 31 2007 - 22:13:38 CST)
  • Re: AMBER: Distance restraint to centre of mass (Sat Mar 31 2007 - 22:13:48 CST)
  • Re: AMBER: DISAVE value1 (Fri Mar 30 2007 - 09:24:27 CST)
  • Re: AMBER: Amber9 Sander Error (Fri Mar 30 2007 - 08:04:40 CST)
  • Re: AMBER: Please check the total charge and your -nc flag (Tue Mar 27 2007 - 16:29:32 CST)
  • Re: AMBER: Amber 9 TI Details (Tue Mar 27 2007 - 16:23:34 CST)
  • Re: AMBER: amber 9: fortran/test failures (Tue Mar 27 2007 - 16:15:50 CST)
  • Re: AMBER: amber 9 - output of forces (Fri Mar 23 2007 - 23:10:21 CST)
  • Re: AMBER: Holding NA Base syn during annealing (Thu Mar 22 2007 - 09:41:30 CST)
  • Re: AMBER: xLeAP: TI calculation: the perturbed charge is not integral (Wed Mar 21 2007 - 13:33:33 CST)
  • Re: AMBER: ntt=1 or ntt= 3? (Wed Mar 21 2007 - 13:29:45 CST)
  • Re: AMBER: Problem while loading Pdb in xleap (Tue Mar 20 2007 - 23:31:42 CST)
  • Re: AMBER: vlimit error (Mon Mar 19 2007 - 17:11:57 CST)
  • Re: AMBER: Essential ions and water molecules in MMPBSA computations (Mon Mar 19 2007 - 09:02:41 CST)
  • Re: AMBER: antechamber (Sun Mar 18 2007 - 17:50:00 CST)
  • Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) (Fri Mar 16 2007 - 14:51:14 CST)
  • Re: AMBER: Problem with anisotropic pressure scaling (Fri Mar 16 2007 - 09:55:51 CST)
  • Re: AMBER: Segmentation Fault when saving prmtop and inpcrd files in xleap (Fri Mar 16 2007 - 09:24:16 CST)
  • Re: AMBER: solvate shell (Thu Mar 15 2007 - 13:36:04 CST)
  • Re: AMBER: van der waals parameters. (Thu Mar 15 2007 - 13:30:34 CST)
  • Re: AMBER: Problem related simulation of dimer (Thu Mar 15 2007 - 11:09:52 CST)
  • Re: AMBER: AMBER hydrophobic Box : script (Wed Mar 14 2007 - 10:22:41 CST)
  • Re: AMBER: AMBER hydrophobic Box : script (Wed Mar 14 2007 - 09:29:47 CST)
  • Re: AMBER: poor performance of sander on a quad-core linux machine (Tue Mar 13 2007 - 11:42:48 CST)
  • Re: AMBER: Can I measure improper torsion by ptarj? (Tue Mar 13 2007 - 10:55:13 CST)
  • Re: AMBER: Can I measure improper torsion by ptarj? (Mon Mar 12 2007 - 10:36:07 CST)
  • Re: AMBER: unable to run test (Mon Mar 12 2007 - 00:54:34 CST)
  • Re: AMBER: rmsd calculation in ptraj II (Sat Mar 10 2007 - 23:55:32 CST)
  • Re: AMBER: problem with ptraj with calculating auto time correlation functions (Sat Mar 10 2007 - 11:34:32 CST)
  • Re: AMBER: problem with ptraj with calculating auto time correlation functions (Fri Mar 09 2007 - 19:01:44 CST)
  • Re: AMBER: Topology file problem in TI ! (Thu Mar 08 2007 - 09:59:22 CST)
  • Re: AMBER: DHAS_10_12 compilation aborted for egb.f (Wed Mar 07 2007 - 12:11:21 CST)
  • Re: AMBER: addles segmentation fault (Wed Mar 07 2007 - 11:23:21 CST)
  • Re: AMBER: how is the standard deviations calculated in mm-pbsa? (Tue Mar 06 2007 - 19:13:55 CST)
  • Re: AMBER: how to modify map.DG-AMBER file? (Tue Mar 06 2007 - 19:06:57 CST)
  • Re: AMBER: DHAS_10_12 compilation aborted for egb.f (Tue Mar 06 2007 - 10:31:10 CST)
  • Re: AMBER: prep file limit exceeding (Mon Mar 05 2007 - 23:25:20 CST)
  • Re: AMBER: pbsa installation problem (Mon Mar 05 2007 - 11:48:13 CST)
  • Re: AMBER: Restraints on modified NA's (Mon Mar 05 2007 - 10:44:56 CST)
  • Re: AMBER: coordinate changes using ptraj (Mon Mar 05 2007 - 10:41:42 CST)
  • Re: AMBER: TI calculation: charge is not zero in the perturbed state (Sat Mar 03 2007 - 15:11:52 CST)
  • Re: AMBER: Amber 9 make parallel fails with mpich (Fri Mar 02 2007 - 11:59:50 CST)
  • Re: AMBER: OpenMPI on MacBook Pro -- problems (Fri Mar 02 2007 - 11:36:28 CST)
  • Re: AMBER: solvent accessible surface area (SASA) (Thu Mar 01 2007 - 12:42:31 CST)
  • AMBER: [rsachdeva@imtech.res.in: A query] (Thu Mar 01 2007 - 11:02:27 CST)
  • Re: AMBER: Disulfide Problem (Thu Mar 01 2007 - 11:00:31 CST)
  • Re: AMBER: momentum and periodic boundary condition (Thu Mar 01 2007 - 10:52:00 CST)
  • Re: AMBER: solvent accessible surface area (SASA) (Thu Mar 01 2007 - 10:47:19 CST)
  • Re: AMBER: problem with atom restraints (Wed Feb 28 2007 - 12:54:58 CST)
  • Re: AMBER: LEaP crashes (Wed Feb 28 2007 - 12:03:29 CST)
  • Re: AMBER: phe-phe molecule (Wed Feb 28 2007 - 12:03:49 CST)
  • Re: AMBER: getting same box dimension (Mon Feb 26 2007 - 20:10:30 CST)
  • AMBER: Re: REMD with torsional restraints- Temperature swapping not occuring (Mon Feb 26 2007 - 17:01:41 CST)
  • Re: AMBER: Modified nucleotides-ATOM TYPES (Mon Feb 26 2007 - 08:21:16 CST)
  • Re: AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8 (Fri Feb 23 2007 - 10:35:34 CST)
  • Re: AMBER: LEaP Problem (Thu Feb 22 2007 - 20:02:11 CST)
  • Re: AMBER: Is this system too large? (Thu Feb 22 2007 - 20:01:52 CST)
  • AMBER: [rsachdeva@imtech.res.in: Pls help - REMD with torsional restraints] (Thu Feb 22 2007 - 20:03:47 CST)
  • Re: AMBER: Amber/ANAL and psf files (Wed Feb 21 2007 - 22:14:42 CST)
  • Re: AMBER: Is this system too large? (Wed Feb 21 2007 - 18:05:39 CST)
  • Re: AMBER: carbohydrate-peptide (Wed Feb 21 2007 - 18:04:59 CST)
  • Re: AMBER: Pseudo-CSA in Amber? (Wed Feb 21 2007 - 18:04:32 CST)
  • Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa (Sat Feb 17 2007 - 15:22:38 CST)
  • Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa (Fri Feb 16 2007 - 19:22:05 CST)
  • Re: AMBER: Problem with dacdif when using cygwin (Fri Feb 16 2007 - 13:44:00 CST)
  • Re: AMBER: Box dimensions (Fri Feb 16 2007 - 10:54:48 CST)
  • Re: AMBER: implicit solvent free energy calcs (Thu Feb 15 2007 - 14:19:53 CST)
  • Re: AMBER: units in hessian matrix (Thu Feb 15 2007 - 12:07:03 CST)
  • Re: AMBER: units in hessian matrix (Thu Feb 15 2007 - 11:31:01 CST)
  • Re: AMBER: NMR violations increase in explicite water (Thu Feb 15 2007 - 10:40:12 CST)
  • Re: AMBER: Membrane Simulation: NPT Issues (Wed Feb 14 2007 - 17:04:47 CST)
  • Re: AMBER: SANDER bug (Wed Feb 14 2007 - 12:11:12 CST)
  • Re: AMBER: Box problems in vacuum minimization with sander.serial 8 (Tue Feb 13 2007 - 13:34:57 CST)
  • Re: AMBER: Lone Pairs (Tue Feb 13 2007 - 10:00:21 CST)
  • Re: AMBER: amber9 possible failure tgtmd (Mon Feb 12 2007 - 23:58:15 CST)
  • Re: AMBER: Lone Pairs (Mon Feb 12 2007 - 15:24:48 CST)
  • Re: AMBER: quasiharnomic analysis (Mon Feb 12 2007 - 10:31:36 CST)
  • Re: AMBER: connect atom (Mon Feb 12 2007 - 10:28:57 CST)
  • Re: AMBER: reporting EPtot and EKtot separately for two molecules (Mon Feb 12 2007 - 10:25:55 CST)
  • Re: AMBER: question about distance restraint on terminal WC of DNA duplex (AMBER9) (Sun Feb 11 2007 - 00:57:27 CST)
  • Re: AMBER: extracting coordinate from crd file (Sat Feb 10 2007 - 10:08:28 CST)
  • Re: AMBER: problem with sander (Sat Feb 10 2007 - 04:08:01 CST)
  • Re: AMBER: assigning charges to a prepi file (Fri Feb 09 2007 - 00:58:08 CST)
  • Re: AMBER: Compiling AMBER 8 on RHEL4 AMD64 (Fri Feb 09 2007 - 00:22:01 CST)
  • Re: AMBER: antechamber for topology file (Thu Feb 08 2007 - 01:08:04 CST)
  • Re: AMBER: problem with AMBER8 installation (Wed Feb 07 2007 - 12:10:51 CST)
  • Re: AMBER: trajectory problem (Wed Feb 07 2007 - 11:52:59 CST)
  • Re: AMBER: MAXGRP error message (Wed Feb 07 2007 - 11:43:33 CST)
  • Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) (Tue Feb 06 2007 - 18:22:03 CST)
  • Re: AMBER: Compile Amber9 for MVAPICH (Tue Feb 06 2007 - 14:23:07 CST)
  • Re: AMBER: Tutorial for chemical shift calculation? (Tue Feb 06 2007 - 10:25:40 CST)
  • Re: AMBER: Glycam (Tue Feb 06 2007 - 10:04:21 CST)
  • Re: AMBER: equilibration in explicit solvent (Sun Feb 04 2007 - 23:27:44 CST)
  • Re: AMBER: equilibration in explicit solvent (Sun Feb 04 2007 - 12:21:18 CST)
  • Re: AMBER: addions (Sun Feb 04 2007 - 11:33:37 CST)
  • Re: AMBER: iRED and corrired (Fri Feb 02 2007 - 12:57:43 CST)
  • Re: AMBER: Example needed for addAtomType command (Thu Feb 01 2007 - 16:30:03 CST)
  • Re: AMBER: xleap (Thu Feb 01 2007 - 10:58:40 CST)
  • Re: AMBER: Charges in TI calculations and leap (Tue Jan 30 2007 - 15:24:33 CST)
  • Re: AMBER: Gas-phase energies (and more) (Sun Jan 28 2007 - 20:23:29 CST)
  • Re: AMBER: Improper angle by Antechamber (Sun Jan 28 2007 - 20:20:26 CST)
  • Re: AMBER: amber9 parralel compiling (Sat Jan 27 2007 - 13:28:27 CST)
  • Re: AMBER: LJ potential (Sat Jan 27 2007 - 12:03:15 CST)
  • Re: AMBER: NVT/NPT equilibration issue in GPCR-membrane simulation (Fri Jan 26 2007 - 19:45:51 CST)
  • Re: AMBER: pmemd install error (Fri Jan 26 2007 - 17:45:14 CST)
  • Re: AMBER: amber9 parralel compiling (Fri Jan 26 2007 - 17:45:25 CST)
  • Re: AMBER: improper dihedral (Fri Jan 26 2007 - 10:09:55 CST)
  • Re: AMBER: coordinates ****** (Thu Jan 25 2007 - 14:08:52 CST)
  • Re: AMBER: nuc.in file (Thu Jan 25 2007 - 13:59:12 CST)
  • Re: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f (Wed Jan 24 2007 - 09:14:24 CST)
  • Re: AMBER: Problem with installation of the leap module of AMBER9 on Linux Suse 10.2 (Wed Jan 24 2007 - 09:09:36 CST)
  • Re: AMBER: minimization using fcap (Wed Jan 24 2007 - 09:05:20 CST)
  • Re: AMBER: Defining BOX INFO during TLEAP (Wed Jan 24 2007 - 09:04:24 CST)
  • Re: AMBER: problem with distance restraints (Mon Jan 22 2007 - 17:41:50 CST)
  • Re: AMBER: problem with distance restraints (Mon Jan 22 2007 - 14:10:12 CST)
  • Re: AMBER: equilibration with amber5, production of MD with amber7 (Sun Jan 21 2007 - 23:28:46 CST)
  • Re: AMBER: Radii for water hydrogens are different (Fri Jan 19 2007 - 12:13:41 CST)
  • Re: AMBER: The convergence criteria for the energy minimization of the DNA molecule (dodecmer duplux) (Fri Jan 19 2007 - 10:36:34 CST)
  • Re: AMBER: perturbed atoms are not bonded on using TIP5P wate (Thu Jan 18 2007 - 11:40:37 CST)
  • Re: AMBER: error when using sander.LES: exceeded MAXLES (Thu Jan 18 2007 - 11:12:23 CST)
  • Re: AMBER: sanger (Thu Jan 18 2007 - 11:05:34 CST)
  • Re: AMBER: vdW parameters for chlorine atom (Wed Jan 17 2007 - 19:55:15 CST)
  • Re: AMBER: Drug bound to the protein (Wed Jan 17 2007 - 10:57:02 CST)
  • Re: AMBER: How are water molecules at cutoff being treated? (Tue Jan 16 2007 - 17:36:07 CST)
  • Re: AMBER: calcium parameter for GB (Tue Jan 16 2007 - 17:33:43 CST)
  • Re: AMBER: perturbed atoms are not bonded on using TIP5P water (Mon Jan 15 2007 - 20:23:17 CST)
  • Re: AMBER: problem compiling Amber 7 (Mon Jan 15 2007 - 11:38:26 CST)
  • Re: AMBER: perturbed atoms are not bonded on using TIP5P water (Sun Jan 14 2007 - 11:39:13 CST)
  • Re: AMBER: solvation of protein using TIP3PBOX in amber 8 (Sat Jan 13 2007 - 23:40:46 CST)
  • Re: AMBER: output (Sat Jan 13 2007 - 23:38:24 CST)
  • Re: AMBER: perturbed atoms are not bonded on using TIP5P water (Thu Jan 11 2007 - 16:12:23 CST)
  • Re: AMBER: amber 9 (Thu Jan 11 2007 - 13:21:09 CST)
  • Re: AMBER: Section missing from AMBER 9 manual? (Wed Jan 10 2007 - 15:02:12 CST)
  • Re: AMBER: Hydrogen in a phosphate ion (Tue Jan 09 2007 - 13:46:43 CST)
  • Re: AMBER: How to change the force field equation in amber by programming... (Mon Jan 08 2007 - 17:00:10 CST)
  • Re: AMBER: question about the testing of AMBER9 (Fri Jan 05 2007 - 22:54:53 CST)
  • Re: AMBER: How to change the force field equation in amber by programming... (Fri Jan 05 2007 - 15:34:41 CST)
  • Re: AMBER: How to get a periodic box of modified water molecules (Thu Jan 04 2007 - 00:04:10 CST)
  • Re: AMBER: amber9 installation error (Wed Jan 03 2007 - 20:05:35 CST)
  • Re: AMBER: installing amber 8 on 5 nodes cluster PC (Wed Jan 03 2007 - 11:26:17 CST)
  • Re: AMBER: torsion angle penalty calculation (Wed Jan 03 2007 - 10:54:33 CST)
  • Re: AMBER: amber9 installation error (Wed Jan 03 2007 - 01:00:50 CST)
  • Re: AMBER: problems trying to modify Amber8 (Tue Jan 02 2007 - 17:53:36 CST)
  • Re: AMBER: Distance Restraints Problem (Tue Jan 02 2007 - 17:37:18 CST)
• David Cerutti
  • AMBER: Solved: Heat capacity calculations not coming out right (Mon Oct 22 2007 - 13:01:32 CDT)
  • Re: AMBER: Addendum: Heat capacity calculations not coming out right (Sat Oct 20 2007 - 17:47:05 CDT)
  • AMBER: Addendum: Heat capacity calculations not coming out right (Fri Oct 19 2007 - 22:31:46 CDT)
  • AMBER: Heat capacity calculations not coming out right (Fri Oct 19 2007 - 21:37:38 CDT)
  • AMBER: Heat capacity, diffusivity way off in this simulation of SPC/E water? (Tue Oct 09 2007 - 00:25:43 CDT)
  • Re: AMBER: 31 integers in the first section of a prmtop file (Wed Oct 03 2007 - 15:04:35 CDT)
  • RE: AMBER: 31 integers in the first section of a prmtop file (Wed Oct 03 2007 - 13:47:42 CDT)
  • AMBER: 31 integers in the first section of a prmtop file (Wed Oct 03 2007 - 11:58:03 CDT)
  • Re: AMBER: Solvation Issues (Sat Sep 29 2007 - 22:55:43 CDT)
  • Re: AMBER: Solvation Issues (Wed Sep 26 2007 - 18:53:11 CDT)
  • Re: AMBER: Water question (Sun Sep 23 2007 - 14:01:24 CDT)
  • Re: AMBER: Problem with Getting SHAKE to work (Mon Sep 17 2007 - 15:36:59 CDT)
  • Re: AMBER: Problem with Getting SHAKE to work (Sun Sep 16 2007 - 11:29:38 CDT)
  • Re: AMBER: Problem with Getting SHAKE to work (Sat Sep 15 2007 - 22:16:10 CDT)
  • AMBER: Problem with Getting SHAKE to work (Sat Sep 15 2007 - 13:04:14 CDT)
  • Re: AMBER: Problem with modelling ammonium ion? (Wed Sep 05 2007 - 00:22:50 CDT)
  • AMBER: Problem with modelling ammonium ion? (Tue Sep 04 2007 - 20:26:22 CDT)
  • Re: AMBER: Scaling for octahedral versus rectilinear boxes (Fri Aug 31 2007 - 08:27:38 CDT)
  • AMBER: Scaling for octahedral versus rectilinear boxes (Fri Aug 31 2007 - 00:32:49 CDT)
  • Re: AMBER: Octahedral box orientation (Tue Aug 21 2007 - 19:07:32 CDT)
  • AMBER: Octahedral box orientation (Tue Aug 21 2007 - 08:08:38 CDT)
  • Re: AMBER: Any experience on Dell two quad core system? (Tue Aug 14 2007 - 10:05:34 CDT)
  • AMBER: Using TLEAP to set up MD in the crystal lattice space? (Mon Aug 13 2007 - 16:09:51 CDT)
  • Re: AMBER: Any experience on Dell two quad core system? (Mon Aug 13 2007 - 15:59:58 CDT)
  • AMBER: BUG? Does TLEAP understand SPC/E water? (Fri Jun 01 2007 - 12:35:02 CDT)
  • Re: AMBER: Pi-pi interactions (Mon May 21 2007 - 08:13:16 CDT)
  • Re: AMBER: Explicit water opinion (Fri Apr 13 2007 - 17:58:32 CDT)
  • AMBER: Extra points... virial computation (Sun Apr 08 2007 - 01:48:11 CDT)
  • AMBER: Extra Points... How to Deal with Them (Tue Apr 03 2007 - 01:39:23 CDT)
  • AMBER: Deriving constraint forces on water molecules based on SETTLE moves (Wed Feb 14 2007 - 18:08:45 CST)
  • Re: AMBER: Positive binding free energy! (Tue Feb 13 2007 - 18:40:35 CST)
  • AMBER: Constraint virial (Tue Feb 13 2007 - 04:22:20 CST)
  • AMBER: Still puzzled about this virial computation (Thu Feb 01 2007 - 02:00:10 CST)
  • AMBER: I need some constant pressure MD help (Tue Jan 30 2007 - 22:39:06 CST)
• David J. Powers
  • RE: AMBER: Compiling Amber 7 (Sat Feb 10 2007 - 09:59:42 CST)
  • RE: AMBER: Compiling Amber 7 (Thu Feb 08 2007 - 13:27:41 CST)
  • AMBER: Compiling Amber 7 (Thu Feb 08 2007 - 09:13:00 CST)
• David LeBard
  • Re: AMBER: amber on AMD opteron-250 (Wed Dec 05 2007 - 14:29:22 CST)
  • Re: AMBER: What is the best computer for running AMBER simulations? (Thu Aug 16 2007 - 17:17:42 CDT)
  • Re: AMBER: Binary file curiosities (Sat Aug 04 2007 - 16:34:23 CDT)
  • AMBER: Binary file curiosities (Fri Aug 03 2007 - 17:59:45 CDT)
  • Re: AMBER: Question about MPI-IO (Mon Jun 11 2007 - 20:59:33 CDT)
  • AMBER: Question about MPI-IO (Mon Jun 11 2007 - 15:58:54 CDT)
  • Re: AMBER: Hardware recommendations please (Thu Jun 07 2007 - 13:31:21 CDT)
  • Re: AMBER: Error on compile amber8 (Tue Apr 24 2007 - 00:45:45 CDT)
  • AMBER: Problems with AMBER8 on 32-bit FC6 (Mon Apr 23 2007 - 13:51:02 CDT)
  • Re: AMBER: Question about loadMol2 (Tue Mar 27 2007 - 16:53:21 CST)
  • Re: AMBER: Question about loadMol2 (Tue Mar 27 2007 - 14:49:10 CST)
  • AMBER: Question about loadMol2 (Tue Mar 27 2007 - 12:31:56 CST)
  • Re: AMBER: read the data (Fri Feb 16 2007 - 13:22:12 CST)
  • Re: AMBER: read the data (Fri Feb 16 2007 - 13:00:10 CST)
  • Re: AMBER: read the data (Fri Feb 16 2007 - 12:31:13 CST)
  • Re: AMBER: read the data (Thu Feb 15 2007 - 15:18:08 CST)
• David Mobley
  • Re: AMBER: replica exchange out files continually overwritten (Fri Dec 14 2007 - 17:04:50 CST)
  • Re: AMBER: replica exchange out files continually overwritten (Fri Dec 14 2007 - 13:18:21 CST)
  • Re: AMBER: replica exchange out files continually overwritten (Fri Dec 14 2007 - 12:47:27 CST)
  • AMBER: replica exchange out files continually overwritten (Fri Dec 14 2007 - 11:02:41 CST)
  • AMBER: LJ parameters for alkynes (Mon Nov 26 2007 - 12:07:37 CST)
  • Re: AMBER: Antechamber (Tue Nov 06 2007 - 14:41:17 CST)
  • Re: AMBER: Antechamber (Tue Nov 06 2007 - 11:15:33 CST)
  • Re: AMBER: prepin file format description; pointers on parameterization (Thu Oct 25 2007 - 15:41:06 CDT)
  • Re: AMBER: prepin file format description; pointers on parameterization (Thu Oct 25 2007 - 15:39:08 CDT)
  • Re: AMBER: prepin file format description; pointers on parameterization (Wed Oct 24 2007 - 19:58:45 CDT)
  • Re: AMBER: prepin file format description; pointers on parameterization (Wed Oct 24 2007 - 18:58:35 CDT)
  • Re: AMBER: prepin file format description; pointers on parameterization (Wed Oct 24 2007 - 18:35:26 CDT)
  • Re: AMBER: prepin file format description; pointers on parameterization (Wed Oct 24 2007 - 15:45:54 CDT)
  • Re: AMBER: prepin file format description; pointers on parameterization (Wed Oct 24 2007 - 14:31:02 CDT)
  • AMBER: prepin file format description; pointers on parameterization (Wed Oct 24 2007 - 12:52:24 CDT)
  • Re: AMBER: An enquiry about "Dynamics of ligand escape from the heme pocket of myoglobin (JACS, 1988, 110, 7690 (Wed Oct 24 2007 - 09:20:43 CDT)
  • Re: AMBER: results from TI (Wed Oct 24 2007 - 09:18:50 CDT)
  • Re: AMBER: results from TI (Tue Oct 23 2007 - 12:09:31 CDT)
  • Re: AMBER: results from TI (Tue Oct 23 2007 - 08:40:26 CDT)
  • Re: AMBER: Confusion about Langevin dymamics (Fri Aug 31 2007 - 11:05:13 CDT)
  • Re: AMBER: Entropy in MM_PBSA (Fri Aug 24 2007 - 11:31:28 CDT)
  • Re: AMBER: Thermodynamic Integration for a CHARGED molecule (Fri Aug 17 2007 - 08:56:33 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Thu Jul 05 2007 - 10:56:43 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Tue Jul 03 2007 - 14:55:54 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Mon Jul 02 2007 - 15:03:17 CDT)
  • Re: AMBER: equilibrium constants via MMPBSA (Mon Jun 04 2007 - 08:11:25 CDT)
  • Fwd: AMBER: missing impropers for nitros? (Mon May 21 2007 - 10:47:04 CDT)
  • Re: AMBER: PMF for DG calculation. (Mon May 14 2007 - 09:06:46 CDT)
  • Re: AMBER: missing impropers for nitros? (Mon May 14 2007 - 08:28:34 CDT)
  • AMBER: Re: missing impropers for nitros? (Fri May 11 2007 - 19:15:11 CDT)
  • AMBER: missing impropers for nitros? (Fri May 11 2007 - 19:03:55 CDT)
  • Re: AMBER: bug in reprocessing with PB? (Thu May 10 2007 - 14:18:23 CDT)
  • Re: AMBER: bug in reprocessing with PB? (Thu May 10 2007 - 14:20:26 CDT)
  • AMBER: bug in reprocessing with PB? (Thu May 10 2007 - 13:08:10 CDT)
  • Re: AMBER: Potential of mean force, how to calculate rate of dissociation? (Fri May 04 2007 - 16:09:36 CDT)
  • Re: AMBER: Rate of Dissociation (Fri May 04 2007 - 12:41:51 CDT)
  • Re: AMBER: Potential of mean force, how to calculate rate of dissociation? (Fri May 04 2007 - 12:39:34 CDT)
  • Re: AMBER: Potential of mean force, how to calculate rate of dissociation? (Thu May 03 2007 - 17:17:31 CDT)
  • Re: AMBER: Steered MD & Jarzynski's equality (Wed May 02 2007 - 09:39:23 CDT)
  • AMBER: bad atom type errors in GB for halides? (Thu Apr 12 2007 - 12:19:51 CDT)
  • Re: AMBER: working with Antechamber (Wed Apr 11 2007 - 13:34:55 CDT)
  • AMBER: temperature artifacts with andersen and GB? (Wed Apr 11 2007 - 11:50:17 CDT)
  • Re: AMBER: sander (AMBER 9) and -y flag -- not working? (Tue Apr 10 2007 - 14:31:56 CDT)
  • Re: AMBER: sander (AMBER 9) and -y flag -- not working? (Tue Apr 10 2007 - 14:04:52 CDT)
  • Re: AMBER: sander (AMBER 9) and -y flag -- not working? (Tue Apr 10 2007 - 13:52:29 CDT)
  • AMBER: sander (AMBER 9) and -y flag -- not working? (Tue Apr 10 2007 - 13:22:39 CDT)
  • Re: AMBER: Question about loadMol2 (Tue Mar 27 2007 - 14:15:26 CST)
  • Re: AMBER: Combining RESP with AM1-BCC (Fri Mar 23 2007 - 17:17:50 CST)
  • AMBER: implicit solvent free energy calcs (Thu Feb 15 2007 - 12:07:37 CST)
  • Re: AMBER: How precise is a MD simulation? (Tue Feb 13 2007 - 14:19:13 CST)
  • Re: AMBER: How precise is a MD simulation? (Tue Feb 13 2007 - 14:11:17 CST)
  • Re: AMBER: How precise is a MD simulation? (Tue Feb 13 2007 - 13:36:17 CST)
  • Re: AMBER: Ligand-Protein Distance Restraints during MD Simulation (Tue Jan 30 2007 - 11:16:19 CST)
• Davide Moiani
  • Re: AMBER: Torsion terms in xleap (Fri Sep 14 2007 - 18:55:37 CDT)
  • Re: AMBER: refc error (Tue Jul 17 2007 - 16:00:20 CDT)
  • Re: AMBER: refc error (Mon Jul 16 2007 - 19:17:18 CDT)
  • Re: AMBER: refc error (Mon Jul 16 2007 - 19:03:42 CDT)
  • Re: AMBER: manganese ion (Wed Jul 11 2007 - 16:47:18 CDT)
  • Re: AMBER: manganese ion (Tue Jul 10 2007 - 11:47:38 CDT)
  • AMBER: manganese ion (Mon Jul 09 2007 - 16:02:31 CDT)
• deepti nayar
  • AMBER: restraining atoms (Sun May 13 2007 - 23:39:15 CDT)
  • AMBER: restraint_wt and fixing chi (Thu May 10 2007 - 05:44:40 CDT)
  • AMBER: REF file problem (Mon May 07 2007 - 01:49:53 CDT)
  • AMBER: md output file (Thu May 03 2007 - 04:06:24 CDT)
  • AMBER: frcmod file (Wed Apr 18 2007 - 01:31:52 CDT)
  • AMBER: vmd and amber (Tue Apr 17 2007 - 06:58:51 CDT)
  • Re: AMBER: problem related to visualizing of structure (Tue Apr 10 2007 - 04:42:58 CDT)
  • Re: AMBER: problem related to visualizing of structure (Tue Apr 10 2007 - 04:18:38 CDT)
  • AMBER: problem related to visualizing of structure (Tue Apr 10 2007 - 01:33:40 CDT)
  • AMBER: restraint command not taken (Mon Apr 02 2007 - 04:54:44 CDT)
  • AMBER: restraint command not taken (Mon Apr 02 2007 - 04:25:12 CDT)
  • AMBER: restraint command not taken (Mon Apr 02 2007 - 05:21:51 CDT)
  • AMBER: RST can not be opened (Fri Mar 30 2007 - 03:21:58 CST)
  • Re: AMBER: minimization energy query (Fri Mar 30 2007 - 03:03:24 CST)
  • AMBER: minimization + simulation (Fri Mar 30 2007 - 01:54:03 CST)
  • Re: AMBER: minimization energy query (Fri Mar 30 2007 - 01:50:56 CST)
  • Re: AMBER: minimization energy query (Thu Mar 29 2007 - 05:35:45 CST)
  • AMBER: minimization energy query (Thu Mar 29 2007 - 04:55:39 CST)
  • Re: AMBER: minimization not running (Thu Mar 29 2007 - 04:51:26 CST)
  • AMBER: minimization not running (Thu Mar 29 2007 - 03:57:15 CST)
  • AMBER: specifying psi and phi for a dipeptide (Wed Mar 28 2007 - 05:50:28 CST)
  • Re: AMBER: phe-phe simulation (Wed Mar 28 2007 - 05:28:51 CST)
  • Re: AMBER: phe-phe simulation (Tue Mar 27 2007 - 06:48:01 CST)
  • Re: AMBER: phe-phe simulation (Mon Mar 26 2007 - 23:12:03 CST)
  • Re: AMBER: restraint in minimization (Mon Mar 26 2007 - 23:10:50 CST)
  • AMBER: phe-phe simulation (Mon Mar 26 2007 - 01:25:19 CST)
  • AMBER: restraint in minimization (Thu Mar 22 2007 - 02:21:32 CST)
  • Re: AMBER: torsion angle (Thu Mar 15 2007 - 00:13:43 CST)
  • AMBER: torsion angle (Wed Mar 14 2007 - 06:03:08 CST)
  • AMBER: NEB tutorial and addles (Tue Mar 13 2007 - 22:28:20 CST)
  • Re: AMBER: addles (Mon Mar 12 2007 - 05:37:27 CST)
  • AMBER: NEB tutorial (Mon Mar 12 2007 - 04:03:17 CST)
  • AMBER: addles (Mon Mar 12 2007 - 00:29:37 CST)
  • Re: AMBER: addles segmentation fault (Thu Mar 08 2007 - 03:35:43 CST)
  • AMBER: addles segmentation fault (Wed Mar 07 2007 - 01:18:39 CST)
  • AMBER: psi , phi angles (Mon Mar 05 2007 - 05:07:41 CST)
  • Re: AMBER: phe-phe molecule (Mon Feb 26 2007 - 22:51:53 CST)
  • Re: AMBER: phe-phe molecule (Mon Feb 26 2007 - 01:46:10 CST)
  • AMBER: phe-phe molecule (Mon Feb 26 2007 - 00:01:26 CST)
  • AMBER: atom types (Wed Feb 21 2007 - 23:43:38 CST)
  • AMBER: connect atom (Mon Feb 12 2007 - 05:01:57 CST)
  • AMBER: assigning charges to a prepi file (Fri Feb 09 2007 - 00:38:27 CST)
  • AMBER: phe-phe prep file (Fri Feb 09 2007 - 00:09:15 CST)
  • Re: AMBER: antechamber for topology file (Thu Feb 08 2007 - 00:55:35 CST)
  • Re: AMBER: antechamber for topology file (Thu Feb 08 2007 - 00:07:22 CST)
  • AMBER: antechamber for topology file (Wed Feb 07 2007 - 04:42:51 CST)
  • Re: AMBER: force fields (Tue Feb 06 2007 - 02:20:05 CST)
  • Re: AMBER: force fields (Tue Feb 06 2007 - 04:33:37 CST)
  • Re: AMBER: force fields (Mon Feb 05 2007 - 23:37:05 CST)
  • AMBER: force fields (Mon Feb 05 2007 - 01:05:09 CST)
  • AMBER: xleap (Thu Feb 01 2007 - 02:04:09 CST)
  • AMBER: xleap (Tue Jan 30 2007 - 04:40:10 CST)
  • AMBER: nuc.in file (Tue Jan 23 2007 - 02:21:27 CST)
  • AMBER: sanger (Thu Jan 18 2007 - 05:29:19 CST)
• Denis Courtier
  • Re: AMBER: vlimit exceeded, polarizable force field (Thu Nov 29 2007 - 07:33:22 CST)
  • AMBER: vlimit exceeded, polarizable force field (Thu Nov 29 2007 - 05:43:45 CST)
  • Re: AMBER: leaprc.ff02polEP.r1into xleap (Thu Nov 29 2007 - 05:01:38 CST)
  • AMBER: leaprc.ff02polEP.r1into xleap (Wed Nov 28 2007 - 11:44:21 CST)
  • AMBER: Polarizable potential (Wed Nov 28 2007 - 08:32:49 CST)
  • AMBER: Polarizable Potential (Tue Nov 27 2007 - 11:40:34 CST)
  • AMBER: Polarizable potentials (Mon Nov 26 2007 - 12:49:33 CST)
• devrani mitra
  • Re: AMBER: error in running sander (Wed May 30 2007 - 18:39:47 CDT)
  • Re: AMBER: error in running sander (Wed May 30 2007 - 18:34:41 CDT)
  • Re: AMBER: error in running sander (Tue May 29 2007 - 20:12:59 CDT)
  • Re: AMBER: error in running sander (Tue May 29 2007 - 19:41:57 CDT)
  • Re: AMBER: error in running sander (Tue May 29 2007 - 17:01:40 CDT)
  • Re: AMBER: error in running sander (Tue May 29 2007 - 16:27:09 CDT)
  • AMBER: error in running sander (Tue May 29 2007 - 15:22:35 CDT)
  • AMBER: parameter file for Fe-S cluster (Thu May 24 2007 - 17:26:05 CDT)
• Dilip Dagade
  • Re: AMBER: EXTRA_PTS: frtype 2 Should not be here (Thu Aug 16 2007 - 11:52:56 CDT)
  • Re: AMBER: EXTRA_PTS: frtype 2 Should not be here (Wed Aug 15 2007 - 23:39:37 CDT)
  • AMBER: EXTRA_PTS: frtype 2 Should not be here (Wed Aug 15 2007 - 11:50:57 CDT)
• Dingguo Xu
  • AMBER: (no subject) (Wed May 09 2007 - 16:29:58 CDT)
• dinko.x.ziher_at_gsk.com
  • AMBER: AMBER 9 - visualization of MD trajectory by MOE (Wed Nov 07 2007 - 06:45:41 CST)
• Douglas Kojetin
  • AMBER: step-by-ste weight changes of dwt -- patch? (Thu Sep 27 2007 - 10:35:01 CDT)
• dpandit_at_brandeis.edu
  • Re: AMBER: AMBER 9 - Force Field Options - Question (Wed Oct 17 2007 - 10:27:12 CDT)
  • AMBER: AMBER 9 - Force Field Options - Question (Tue Oct 16 2007 - 15:41:33 CDT)
• Dr M. Blomberg
  • AMBER: prep file new residue (Mon Apr 23 2007 - 03:48:27 CDT)
  • AMBER: rigid epoxide substrate (Fri Apr 20 2007 - 06:24:13 CDT)
• Dr. Devanathan Raghunathan
  • AMBER: implicit minimization (Thu Sep 27 2007 - 21:21:14 CDT)
• Du, Shiyu
  • AMBER: Question on TIP4P model (Mon Jul 09 2007 - 19:01:58 CDT)
  • Re: AMBER: Installing amber9 in IBM P5? (Wed Jun 13 2007 - 16:20:37 CDT)
  • Re: AMBER: Installing amber9 in IBM P5? (Wed Jun 13 2007 - 12:52:11 CDT)
  • Re: AMBER: Installing amber9 in IBM P5? (Wed Jun 13 2007 - 00:01:56 CDT)
  • AMBER: Installing amber9 in IBM P5? (Tue Jun 12 2007 - 21:09:34 CDT)
• dykyy
  • AMBER: Question (Tue Nov 06 2007 - 07:12:46 CST)
• ebright HMS
  • Re: AMBER: abnormal high temperature during NPT ensembles MD (Wed Feb 28 2007 - 10:29:41 CST)
  • AMBER: abnormal high temperature during NPT ensembles MD (Tue Feb 27 2007 - 17:13:29 CST)
• Ed Pate
  • AMBER: dihedrals (Mon Oct 01 2007 - 18:07:47 CDT)
  • AMBER: IFVARI parameter (Tue Feb 27 2007 - 15:22:43 CST)
  • AMBER: problem with atom restraints (Sun Feb 25 2007 - 22:53:31 CST)
  • Re: AMBER: problem with distance restraints (Mon Jan 22 2007 - 16:29:15 CST)
  • AMBER: problem with distance restraints (Mon Jan 22 2007 - 13:43:58 CST)
  • AMBER: improper torsions (Mon Jan 08 2007 - 13:08:36 CST)
• Eddie Men
  • Re: AMBER: PME and counter ions (Wed Dec 19 2007 - 15:40:24 CST)
  • Re: AMBER: bondi radii problems (Wed Nov 28 2007 - 12:45:34 CST)
  • AMBER: PB warning in pb_miccg(): CG maxitn exceeded! (Tue Nov 27 2007 - 22:35:17 CST)
  • Re: AMBER: restraints to individual atoms (Tue Nov 27 2007 - 21:54:30 CST)
  • AMBER: bondi radii problems (Tue Nov 27 2007 - 21:31:19 CST)
  • AMBER: restraints to individual atoms (Mon Nov 26 2007 - 21:02:11 CST)
  • Re: AMBER: Hello (Sat Nov 24 2007 - 12:47:11 CST)
  • AMBER: Hello (Fri Nov 23 2007 - 20:44:05 CST)
  • Re: AMBER: BELLY (Thu Nov 22 2007 - 16:30:38 CST)
  • AMBER: BELLY (Thu Nov 22 2007 - 15:16:39 CST)
  • AMBER: BELLY issues (Thu Nov 22 2007 - 04:03:52 CST)
  • AMBER: Implicit/Explicit solvation (Wed Nov 21 2007 - 01:03:12 CST)
  • Re: AMBER: newby question on converting xyz format to pdb format after energy minimization (Tue Nov 20 2007 - 15:24:56 CST)
  • AMBER: RESP question (Fri Nov 09 2007 - 18:33:16 CST)
  • Re: AMBER: Energy minimization problem of -SO3H group (Tue Nov 06 2007 - 23:52:09 CST)
  • Re: AMBER: &dipoles output in QM/MM simulations (Fri Nov 02 2007 - 06:01:10 CST)
  • Re: AMBER: antechamber fails with large molecules (Fri Nov 02 2007 - 02:50:57 CST)
  • Re: AMBER: anal calculatons (Mon Oct 15 2007 - 02:43:02 CDT)
  • AMBER: BOMB! (Thu Oct 11 2007 - 05:12:49 CDT)
  • Re: AMBER: Quick QUESTION (Tue Oct 09 2007 - 00:02:10 CDT)
  • AMBER: Quick QUESTION (Mon Oct 08 2007 - 23:23:49 CDT)
  • Re: AMBER: PB Bomb (Sun Oct 07 2007 - 03:03:52 CDT)
  • AMBER: PB Bomb (Sun Oct 07 2007 - 02:10:59 CDT)
  • Re: AMBER: Problems with cpin file (Thu Oct 04 2007 - 15:46:22 CDT)
  • Re: AMBER: Problems with cpin file (Thu Oct 04 2007 - 00:07:11 CDT)
  • AMBER: Problems with cpin file (Tue Oct 02 2007 - 07:47:50 CDT)
  • AMBER: constant pH (Tue Oct 02 2007 - 04:45:34 CDT)
  • AMBER: Constant pH (Tue Oct 02 2007 - 04:41:31 CDT)
  • Re: AMBER: Solvation Issues (Sat Sep 29 2007 - 01:31:26 CDT)
  • AMBER: force field question (Thu Sep 27 2007 - 02:31:42 CDT)
  • AMBER: solvation issues (Wed Sep 26 2007 - 18:19:47 CDT)
  • AMBER: Solvation Issues (Wed Sep 26 2007 - 17:48:21 CDT)
  • AMBER: Water question (Sun Sep 23 2007 - 10:21:48 CDT)
  • AMBER: Water Question (Sun Sep 23 2007 - 03:09:21 CDT)
  • Re: AMBER: Problems loading parameter file in tleap (Fri Sep 21 2007 - 06:27:35 CDT)
• Edoardo Saccenti
  • Re: AMBER: Problem with PCSHIFT module (Thu Apr 12 2007 - 07:40:55 CDT)
  • Re: AMBER: Problem with PCSHIFT module (Tue Apr 03 2007 - 03:08:38 CDT)
  • AMBER: Problem with PCSHIFT module (Fri Mar 30 2007 - 05:20:37 CST)
• Eduardo Mendez
  • AMBER: hey (Sun Oct 07 2007 - 00:19:36 CDT)
  • Re: AMBER: Problems with cpin file (Thu Oct 04 2007 - 16:11:06 CDT)
  • AMBER: Problems loading parameter file in tleap (Fri Sep 21 2007 - 05:58:48 CDT)
  • Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- (Thu Sep 20 2007 - 05:38:08 CDT)
  • Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- (Wed Sep 19 2007 - 06:33:48 CDT)
  • Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- (Tue Sep 18 2007 - 18:52:18 CDT)
  • Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- (Tue Sep 18 2007 - 18:41:33 CDT)
  • Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- (Mon Sep 17 2007 - 22:16:02 CDT)
  • AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- (Mon Sep 17 2007 - 21:32:22 CDT)
  • AMBER: AMBER sander (Fri Sep 14 2007 - 18:42:38 CDT)
  • AMBER: AMBER parametrization (??) for OAA and Mg++ (Mon Sep 10 2007 - 23:39:43 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Fri Sep 07 2007 - 00:56:00 CDT)
• Eduardo Mendez-Villuendas
  • AMBER: AMBER at WESTGRID (Thu Aug 30 2007 - 06:49:07 CDT)
• Emilia Wu
  • AMBER: bad atom type:F (Thu Aug 30 2007 - 07:36:14 CDT)
  • Re: RE: RE: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f (Mon Jan 22 2007 - 20:45:46 CST)
  • Re: RE: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f (Mon Jan 22 2007 - 18:22:39 CST)
  • Re: RE: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f (Sun Jan 21 2007 - 19:42:18 CST)
  • Re: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f (Fri Jan 19 2007 - 19:54:27 CST)
  • AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f (Fri Jan 19 2007 - 07:15:56 CST)
• emine cebe
  • AMBER: personal computer configuration for parallel computing (Sun Aug 26 2007 - 06:36:28 CDT)
  • AMBER: united atom parameters for -NH2 and -OH groups (Mon Jan 22 2007 - 13:47:12 CST)
• Eric Shamay
  • AMBER: Problem compiling AMBER 9 on ppc64 (Tue Sep 04 2007 - 11:14:07 CDT)
  • Re: AMBER: amber 9 - output of forces (Tue Mar 27 2007 - 14:36:34 CST)
  • Re: AMBER: amber 9 - output of forces (Mon Mar 26 2007 - 16:08:58 CST)
  • Re: AMBER: Error - must define AMBERHOME environment variable (Sat Mar 24 2007 - 18:32:40 CST)
  • Re: AMBER: Error - must define AMBERHOME environment variable (Fri Mar 23 2007 - 16:26:02 CST)
  • Re: AMBER: amber 9 - output of forces (Sat Mar 24 2007 - 00:27:41 CST)
  • AMBER: amber 9 - output of forces (Fri Mar 23 2007 - 17:00:39 CST)
  • Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) (Wed Mar 14 2007 - 20:18:55 CST)
  • AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) (Wed Mar 14 2007 - 19:12:49 CST)
• Esther Brugger
  • AMBER: radial distribution by Ptraj (Wed Nov 28 2007 - 08:35:49 CST)
  • AMBER: principal mask dorotation (Thu Apr 05 2007 - 16:46:51 CDT)
  • AMBER: principal axis calculation in Ptraj (Tue Apr 03 2007 - 16:05:44 CDT)
  • AMBER: water density (Fri Mar 23 2007 - 16:47:33 CST)
  • Re: AMBER: solvent accessible surface area (SASA) (Thu Mar 01 2007 - 17:58:50 CST)
  • Re: AMBER: solvent accessible surface area (SASA) (Thu Mar 01 2007 - 13:15:51 CST)
  • Re: AMBER: solvent accessible surface area (SASA) (Thu Mar 01 2007 - 11:03:34 CST)
  • Re: AMBER: solvent accessible surface area (SASA) (Thu Mar 01 2007 - 10:40:16 CST)
  • Re: AMBER: solvent accessible surface area (SASA) (Thu Mar 01 2007 - 09:23:04 CST)
  • Re: AMBER: solvent accessible surface area (SASA) (Wed Feb 28 2007 - 17:54:51 CST)
  • AMBER: solvent accessible surface area (SASA) (Wed Feb 28 2007 - 12:38:55 CST)
  • Re: AMBER: read the data (Sat Feb 17 2007 - 14:22:50 CST)
  • Re: AMBER: read the data (Fri Feb 16 2007 - 13:01:27 CST)
  • Re: AMBER: read the data (Fri Feb 16 2007 - 12:40:45 CST)
  • Re: AMBER: read the data (Fri Feb 16 2007 - 10:54:06 CST)
  • Re: AMBER: read the data (Thu Feb 15 2007 - 17:00:39 CST)
  • Re: AMBER: read the data (Fri Feb 16 2007 - 11:43:39 CST)
  • AMBER: read the data (Thu Feb 15 2007 - 13:53:45 CST)
  • AMBER: H-Bond (Thu Feb 08 2007 - 11:06:57 CST)
  • Re: AMBER: side chain orientation (Wed Feb 07 2007 - 09:23:55 CST)
  • AMBER: side chain orientation (Tue Feb 06 2007 - 17:36:48 CST)
  • Re: AMBER: angle command in Ptraj (Fri Feb 02 2007 - 18:36:01 CST)
  • AMBER: angle command in Ptraj (Fri Feb 02 2007 - 18:20:34 CST)
  • AMBER: Ptraj: watershell and distance (Tue Jan 30 2007 - 15:26:17 CST)
  • Re: AMBER: radius of gyration (Mon Jan 29 2007 - 16:27:34 CST)
  • Re: AMBER: radius of gyration (Mon Jan 29 2007 - 15:06:00 CST)
  • Re: AMBER: radius of gyration (Mon Jan 29 2007 - 09:51:26 CST)
  • AMBER: radius of gyration (Fri Jan 26 2007 - 14:17:37 CST)
  • Re: AMBER: dihedral angle by Ptraj (Wed Jan 24 2007 - 11:08:15 CST)
  • Re: AMBER: dihedral angle by Ptraj (Wed Jan 24 2007 - 10:02:38 CST)
  • Re: AMBER: dihedral angle by Ptraj (Tue Jan 23 2007 - 17:02:00 CST)
  • AMBER: dihedral angle by Ptraj (Tue Jan 23 2007 - 12:24:42 CST)
  • Re: AMBER: Distance Restraints (Fri Jan 05 2007 - 09:17:38 CST)
  • Re: Re : AMBER: intra-molecular h-bonds in ptraj (Fri Jan 05 2007 - 09:11:43 CST)
  • Re: AMBER: Distance Restraints (Wed Jan 03 2007 - 16:04:03 CST)
  • AMBER: Distance Restraints (Wed Jan 03 2007 - 14:29:26 CST)
  • AMBER: Distance Restraints Problem (Tue Jan 02 2007 - 16:00:16 CST)
• Evan Kelly
  • AMBER: Ligand-Residue interaction tracking (Mon Dec 10 2007 - 12:20:29 CST)
  • AMBER: SASA per residue (Mon Oct 22 2007 - 11:59:26 CDT)
  • AMBER: Substitute for GAFF (Fri Jul 06 2007 - 12:32:50 CDT)
  • AMBER: QM/MM LJ parameters (Thu Jul 05 2007 - 18:31:35 CDT)
  • Re: AMBER: Sander (Amber 9) crash on cortex (Thu May 10 2007 - 20:10:46 CDT)
  • AMBER: Sander (Amber 9) crash on cortex (Thu May 10 2007 - 13:57:20 CDT)
  • Re: AMBER: ptraj hbond (Sun Apr 08 2007 - 21:00:29 CDT)
  • AMBER: ptraj hbond (Sun Apr 08 2007 - 19:37:04 CDT)
  • AMBER: Distance restraint to centre of mass (Fri Mar 30 2007 - 16:41:32 CST)
  • AMBER: AM1-bcc (Tue Feb 27 2007 - 18:26:22 CST)
  • AMBER: ptraj dipole calculation in QMMM simulation (Fri Feb 09 2007 - 12:36:30 CST)
  • AMBER: test submission through PBS queue (Wed Jan 10 2007 - 13:20:45 CST)
• Falck da Silva Eirik
  • RE: AMBER: Heat of Vaporization (Tue May 15 2007 - 15:00:31 CDT)
• fatima.chami_at_durham.ac.uk
  • Fwd: Re: AMBER: leap restrainTorsion (Wed Dec 05 2007 - 12:45:24 CST)
  • AMBER: leap restrainTorsion (Wed Dec 05 2007 - 04:24:30 CST)
  • Re: AMBER: antechamber: read in charges (Wed Nov 28 2007 - 12:52:41 CST)
  • AMBER: antechamber: read in charges (Tue Nov 27 2007 - 09:40:13 CST)
  • AMBER: dihedral driver (Sun Nov 04 2007 - 06:51:22 CST)
  • Re: AMBER: problem compiling Amber9 on 64-machine (Wed Aug 01 2007 - 10:55:26 CDT)
  • Re: AMBER: problem compiling Amber9 on 64-machine (Wed Aug 01 2007 - 10:52:13 CDT)
  • AMBER: problem compiling Amber9 on 64-machine (Wed Aug 01 2007 - 06:03:48 CDT)
• Fenghui Fan
  • AMBER: During the Sander process, does the pH of the solution change orr not (Mon Dec 03 2007 - 19:58:44 CST)
  • Re: AMBER: adding water molecules in lipid bilayer model (Mon Jul 09 2007 - 18:11:45 CDT)
  • Re: AMBER: pdb flie format (Sun Jun 03 2007 - 12:57:02 CDT)
  • AMBER: simulation of the phosphorylated protein (Wed Mar 07 2007 - 19:20:09 CST)
  • RE: AMBER: Is this system too large? (Wed Feb 21 2007 - 16:55:57 CST)
  • Re: AMBER: Is this system too large? (Tue Feb 20 2007 - 22:53:26 CST)
  • Re: AMBER: How precise is a MD simulation? (Mon Feb 12 2007 - 19:47:09 CST)
  • Re: AMBER: simulating part of a molecule with homology modeling (Sat Feb 10 2007 - 22:26:41 CST)
  • Re: AMBER: side chain orientation (Tue Feb 06 2007 - 18:11:47 CST)
  • Re: AMBER: DNA structure analysis (Wed Jan 17 2007 - 09:31:00 CST)
  • Re: AMBER: improper torsions (Mon Jan 08 2007 - 13:45:09 CST)
  • Re: AMBER: enzyme kinetics in silico (Thu Jan 04 2007 - 15:34:41 CST)
• Florian Haberl
  • Re: AMBER: membrane simulation (Mon Apr 16 2007 - 09:04:04 CDT)
  • Re: AMBER: read the data (Thu Feb 15 2007 - 14:11:16 CST)
• Francesco Pietra
  • AMBER: About RAMD (Mon Dec 31 2007 - 09:27:36 CST)
  • Re: AMBER: RESP charge fitting using antechamber (Mon Dec 31 2007 - 01:19:42 CST)
  • AMBER: About protein-ligand binding (Fri Dec 21 2007 - 08:52:00 CST)
  • Re: AMBER: amber9/mmtsb (Tue Dec 18 2007 - 11:15:55 CST)
  • AMBER: Scripts for md analysis (Tue Dec 18 2007 - 05:05:24 CST)
  • AMBER: amber9/mmtsb (Tue Dec 18 2007 - 04:21:31 CST)
  • RE: AMBER: Time step & non-bonded interactions updating (Sun Dec 16 2007 - 10:36:46 CST)
  • AMBER: Time step & non-bonded interactions updating (Sat Dec 15 2007 - 12:39:48 CST)
  • AMBER: protein-ligand binding affinity (Thu Dec 13 2007 - 08:00:17 CST)
  • Re: AMBER: pmend vs sander.MPI (Sun Dec 09 2007 - 11:35:48 CST)
  • AMBER: Fwd: ptraj with protein-ligand (Sun Dec 09 2007 - 04:18:24 CST)
  • AMBER: ptraj with protein-ligand (Sun Dec 09 2007 - 04:11:30 CST)
  • AMBER: pmend vs sander.MPI (Thu Dec 06 2007 - 09:13:39 CST)
  • RE: AMBER: Restraintmask syntax (Wed Dec 05 2007 - 12:00:49 CST)
  • RE: AMBER: Restraintmask syntax (Tue Dec 04 2007 - 11:44:01 CST)
  • AMBER: Restraintmask syntax (Tue Dec 04 2007 - 09:30:50 CST)
  • Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault (Mon Dec 03 2007 - 16:18:01 CST)
  • Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault (Mon Dec 03 2007 - 15:45:14 CST)
  • Fwd: Re: AMBER: Minimization amber9 segmentation fault (Mon Dec 03 2007 - 10:30:11 CST)
  • Re: AMBER: Minimization amber9 segmentation fault (Sun Dec 02 2007 - 03:51:42 CST)
  • Re: AMBER: Minimization amber9 segmentation fault (Sat Dec 01 2007 - 12:48:01 CST)
  • AMBER: Minimization amber9 segmentation fault (Sat Dec 01 2007 - 09:46:23 CST)
  • Re: AMBER: Group input for restrained atoms (Fri Nov 30 2007 - 15:12:42 CST)
  • AMBER: Group input for restrained atoms (Fri Nov 30 2007 - 10:28:50 CST)
  • RE: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated (Thu Nov 29 2007 - 09:44:33 CST)
  • AMBER: About RAMD (Thu Nov 29 2007 - 01:26:45 CST)
  • AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated (Wed Nov 28 2007 - 09:01:37 CST)
  • AMBER: solvatebox vs solvateoct (Sun Nov 25 2007 - 12:27:06 CST)
  • Re: AMBER: About TER records (Sat Nov 24 2007 - 15:34:59 CST)
  • Re: AMBER: Fwd: About TER records (Sat Nov 24 2007 - 15:27:11 CST)
  • Re: AMBER: Fwd: About TER records (Sat Nov 24 2007 - 12:29:15 CST)
  • AMBER: Fwd: About TER records (Fri Nov 23 2007 - 09:23:41 CST)
  • AMBER: About TER records (Fri Nov 23 2007 - 02:15:05 CST)
  • Re: AMBER: pmemd with openmpi (Mon Nov 19 2007 - 14:31:56 CST)
  • Re: AMBER: Puzzle with WAT (Sun Nov 18 2007 - 02:09:27 CST)
  • AMBER: Puzzle with WAT (Sat Nov 17 2007 - 12:14:38 CST)
  • Fwd: Re: AMBER: Fwd: [chirality.c] Atom did not match (Sat Nov 17 2007 - 10:16:09 CST)
  • Re: AMBER: Fwd: [chirality.c] Atom did not match (Sat Nov 17 2007 - 04:56:01 CST)
  • AMBER: Fwd: [chirality.c] Atom did not match (Fri Nov 16 2007 - 15:59:40 CST)
  • Re: AMBER: [chirality.c] Atom did not match (Fri Nov 16 2007 - 13:38:20 CST)
  • AMBER: [chirality.c] Atom did not match (Fri Nov 16 2007 - 11:09:10 CST)
  • Re: AMBER:antechamber fails with large molecules (Sun Nov 11 2007 - 05:13:56 CST)
  • Re: AMBER:antechamber fails with large molecules (Sun Nov 11 2007 - 05:13:56 CST)
  • Re: AMBER: make test.parallel (Thu Nov 08 2007 - 11:30:36 CST)
  • AMBER: make test.parallel (Thu Nov 08 2007 - 02:33:21 CST)
  • AMBER: "Atom valence violated" from LEaP (Mon Nov 05 2007 - 05:00:28 CST)
  • Re: AMBER: antechamber fails with large molecules (Sat Nov 03 2007 - 08:01:41 CST)
  • AMBER: Failure to recompile antechamber (Fri Nov 02 2007 - 17:05:45 CST)
  • AMBER: Compiling single programs (Fri Nov 02 2007 - 11:44:09 CST)
  • Re: AMBER: antechamber fails with large molecules (Fri Nov 02 2007 - 11:07:52 CST)
  • Re: AMBER: antechamber fails with large molecules (Thu Nov 01 2007 - 02:29:26 CST)
  • Re: AMBER: Getting prmtop and inpcrd (Mon Oct 29 2007 - 10:51:23 CST)
  • AMBER: Getting prmtop and inpcrd (Mon Oct 29 2007 - 09:43:44 CST)
  • Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- (Wed Sep 19 2007 - 01:52:48 CDT)
  • AMBER: Tutorial protein-small-molecule-associates (Tue Sep 11 2007 - 11:26:01 CDT)
  • AMBER: solvent box pyridine (Sat Sep 08 2007 - 09:46:37 CDT)
  • AMBER: Fwd: System extending beyond of (non existent) virtual box (Sat Sep 08 2007 - 03:33:34 CDT)
  • AMBER: System extending beyond of (non existent) virtual box (Fri Sep 07 2007 - 12:17:36 CDT)
  • AMBER: Fwd: Comparing explicit solvent/vacuum qmmm (Wed Sep 05 2007 - 06:05:07 CDT)
  • AMBER: Comparing explicit solvent/vacuum qmmm (Wed Sep 05 2007 - 02:31:32 CDT)
  • Re: AMBER: Running mpirun -np 1 on different processors (Tue Sep 04 2007 - 09:39:40 CDT)
  • AMBER: Running mpirun -np 1 on different processors (Tue Sep 04 2007 - 08:37:27 CDT)
  • AMBER: Solvent in closest contact with solute (Sat Sep 01 2007 - 09:15:11 CDT)
  • AMBER: Fwd: Schedule for QM-MM with Amber9/Amber10 (Thu Aug 30 2007 - 08:17:41 CDT)
  • AMBER: Schedule for QM-MM with Amber9/Amber10 (Thu Aug 30 2007 - 01:30:10 CDT)
  • Re: AMBER: Criteria for classical md being OK to move to QM-MM (Wed Aug 29 2007 - 12:40:36 CDT)
  • AMBER: Criteria for classical md being OK to move to QM-MM (Wed Aug 29 2007 - 11:51:15 CDT)
  • AMBER: heating up system (Tue Aug 28 2007 - 11:16:57 CDT)
  • Fwd: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB (Mon Aug 27 2007 - 01:24:33 CDT)
  • Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB (Sun Aug 26 2007 - 11:28:14 CDT)
  • AMBER: Fwd: SCC convergence failure in QM-MM DFTB (Sun Aug 26 2007 - 09:34:57 CDT)
  • AMBER: Fwd: SCC convergence failure in QM-MM DFTB (Sun Aug 26 2007 - 02:26:42 CDT)
  • AMBER: SCC convergence failure in QM-MM DFTB (Sat Aug 25 2007 - 12:54:12 CDT)
  • RE: AMBER: solvateCap minin and mdin for qm-mm dftb (Fri Aug 24 2007 - 16:37:12 CDT)
  • Re: AMBER: solvateCap minin and mdin for qm-mm dftb (Fri Aug 24 2007 - 15:42:50 CDT)
  • RE: AMBER: solvateCap minin and mdin for qm-mm dftb (Fri Aug 24 2007 - 12:28:32 CDT)
  • Re: AMBER: solvateCap minin and mdin for qm-mm dftb (Fri Aug 24 2007 - 11:01:31 CDT)
  • AMBER: solvateCap minin and mdin for qm-mm dftb (Fri Aug 24 2007 - 05:19:30 CDT)
  • Re: AMBER: Thermodynamic Integration for conformational changes? (Wed Aug 22 2007 - 01:53:15 CDT)
  • AMBER: Thermodynamic Integration for conformational changes? (Tue Aug 21 2007 - 11:57:47 CDT)
  • AMBER: CRESP charges in antechamber prepin (Mon Aug 20 2007 - 02:23:24 CDT)
  • AMBER: DFTB email address (Sat Aug 18 2007 - 02:14:53 CDT)
  • Re: AMBER: about parallelization in QM-MM (Fri Aug 17 2007 - 01:41:02 CDT)
  • Re: AMBER: antechamber, how does it work (Thu Aug 16 2007 - 12:25:35 CDT)
  • Re: AMBER: antechamber, how does it work (Thu Aug 16 2007 - 00:53:34 CDT)
  • Re: AMBER: antechamber, how does it work (Wed Aug 15 2007 - 16:53:55 CDT)
  • Re: AMBER: antechamber, how does it work (Wed Aug 15 2007 - 11:08:37 CDT)
  • Re: AMBER: antechamber, how does it work (Wed Aug 15 2007 - 10:05:31 CDT)
  • Re: AMBER: antechamber, how does it work (Wed Aug 15 2007 - 09:25:12 CDT)
  • AMBER: antechamber, how does it work (Wed Aug 15 2007 - 03:43:45 CDT)
  • AMBER: Parallelizin antechamber? (Tue Aug 14 2007 - 08:29:11 CDT)
  • RE: AMBER: Failure to SCF convergence & parallelization and memory (Sun Aug 12 2007 - 02:37:33 CDT)
  • AMBER: Neutralize charges for simulated annealing? (Sat Aug 11 2007 - 17:35:30 CDT)
  • AMBER: Failure to SCF convergence (Sat Aug 11 2007 - 11:56:53 CDT)
  • AMBER: Positive EPtot in QM-MM (Tue Aug 07 2007 - 09:34:35 CDT)
  • Re: AMBER: Fwd: QM region + cutoff larger that box (Mon Aug 06 2007 - 10:07:09 CDT)
  • RE: AMBER: Fwd: QM region + cutoff larger that box (Mon Aug 06 2007 - 01:28:13 CDT)
  • Re: AMBER: Fwd: QM region + cutoff larger that box (Sat Aug 04 2007 - 11:42:33 CDT)
  • AMBER: Fwd: QM region + cutoff larger that box (Sat Aug 04 2007 - 09:33:35 CDT)
  • AMBER: Fwd: QM region + cutoff larger that box (Sat Aug 04 2007 - 03:32:40 CDT)
  • AMBER: Fwd: unable to save prmtop/inpcrd for chcl3box (Fri Aug 03 2007 - 07:24:24 CDT)
  • AMBER: unable to save prmtop/inpcrd for chcl3box (Fri Aug 03 2007 - 05:09:03 CDT)
  • AMBER: Calculating cumulative average (Thu Aug 02 2007 - 12:00:10 CDT)
  • Fwd: RE: AMBER: Average potential energies and conformer ratios (Wed Aug 01 2007 - 08:58:02 CDT)
  • RE: AMBER: Average potential energies and conformer ratios (Tue Jul 31 2007 - 00:09:02 CDT)
  • RE: AMBER: QM-MM output interpretation (Mon Jul 30 2007 - 12:59:13 CDT)
  • AMBER: QM-MM output interpretation (Mon Jul 30 2007 - 09:08:36 CDT)
  • AMBER: thermodynamic data for conformers (Sun Jul 29 2007 - 12:11:11 CDT)
  • Fwd: Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 17:01:40 CDT)
  • Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 15:43:08 CDT)
  • RE: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 12:07:15 CDT)
  • Re: AMBER: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 09:44:46 CDT)
  • Re: AMBER: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 09:00:58 CDT)
  • AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 08:24:10 CDT)
  • AMBER: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 01:24:22 CDT)
  • Re: Re: Re: Fwd: Re: Re: AMBER: parallel compilation (Wed Jul 25 2007 - 01:10:17 CDT)
  • Re: Re: Fwd: Re: Re: AMBER: parallel compilation (Tue Jul 24 2007 - 10:02:01 CDT)
  • Re: Fwd: Re: Re: AMBER: parallel compilation (Tue Jul 24 2007 - 09:07:10 CDT)
  • Fwd: Re: Re: AMBER: parallel compilation (Tue Jul 24 2007 - 02:19:58 CDT)
  • Re: Re: AMBER: parallel compilation (Tue Jul 24 2007 - 02:17:03 CDT)
  • Re: AMBER: parallel compilation (Tue Jul 24 2007 - 01:19:56 CDT)
  • AMBER: md potential energy (Mon Jul 23 2007 - 11:14:48 CDT)
  • AMBER: parallel compilation (Mon Jul 23 2007 - 05:16:35 CDT)
  • AMBER: RE Amber: Simulated Annealing (Sat Jul 21 2007 - 10:13:11 CDT)
  • Fwd: Re: AMBER: Could not find cntrl namelist (Wed Jul 11 2007 - 16:52:25 CDT)
  • Re: AMBER: Could not find cntrl namelist (Wed Jul 11 2007 - 16:50:37 CDT)
  • Re: AMBER: Could not find cntrl namelist (Wed Jul 11 2007 - 10:10:42 CDT)
  • RE: AMBER: Could not find cntrl namelist (Wed Jul 11 2007 - 01:48:59 CDT)
  • Re: AMBER: Could not find cntrl namelist (Wed Jul 11 2007 - 05:14:51 CDT)
  • Re: AMBER: Could not find cntrl namelist (Wed Jul 11 2007 - 01:48:41 CDT)
  • RE: AMBER: Could not find cntrl namelist (Tue Jul 10 2007 - 16:11:48 CDT)
  • RE: AMBER: Could not find cntrl namelist (Tue Jul 10 2007 - 01:26:54 CDT)
  • Re: AMBER: antechamber (Tue Jul 10 2007 - 02:04:39 CDT)
  • Re: AMBER: antechamber (Mon Jul 09 2007 - 16:57:45 CDT)
  • Re: AMBER: Could not find cntrl namelist (Mon Jul 09 2007 - 16:31:18 CDT)
  • Re: AMBER: Could not find cntrl namelist (Mon Jul 09 2007 - 16:22:30 CDT)
  • Re: AMBER: Could not find cntrl namelist (Mon Jul 09 2007 - 15:53:43 CDT)
  • AMBER: Could not find cntrl namelist (Mon Jul 09 2007 - 11:56:58 CDT)
  • AMBER: Simulated Annealing - Best way to create randomness (Sat Jul 07 2007 - 09:56:41 CDT)
  • Re: AMBER: Nudget Elastic Band query (Thu Jul 05 2007 - 15:28:31 CDT)
  • Re: AMBER: Nudget Elastic Band query (Thu Jul 05 2007 - 14:02:19 CDT)
  • AMBER: Nudget Elastic Band query (Thu Jul 05 2007 - 12:43:43 CDT)
  • Re: AMBER: Fwd: antechamber save prmtop inpcrd (Wed Jul 04 2007 - 16:08:02 CDT)
  • Re: AMBER: Fwd: antechamber save prmtop inpcrd (Wed Jul 04 2007 - 11:54:08 CDT)
  • Re: AMBER: Simulated annealing - Nudget Elastic Band (Wed Jul 04 2007 - 08:13:41 CDT)
  • AMBER: Simulated annealing - Nudget Elastic Band (Wed Jul 04 2007 - 02:01:58 CDT)
  • AMBER: Fwd: antechamber save prmtop inpcrd (Wed Jul 04 2007 - 01:14:23 CDT)
  • AMBER: antechamber save prmtop inpcrd (Tue Jul 03 2007 - 12:55:11 CDT)
  • Fwd: Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH (Sun Jul 01 2007 - 15:50:39 CDT)
  • Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH (Sun Jul 01 2007 - 09:38:03 CDT)
  • Re: AMBER: Problem with leaprc (Sat Jun 30 2007 - 11:23:59 CDT)
  • Re: Fwd: Re: AMBER: make test serial (Sat Jun 30 2007 - 11:18:38 CDT)
  • Fwd: Re: AMBER: make test serial (Sat Jun 30 2007 - 08:42:56 CDT)
  • Fwd: Re: AMBER: make serial failure for xleap (Sat Jun 30 2007 - 08:00:31 CDT)
  • Re: AMBER: make serial failure for xleap (Sat Jun 30 2007 - 03:39:32 CDT)
  • AMBER: make serial failure for xleap (Fri Jun 29 2007 - 16:05:52 CDT)
  • AMBER: Serial "make" failure (Fri Jun 29 2007 - 15:59:42 CDT)
  • Re: AMBER: Serial "make" failure with xleap (Fri Jun 29 2007 - 15:53:52 CDT)
  • AMBER: Fwd: Serial "make" failure with xleap (Fri Jun 29 2007 - 12:26:54 CDT)
  • AMBER: Serial "make" failure with xleap (Fri Jun 29 2007 - 12:17:39 CDT)
  • Fwd: RE: Re: AMBER: $AMBERHOME on PATH (Fri Jun 29 2007 - 00:58:19 CDT)
  • RE: Re: AMBER: $AMBERHOME on PATH (Thu Jun 28 2007 - 15:55:53 CDT)
  • Re: AMBER: Math libraries (Thu Jun 28 2007 - 15:12:28 CDT)
  • RE: Re: AMBER: $AMBERHOME on PATH (Thu Jun 28 2007 - 15:01:11 CDT)
  • RE: Re: AMBER: $AMBERHOME on PATH (Thu Jun 28 2007 - 12:12:43 CDT)
  • RE: Re: AMBER: $AMBERHOME on PATH (Thu Jun 28 2007 - 09:40:09 CDT)
  • AMBER: Math libraries (Thu Jun 28 2007 - 04:56:45 CDT)
  • Re: AMBER: bugfix.all (Thu Jun 28 2007 - 01:14:33 CDT)
  • AMBER: bugfix.all (Wed Jun 27 2007 - 15:26:15 CDT)
  • Fwd: Re: AMBER: $AMBERHOME on PATH (Wed Jun 27 2007 - 09:59:02 CDT)
  • Fwd: Re: AMBER: $AMBERHOME on PATH & compilations (Wed Jun 27 2007 - 11:10:38 CDT)
  • Fwd: Re: AMBER: $AMBERHOME on PATH (Wed Jun 27 2007 - 09:30:09 CDT)
  • Re: AMBER: $AMBERHOME on PATH (Tue Jun 26 2007 - 15:15:11 CDT)
  • AMBER: $AMBERHOME on PATH (Tue Jun 26 2007 - 12:38:35 CDT)
  • AMBER: environment variables (Mon Jun 25 2007 - 10:51:05 CDT)
  • AMBER: Compile openmpi (Thu Jun 14 2007 - 12:11:02 CDT)
  • Re: AMBER: antechamber/charges/conformation (Mon Jun 11 2007 - 04:44:21 CDT)
  • AMBER: antechamber/charges/conformation (Sun Jun 10 2007 - 02:02:15 CDT)
  • RE: AMBER: Compiling openmpi/icc/icpc (Sat Jun 09 2007 - 01:04:45 CDT)
  • AMBER: Compiling openmpi/icc/icpc (Fri Jun 08 2007 - 12:27:20 CDT)
  • Re: AMBER: Solvent models (Fri Jun 01 2007 - 02:00:36 CDT)
  • AMBER: Solvent models (Thu May 31 2007 - 10:23:56 CDT)
  • Re: AMBER: Antechamber (Mon May 28 2007 - 02:20:55 CDT)
  • AMBER: Amber 9 install on Debian Linux amd64 (Mon May 28 2007 - 02:14:49 CDT)
  • Re: AMBER: antechamber question (Sun May 20 2007 - 10:36:28 CDT)
  • AMBER: antechamber question (Sun May 20 2007 - 02:05:59 CDT)
• francesco zonta
  • Re: AMBER: problems compiling amber on mac OSX (Sat Oct 27 2007 - 07:03:51 CDT)
  • AMBER: HG atoms in CYX residues (Fri Oct 26 2007 - 04:45:32 CDT)
  • AMBER: problems compiling amber on mac OSX (Thu Oct 25 2007 - 08:50:04 CDT)
• Franck Vendeix
  • Re: AMBER: (no subject) (Thu Jun 14 2007 - 08:32:54 CDT)
  • Re: AMBER: (no subject) (Thu Jun 14 2007 - 08:32:54 CDT)
  • Re: AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain? (Fri Feb 16 2007 - 16:04:48 CST)
  • Re: AMBER: Umbrella sampling (Wed Feb 14 2007 - 21:13:31 CST)
  • AMBER: Umbrella sampling (Fri Feb 09 2007 - 08:37:35 CST)
• Francois Theillet
  • Re: AMBER: iRED and corrired (Fri Feb 02 2007 - 15:05:41 CST)
  • AMBER: iRED and corrired (Fri Feb 02 2007 - 11:07:47 CST)
• Fred Baba
  • AMBER: "FATAL: Atom xxx does not have a type." (Tue Jun 26 2007 - 12:59:51 CDT)
  • AMBER: [ProblemSolved]Re: SANDER error: 'angles are not correct' (Thu Jun 14 2007 - 12:08:47 CDT)
  • AMBER: SANDER error: 'angles are not correct' (Wed Jun 13 2007 - 16:47:14 CDT)
• FyD
  • Re: AMBER: RESP charge fitting using antechamber (Mon Dec 31 2007 - 09:40:11 CST)
  • Re: AMBER: RESP charge fitting using antechamber (Mon Dec 31 2007 - 08:06:34 CST)
  • Re: AMBER: RESP charge fitting using antechamber (Sun Dec 30 2007 - 08:54:59 CST)
  • Re: AMBER: xleap loading files (Sat Dec 15 2007 - 07:04:46 CST)
  • Re: AMBER: phosphorylation (Thu Dec 06 2007 - 14:07:57 CST)
  • Re: AMBER: THF parameters (Wed Dec 05 2007 - 14:42:29 CST)
  • Re: AMBER: THF parameters (Wed Dec 05 2007 - 08:32:27 CST)
  • Re: AMBER: Error reading radii of Cu during ESP caculation. (Thu Nov 29 2007 - 02:07:07 CST)
  • Re: AMBER: Error reading radii of Cu during ESP caculation. (Wed Nov 28 2007 - 06:19:35 CST)
  • AMBER: R.E.D.-III bug fixes (Sun Nov 18 2007 - 11:22:47 CST)
  • Re: AMBER: calculating charges to modified 4GA unit (Wed Nov 07 2007 - 07:21:03 CST)
  • Re: AMBER: RED-vIII fails (Mon Nov 05 2007 - 12:27:33 CST)
  • Re: AMBER: paper request (Mon Nov 05 2007 - 03:13:38 CST)
  • Re: AMBER: antechamber fails with large molecules (Sun Nov 04 2007 - 06:29:09 CST)
  • Re: AMBER: antechamber fails with large molecules (Wed Oct 31 2007 - 08:02:36 CST)
  • Re: AMBER: RED-vIII fails (Tue Oct 30 2007 - 15:38:03 CST)
  • Re: AMBER: RED-vIII fails (Mon Oct 29 2007 - 10:25:09 CST)
  • Re: AMBER: prepin file format description; pointers on parameterization (Fri Oct 26 2007 - 07:45:10 CDT)
  • Re: AMBER: prepin file format description; pointers on parameterization (Fri Oct 26 2007 - 01:40:46 CDT)
  • Re: AMBER: prepin file format description; pointers on parameterization (Thu Oct 25 2007 - 08:15:52 CDT)
  • Re: AMBER: prepin file format description; pointers on parameterization (Thu Oct 25 2007 - 01:54:33 CDT)
  • Re: AMBER: prepin file format description; pointers on parameterization (Thu Oct 25 2007 - 00:27:33 CDT)
  • Re: AMBER: prepin file format description; pointers on parameterization (Thu Oct 25 2007 - 00:14:32 CDT)
  • Re: AMBER: prepin file format description; pointers on parameterization (Wed Oct 24 2007 - 15:13:37 CDT)
  • Re: AMBER: prepin file format description; pointers on parameterization (Wed Oct 24 2007 - 14:09:09 CDT)
  • Re: AMBER: how to simulate a ligand bound to a residue (Thu Oct 18 2007 - 16:02:13 CDT)
  • Re: AMBER: using amber for cyclic peptides (Mon Oct 15 2007 - 12:53:54 CDT)
  • Re: AMBER: RED III (Mon Oct 15 2007 - 05:20:47 CDT)
  • Re: AMBER: Resp: "Statistics of the Fitting" (Tue Oct 09 2007 - 23:53:05 CDT)
  • Re: AMBER: dihedrals (Tue Oct 02 2007 - 01:36:30 CDT)
  • Re: AMBER: cyclohexane and decalin on amber (Mon Oct 01 2007 - 02:20:29 CDT)
  • Re: AMBER: fragment parametrization tutorial? (Sun Sep 30 2007 - 02:12:41 CDT)
  • Re: AMBER: cyclohexane and decalin on amber (Sun Sep 30 2007 - 02:20:29 CDT)
  • Re: AMBER: Re: using RESP (Wed Sep 26 2007 - 01:14:58 CDT)
  • Re: AMBER: Problems loading parameter file in tleap (Fri Sep 21 2007 - 06:55:39 CDT)
  • Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- (Thu Sep 20 2007 - 07:14:29 CDT)
  • Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- (Thu Sep 20 2007 - 06:54:23 CDT)
  • Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- (Thu Sep 20 2007 - 03:37:30 CDT)
  • Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- (Wed Sep 19 2007 - 02:50:14 CDT)
  • Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- (Wed Sep 19 2007 - 00:57:29 CDT)
  • Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- (Tue Sep 18 2007 - 02:06:51 CDT)
  • Re: AMBER: AMBER parametrization (??) for OAA and Mg++ (Tue Sep 11 2007 - 02:28:46 CDT)
  • Re: AMBER: adding organic molecule to polypeptide residue (Sat Jul 28 2007 - 04:05:18 CDT)
  • Re: AMBER: Re: RED problem (Mon Jul 23 2007 - 07:08:14 CDT)
  • AMBER: ptraj error (Fri Jul 20 2007 - 16:21:17 CDT)
  • Re: AMBER: Non-standard amino acid residue (Thu Jul 19 2007 - 06:26:39 CDT)
  • Re: AMBER: running_RED-III (Wed Jul 18 2007 - 20:33:20 CDT)
  • Re: AMBER: Non-standard amino acid residue (Wed Jul 18 2007 - 09:50:55 CDT)
  • Re: AMBER: Non-standard amino acid residue (Tue Jul 17 2007 - 08:41:57 CDT)
  • Re: AMBER: RESP_compilation (Mon Jul 16 2007 - 17:59:06 CDT)
  • Re: AMBER: RESP_compilation (Mon Jul 16 2007 - 17:55:20 CDT)
  • Re: AMBER: Non-standard amino acid residue (Mon Jul 16 2007 - 11:45:07 CDT)
  • Re: AMBER: Input required for RESP (Wed Jul 11 2007 - 01:21:42 CDT)
  • Re: AMBER: RESP charge generation (Sun Jul 08 2007 - 05:19:16 CDT)
  • Re: AMBER: S-nitrocysteine (Wed Jun 13 2007 - 16:44:59 CDT)
  • Re: AMBER: antechamber/charges/conformation (Mon Jun 11 2007 - 03:40:11 CDT)
  • Re: AMBER: Solvent models (Fri Jun 01 2007 - 03:14:20 CDT)
  • Re: AMBER: Solvent models (Thu May 31 2007 - 15:41:24 CDT)
  • Re: AMBER: Protonation/deprotonation of terminal residues (Wed Apr 18 2007 - 13:26:47 CDT)
  • Re: AMBER: using glycam04 parameters (Wed Apr 18 2007 - 05:57:02 CDT)
  • AMBER: Release of the R.E.D.-III tools (Sun Apr 15 2007 - 05:10:25 CDT)
  • Re: AMBER: Combining RESP with AM1-BCC (Sat Mar 24 2007 - 03:03:37 CST)
  • Re: AMBER: Generating structure of polyethylene glycol in AMBER (Thu Mar 22 2007 - 16:57:55 CST)
  • Re: AMBER: Generating structure of polyethylene glycol in AMBER (Thu Mar 22 2007 - 16:11:07 CST)
  • Re: AMBER: basis set for RESP calculation (Wed Mar 21 2007 - 11:17:44 CST)
  • Re: AMBER: Modified Nucleic Acid Problem (Wed Mar 21 2007 - 08:20:34 CST)
  • Re: AMBER: Modified Nucleic Acid Problem (Wed Mar 21 2007 - 08:19:09 CST)
  • Re: AMBER: basis set for RESP calculation (Wed Mar 21 2007 - 02:03:15 CST)
  • Re: AMBER: RESP calculation of modified nucleotides (Sun Feb 25 2007 - 11:49:55 CST)
  • Re: AMBER: LeaP: Mol2 files (Wed Feb 14 2007 - 11:47:40 CST)
  • Re: AMBER: Modified nucleotides (Wed Feb 14 2007 - 06:30:50 CST)
  • Re: AMBER: antechamber for topology file (Thu Feb 08 2007 - 02:10:29 CST)
  • Re: AMBER: antechamber for topology file (Wed Feb 07 2007 - 07:28:58 CST)
  • Re: AMBER: organic solvent : hexan octan (Wed Jan 24 2007 - 22:50:33 CST)
  • Re: AMBER: Antechamber esp calculation (Tue Jan 23 2007 - 00:05:46 CST)
  • Re: AMBER: HF/6-31G* ESP Charges do not match with ff02 charges (Fri Jan 19 2007 - 14:30:43 CST)
  • AMBER: Dihedral FF parameters (Fri Jan 19 2007 - 09:40:10 CST)
  • Re: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand (Fri Jan 19 2007 - 07:19:17 CST)
  • Re: AMBER: HF/6-31G* ESP Charges do not match with ff02 charges (Fri Jan 19 2007 - 02:31:46 CST)
  • Re: AMBER: RESP charges for charged species (Tue Jan 16 2007 - 23:13:51 CST)
• Gabbar S. Daaku
  • AMBER: reporting EPtot and EKtot separately for two molecules (Mon Feb 12 2007 - 10:15:09 CST)
  • AMBER: Re: reporting EPtot and EKtot separately for two molecules (Mon Feb 12 2007 - 10:16:45 CST)
• Gabriele Viliani
  • AMBER: (no subject) (Wed Nov 28 2007 - 10:56:32 CST)
• Geoff Wood
  • AMBER: replica exchange (Sun Oct 28 2007 - 10:29:42 CST)
  • Re: AMBER: NETCDF (Mon Aug 27 2007 - 02:18:48 CDT)
  • AMBER: NETCDF (Fri Aug 24 2007 - 05:43:11 CDT)
  • Re: AMBER: netcdf support needed (Amber 9, sander imin = 5, -y flag) (Mon Jul 23 2007 - 12:23:46 CDT)
  • AMBER: Re: amber-developers: -y option in sander (Thu Jul 19 2007 - 08:54:47 CDT)
  • Re: AMBER: hybrid remd (Thu May 10 2007 - 14:24:55 CDT)
  • Re: AMBER: hybrid remd (Thu May 10 2007 - 06:49:59 CDT)
  • Re: AMBER: hybrid remd (Wed May 09 2007 - 16:30:50 CDT)
  • Re: AMBER: hybrid remd (Wed May 09 2007 - 16:13:32 CDT)
  • Re: AMBER: hybrid remd (Wed May 09 2007 - 15:38:45 CDT)
  • AMBER: hybrid remd (Wed May 09 2007 - 06:22:09 CDT)
  • AMBER: hybrid remd (Wed May 09 2007 - 05:15:16 CDT)
• Giacomo Bastianelli
  • AMBER: Charge not integral. Head-to-tail cyclic peptides (Mon Jun 18 2007 - 08:55:46 CDT)
• Gianluca Degliesposti
  • AMBER: mmpbsa free energy pairwise decomposition (Wed Mar 14 2007 - 12:54:32 CST)
• Giulio Rastelli
  • AMBER: correlation between PBTOT and GBTOT values in a MD trajectory (Fri May 11 2007 - 09:47:39 CDT)
  • AMBER: Print individual free energies in MD trajectories using MM_PBSA (Fri Apr 27 2007 - 11:05:39 CDT)
  • AMBER: entropy units (Mon Jan 08 2007 - 04:33:19 CST)
• Gobind Singh Bisht
  • AMBER: format of .xyz files and pdb (Wed Jan 31 2007 - 16:05:24 CST)
  • Re: AMBER: How to change the force field equation in amber by programming... (Sun Jan 07 2007 - 08:06:06 CST)
  • AMBER: How to change the force field equation in amber by programming... (Fri Jan 05 2007 - 13:55:22 CST)
• Gohlke_at_bioinformatik.uni-frankfurt.de
  • Re: Re: AMBER: parse radii (Mon Apr 09 2007 - 04:35:06 CDT)
  • Re: AMBER: Comparison of normal modes with ptraj? (Wed Feb 14 2007 - 07:08:38 CST)
  • Re: AMBER: iRED and corrired (Sun Feb 04 2007 - 07:01:17 CST)
• gong wb
  • Re: AMBER: Test fails in Parallel version Amber9 (Tue Oct 23 2007 - 20:37:20 CDT)
  • Re: AMBER: Test fails in Parallel version Amber9 (Mon Oct 22 2007 - 01:52:48 CDT)
  • Re: AMBER: Test fails in Parallel version Amber9 (Thu Oct 18 2007 - 21:00:44 CDT)
  • Re: AMBER: Test fails in Parallel version Amber9 (Wed Oct 17 2007 - 03:04:13 CDT)
  • Re: AMBER: Test fails in Parallel version Amber9 (Wed Oct 17 2007 - 02:54:30 CDT)
  • AMBER: Test fails in Parallel version Amber9 (Tue Oct 16 2007 - 01:42:45 CDT)
• Greg Gannon
  • AMBER: edit.out amber version 9 (Thu Aug 02 2007 - 13:21:31 CDT)
  • Re: AMBER: FLAG LENNARD_JONES_ACOEF NAN (Fri Jul 27 2007 - 10:55:52 CDT)
  • AMBER: FLAG LENNARD_JONES_ACOEF NAN (Fri Jul 27 2007 - 09:41:46 CDT)
• gsciaini_at_qi.fcen.uba.ar
  • Re: AMBER: MD simulations with Pt atom - how to keep square planar geometry? (Thu Nov 08 2007 - 10:09:31 CST)
  • Re: AMBER: AMBER MINIMIZATION (Mon Apr 30 2007 - 16:08:47 CDT)
• Guillaume Bollot
  • AMBER: Amber 8.0 : how to represent EPS with VMD? (Fri Jan 12 2007 - 08:49:28 CST)
• Guillaume Renvez
  • Re: AMBER: gb minimization using nab (Tue Nov 13 2007 - 08:49:48 CST)
  • AMBER: gb minimization using nab (Tue Nov 13 2007 - 05:06:13 CST)
  • AMBER: H bond (Tue Jun 19 2007 - 03:18:45 CDT)
  • AMBER: [Fwd: Tr: H bonds] (Wed Jun 13 2007 - 07:37:20 CDT)
  • AMBER: hydrogen bond (Wed Jun 13 2007 - 03:49:22 CDT)
• Guillermo Mulliert Carlín
  • Re: AMBER: manganese ion (Tue Jul 10 2007 - 03:39:40 CDT)
  • Re: AMBER: Drug bound to the protein (Wed Jan 17 2007 - 09:27:45 CST)
• gurpreet singh
  • AMBER: regarding anal calculations (Wed Oct 24 2007 - 13:50:49 CDT)
  • AMBER: anal (Wed Oct 17 2007 - 23:35:23 CDT)
  • Re: AMBER: error while Running TMD (Wed Oct 17 2007 - 23:19:54 CDT)
  • AMBER: error while Running TMD (Wed Oct 17 2007 - 13:21:18 CDT)
  • AMBER: anal error (Wed Oct 17 2007 - 13:14:52 CDT)
  • AMBER: anal calculation error (Tue Oct 16 2007 - 12:07:20 CDT)
  • Re: AMBER: anal calculatons (Mon Oct 15 2007 - 23:17:47 CDT)
  • AMBER: anal calculatons (Mon Oct 15 2007 - 02:19:33 CDT)
  • AMBER: interaction energy calculations (Tue Oct 09 2007 - 12:06:24 CDT)
  • AMBER: regrading interaction energy calculations (Sun Oct 07 2007 - 23:52:23 CDT)
  • AMBER: regarding non bonded energy caculations (Mon Oct 01 2007 - 00:41:47 CDT)
  • AMBER: regarding energy calculation (Wed Sep 26 2007 - 00:16:41 CDT)
  • AMBER: energy calculation (Tue Sep 25 2007 - 00:54:16 CDT)
  • AMBER: regarding implicit simulation (Tue Aug 14 2007 - 01:21:35 CDT)
  • Re: AMBER: (no subject) (Thu Aug 02 2007 - 03:39:07 CDT)
  • Re: AMBER: Problem with antechamber (Thu Aug 02 2007 - 03:24:18 CDT)
  • AMBER: regarding distance restraints (Mon Jul 23 2007 - 05:46:39 CDT)
  • Re: AMBER: Re: Strange shape in my MD simulations (Wed Jun 20 2007 - 02:58:03 CDT)
  • Re: AMBER: building water box with desired number of molecules (Tue Jun 12 2007 - 04:09:10 CDT)
  • Re: AMBER: problem regarding implicit simulation (Tue Apr 24 2007 - 06:18:57 CDT)
  • AMBER: problem regarding implicit simulation (Mon Apr 23 2007 - 01:16:35 CDT)
  • AMBER: Fwd: problem regarding water handling in explicit simu (Fri Mar 30 2007 - 03:36:52 CST)
  • AMBER: problem regarding water handling in explicit simu (Fri Mar 30 2007 - 03:35:49 CST)
  • AMBER: problem in implcit simulation (Wed Mar 28 2007 - 22:25:53 CST)
  • AMBER: targetedMD problem (Sun Mar 18 2007 - 07:32:40 CST)
  • AMBER: targeted MD problem (Sat Mar 17 2007 - 06:17:27 CST)
  • AMBER: rmsd calculation in ptraj II (Sat Mar 10 2007 - 22:37:10 CST)
  • AMBER: rmsd calculation in ptraj (Sat Mar 10 2007 - 07:38:28 CST)
  • AMBER: rmsd calculation in ptraj (Sat Mar 10 2007 - 07:24:50 CST)
  • AMBER: prep file limit exceeding (Mon Mar 05 2007 - 01:52:49 CST)
  • AMBER: Residence time of WATER (Mon Feb 19 2007 - 02:33:59 CST)
  • AMBER: extracting coordinate from crd file (Sat Feb 10 2007 - 04:05:20 CST)
  • AMBER: extracting coordinates from crd file (Sat Feb 10 2007 - 02:40:44 CST)
• Gustavo Seabra
  • Re: AMBER: help in QM/MM simulation (Wed Dec 19 2007 - 08:42:19 CST)
  • Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine (Tue Dec 11 2007 - 18:23:49 CST)
  • Re: AMBER: questions about smd of amber 9 (Thu Nov 29 2007 - 08:53:24 CST)
  • Re: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated (Wed Nov 28 2007 - 15:04:32 CST)
  • Re: AMBER: restraints to individual atoms (Tue Nov 27 2007 - 10:34:14 CST)
  • Re: AMBER: RESP question (Fri Nov 09 2007 - 23:01:09 CST)
  • Re: AMBER: make test.parallel (Fri Nov 09 2007 - 10:28:23 CST)
  • Re: AMBER: binary restart file (Fri Oct 05 2007 - 22:56:02 CDT)
  • Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! (Fri Oct 05 2007 - 22:48:59 CDT)
  • Re: AMBER: LINMIN Failure vs Parallelization (Thu Sep 13 2007 - 08:26:45 CDT)
  • Re: AMBER: Schedule for QM-MM with Amber9/Amber10 (Fri Aug 31 2007 - 12:41:18 CDT)
  • Re: AMBER: AMBER at WESTGRID (Thu Aug 30 2007 - 07:35:49 CDT)
  • Re: AMBER: Criteria for classical md being OK to move to QM-MM (Wed Aug 29 2007 - 13:13:05 CDT)
  • Re: AMBER: How to perform MD simulation in NVT ensemble? (Wed Aug 29 2007 - 09:53:11 CDT)
  • Re: AMBER: QM/MM in reaction pathways? (Tue Aug 28 2007 - 09:55:20 CDT)
  • Re: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB (Mon Aug 27 2007 - 15:50:40 CDT)
  • Re: AMBER: generating a .rst file from an .mdcrd file (Mon Aug 27 2007 - 14:15:23 CDT)
  • Re: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB (Mon Aug 27 2007 - 14:12:23 CDT)
  • Re: AMBER: SCC convergence failure in QM-MM DFTB (Mon Aug 27 2007 - 12:20:37 CDT)
  • Re: AMBER: How to perform MD simulation in NVT ensemble? (Fri Aug 24 2007 - 21:21:59 CDT)
  • Re: AMBER: ow to split MDCRD file using ptraj (Fri Aug 24 2007 - 21:17:27 CDT)
  • Re: AMBER: Thermodynamic Integration for conformational changes? (Tue Aug 21 2007 - 22:41:23 CDT)
  • Re: AMBER: Thermodynamic Integration for conformational changes? (Tue Aug 21 2007 - 22:33:36 CDT)
  • Re: AMBER: antechamber, how does it work (Wed Aug 15 2007 - 09:15:48 CDT)
  • Re: AMBER: Building parallel Amber 9.0 (Wed Aug 15 2007 - 08:46:59 CDT)
  • Re: AMBER: Cygwin error (Thu Aug 09 2007 - 16:40:14 CDT)
  • Re: AMBER: Cygwin error (Thu Aug 09 2007 - 15:30:19 CDT)
  • Re: AMBER: Cygwin error (Thu Aug 09 2007 - 14:08:27 CDT)
  • Re: AMBER: Cygwin error (Wed Aug 08 2007 - 18:36:29 CDT)
  • Re: AMBER: Cygwin error (Wed Aug 08 2007 - 17:21:01 CDT)
  • RE: AMBER: Fwd: QM region + cutoff larger that box (Mon Aug 06 2007 - 10:38:19 CDT)
  • RE: AMBER: Fwd: QM region + cutoff larger that box (Sat Aug 04 2007 - 10:33:12 CDT)
  • RE: AMBER: (no subject) (Thu Aug 02 2007 - 15:19:05 CDT)
  • RE: AMBER: QMMM to follow reaction involving water (Mon Jul 30 2007 - 14:41:17 CDT)
  • RE: AMBER: FW: MPI error message (Tue Jul 24 2007 - 14:32:52 CDT)
  • RE: AMBER: Offending restraints???? (Tue Jun 26 2007 - 09:09:18 CDT)
  • RE: AMBER: problems in adding ACE and NME group (Wed Jun 20 2007 - 09:14:26 CDT)
  • Re: AMBER: Installing on windows (Mon Jun 11 2007 - 13:56:48 CDT)
  • Re: AMBER: Installing on windows (Mon Jun 11 2007 - 10:41:05 CDT)
  • Re: AMBER: Installing on windows (Mon Jun 11 2007 - 08:59:29 CDT)
  • Re: AMBER: Installing on windows (Sun Jun 10 2007 - 21:20:05 CDT)
  • Re: AMBER: Installing on windows (Sun Jun 10 2007 - 19:28:01 CDT)
  • Re: AMBER: software to extract data from the output file?? (Sat May 26 2007 - 09:09:08 CDT)
  • Re: AMBER: QM/MM-DRFTB (Mon May 21 2007 - 14:18:10 CDT)
  • Re: AMBER: QM/MM-DRFTB (Mon May 21 2007 - 10:43:43 CDT)
  • Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj (Tue May 15 2007 - 14:11:21 CDT)
  • Re: AMBER: FW: Query regarding using tleap for preparing carbohydrate molecule (Mon May 07 2007 - 07:36:15 CDT)
  • Re: AMBER: Potential of mean force, how to calculate rate of dissociation? (Mon May 07 2007 - 07:26:55 CDT)
  • Re: AMBER: REF file problem (Mon May 07 2007 - 07:20:10 CDT)
  • distance constraint [Was: Re: AMBER: Steered MD & Jarzynski's equality] (Thu May 03 2007 - 06:53:33 CDT)
  • Re: AMBER: md output file (Thu May 03 2007 - 06:32:56 CDT)
  • Re: AMBER: Problem with SCC-DFTB parameter files (Wed May 02 2007 - 10:27:00 CDT)
  • Re: AMBER: Problem with SCC-DFTB parameter files (Wed May 02 2007 - 06:46:58 CDT)
  • Re: AMBER: Steered MD & Jarzynski's equality (Wed May 02 2007 - 06:37:51 CDT)
  • Re: AMBER: Employing SCC-DFTB with a periodic boundary condtion (Thu Apr 26 2007 - 08:18:32 CDT)
  • Re: AMBER: QM/MM simulation with SCC-DFTB (Tue Apr 24 2007 - 05:48:11 CDT)
  • Re: AMBER: regarding frcmod file (Thu Apr 19 2007 - 10:50:44 CDT)
  • Re: AMBER: problem with calculating RMSD (Wed Apr 18 2007 - 09:50:21 CDT)
  • Re: AMBER: problem with calculating RMSD (Tue Apr 17 2007 - 07:41:26 CDT)
  • Re: AMBER: vmd and amber (Tue Apr 17 2007 - 07:33:48 CDT)
  • Re: AMBER: is possible to compile pmemd using scali MPI? (Fri Mar 30 2007 - 14:21:39 CST)
  • Re: AMBER: sander/topology problem (Fri Mar 23 2007 - 09:15:21 CST)
  • Re: AMBER: Need help in Analysis (Wed Mar 14 2007 - 04:39:51 CST)
  • Re: AMBER: The parallel test fails while sander.MPI seems to be installed correctly (Mon Mar 12 2007 - 07:23:50 CST)
  • Re: AMBER: Restart Files (Fri Mar 02 2007 - 15:28:26 CST)
  • Re: AMBER: Restart Files (Fri Mar 02 2007 - 12:06:16 CST)
  • Re: AMBER: Difference in Equilibration & Production MD in Amber (Wed Feb 28 2007 - 14:54:13 CST)
  • Re: AMBER: Box dimensions (Fri Feb 16 2007 - 10:19:39 CST)
  • Re: AMBER: How to place torsion restraint (Tue Feb 13 2007 - 10:48:08 CST)
  • Re: AMBER: ptraj dipole calculation in QMMM simulation (Fri Feb 09 2007 - 12:54:04 CST)
  • Re: AMBER: ab initio modeling using Amber (Thu Feb 01 2007 - 22:07:45 CST)
  • Re: AMBER: xleap (Tue Jan 30 2007 - 09:57:11 CST)
  • Re: AMBER: Fwd: a request (Tue Jan 30 2007 - 09:53:33 CST)
  • Re: AMBER: Fwd: a request (Mon Jan 29 2007 - 11:24:12 CST)
  • Re: AMBER: Fwd: a request (Sat Jan 27 2007 - 22:52:08 CST)
  • Re: AMBER: Fwd: a request (Thu Jan 25 2007 - 09:49:49 CST)
  • Re: AMBER: error when compiling Moilview (Thu Jan 25 2007 - 09:50:57 CST)
  • Re: AMBER: Fwd: a request (Thu Jan 25 2007 - 06:44:58 CST)
  • Re: AMBER: organic solvent : hexan octan (Wed Jan 24 2007 - 13:12:40 CST)
  • Re: AMBER: Fatal error: Command failed for target `test.sander.no_lmod' (Tue Jan 23 2007 - 10:54:09 CST)
  • Re: AMBER: Installation help - SGI Altix 350 (Wed Jan 10 2007 - 10:07:26 CST)
• hadi behzadi
  • AMBER: resp (Tue Jul 31 2007 - 12:15:37 CDT)
  • AMBER: Resp (Tue Jul 31 2007 - 09:15:15 CDT)
  • AMBER: heme force field (Mon Jul 30 2007 - 06:55:07 CDT)
• Hai Long
  • AMBER: Weird restart file with ioutfm=0, iwrap=1 and ntwprt >0 (Mon Nov 26 2007 - 11:41:18 CST)
• Hannes Loeffler
  • Re: AMBER: Reply regarding PCA with ptraj and IED (Tue Jun 19 2007 - 21:43:21 CDT)
• Hannes Wallnoefer
  • Re: AMBER: ptraj frames maximum (Mon Nov 05 2007 - 10:07:00 CST)
  • AMBER: ptraj frames maximum (Mon Nov 05 2007 - 08:19:25 CST)
• Hans Lee
  • Re: AMBER: ptraj and quasi harmonic analysis (Fri Apr 20 2007 - 11:35:49 CDT)
  • Re: AMBER: ptraj and quasi harmonic analysis (Thu Apr 19 2007 - 20:46:38 CDT)
  • Re: AMBER: ptraj and quasi harmonic analysis (Wed Apr 18 2007 - 09:47:11 CDT)
  • AMBER: ptraj and quasi harmonic analysis (Mon Apr 16 2007 - 16:19:34 CDT)
  • AMBER: quasiharnomic analysis (Sun Feb 11 2007 - 15:12:52 CST)
• Hans Martin Senn
  • AMBER: GAFF atom typing for flavin (Sat Aug 04 2007 - 11:15:30 CDT)
• Harald Lanig
  • AMBER: Projecting trajectories onto normal modes (Mon Apr 16 2007 - 09:50:38 CDT)
  • AMBER: Comparison of normal modes with ptraj? (Wed Feb 14 2007 - 04:10:19 CST)
• Harianto Tjong
  • Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! (Wed Sep 26 2007 - 11:23:14 CDT)
• Hashem Taha
  • Re: AMBER: MPI script (Tue Jul 17 2007 - 15:10:46 CDT)
  • Re: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help (Thu Jul 12 2007 - 16:45:50 CDT)
  • AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help (Thu Jul 12 2007 - 15:31:59 CDT)
  • AMBER: TIP4P MD simulations (Mon Jul 09 2007 - 12:53:28 CDT)
• Hayden Eastwood
  • RE: AMBER: invalid digit '*' in the input file (Mon Nov 12 2007 - 09:10:03 CST)
  • RE: AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler (Wed Sep 19 2007 - 12:25:21 CDT)
  • AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler (Wed Sep 19 2007 - 09:24:34 CDT)
  • AMBER: Explicit water in implicit enviornment? (Sun Sep 09 2007 - 14:57:26 CDT)
  • AMBER: Confusion about Langevin dymamics (Fri Aug 31 2007 - 08:46:28 CDT)
  • AMBER: Setting nonbonded cutoff to 1 (Mon Jul 16 2007 - 12:27:45 CDT)
  • RE: AMBER: Simulated Annealing (Tue Jun 26 2007 - 04:14:57 CDT)
  • AMBER: Minimization increases energy (Wed May 23 2007 - 11:24:15 CDT)
  • AMBER: Minimization increases energy (Wed May 23 2007 - 11:21:35 CDT)
  • RE: AMBER: Average PDB - Unusual Bonds (Fri May 04 2007 - 09:45:01 CDT)
  • RE: AMBER: mm-pbsa error with nm = 1 (Wed May 02 2007 - 06:10:10 CDT)
  • RE: AMBER: mm-pbsa error with nm = 1 (Wed May 02 2007 - 05:36:55 CDT)
  • AMBER: mm-pbsa error with nm = 1 (Tue May 01 2007 - 12:21:22 CDT)
  • RE: AMBER: PDB files (Mon Apr 30 2007 - 12:20:14 CDT)
  • RE: AMBER: PDB files (Mon Apr 30 2007 - 12:12:01 CDT)
  • AMBER: Problem with calcpka.pl and constant pH (Mon Apr 30 2007 - 08:04:11 CDT)
  • AMBER: Problem with calcpka.pl and constant pH (Mon Apr 30 2007 - 06:35:23 CDT)
  • AMBER: Explicit water opinion (Fri Apr 13 2007 - 13:39:19 CDT)
• Hector A. Baldoni
  • AMBER: chiral surfaces (Wed Sep 05 2007 - 18:35:42 CDT)
• Heike.Meiselbach_at_chemie.uni-erlangen.de
  • Re: AMBER: Need help in Analysis (Wed Mar 14 2007 - 04:35:34 CST)
• Henar Martínez García
  • AMBER: Problem with MM-PBSA statistics (Mon Apr 30 2007 - 04:53:38 CDT)
• Henk Meij
  • Re: AMBER: problem in installing amber9 SOLVED! (Wed Jun 13 2007 - 15:43:06 CDT)
  • Re: AMBER: problem in installing amber9 (Wed Jun 13 2007 - 15:32:18 CDT)
  • Re: AMBER: amber9 compile problem (Tue Jun 12 2007 - 13:30:54 CDT)
  • Re: AMBER: problem in installing amber9 (Wed Jun 13 2007 - 12:30:59 CDT)
  • Re: AMBER: problem in installing amber9 (Wed Jun 13 2007 - 08:41:27 CDT)
  • Re: AMBER: amber9 compile problem (Tue Jun 12 2007 - 09:13:01 CDT)
  • Re: AMBER: amber9 compile problem (Mon Jun 11 2007 - 14:04:05 CDT)
  • Re: AMBER: amber9 compile problem (Mon Jun 11 2007 - 08:51:12 CDT)
  • Re: AMBER: amber9 compile problem (Mon Jun 11 2007 - 08:20:17 CDT)
• HL Eastwood
  • AMBER: mobile proton algorithm (Tue Apr 24 2007 - 14:25:10 CDT)
  • AMBER: How do I make and enter new ff parameters into AMBER (Fri Feb 02 2007 - 15:26:46 CST)
  • Re: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand (Fri Feb 02 2007 - 11:41:50 CST)
  • Re: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand (Fri Feb 02 2007 - 11:40:10 CST)
• hmeij_at_wesleyan.edu
  • AMBER: amber9 compile problem (Sun Jun 10 2007 - 08:58:54 CDT)
• Holger Gohlke
  • Re: AMBER: Amber 9 - bugfix.40 fails (Wed Dec 05 2007 - 11:56:23 CST)
  • Re: AMBER: secstruct command (Thu Jul 19 2007 - 13:22:37 CDT)
  • Re: AMBER: parse radii (Wed Apr 04 2007 - 04:24:17 CDT)
  • Re: AMBER: iRED and corrired (Mon Feb 05 2007 - 10:09:15 CST)
• Holly Freedman
  • Re: AMBER: results from TI (Tue Oct 23 2007 - 15:29:00 CDT)
  • Re: AMBER: results from TI (Tue Oct 23 2007 - 11:57:42 CDT)
  • Re: AMBER: results from TI (Mon Oct 22 2007 - 14:03:20 CDT)
  • AMBER: results from TI (Mon Oct 22 2007 - 11:42:26 CDT)
  • Re: AMBER: neb for path between binding sites (Tue Oct 09 2007 - 18:37:20 CDT)
  • Re: AMBER: neb for path between binding sites (Tue Oct 09 2007 - 18:35:19 CDT)
  • AMBER: neb for path between binding sites (Tue Oct 09 2007 - 16:09:50 CDT)
  • AMBER: tgtrmsmask and tgtfitmask (Mon Jul 09 2007 - 21:03:39 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Wed Jul 04 2007 - 14:53:01 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Tue Jul 03 2007 - 12:14:29 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Mon Jul 02 2007 - 15:51:12 CDT)
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Sun Jul 01 2007 - 14:54:11 CDT)
  • AMBER: large RMS fluctuations in turning off VDW interactions by TI (Sun Jul 01 2007 - 14:13:17 CDT)
• Hopkins, Robert
  • Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine (Tue Dec 11 2007 - 17:50:17 CST)
  • Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine (Sun Dec 09 2007 - 15:44:34 CST)
  • AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine (Mon Nov 12 2007 - 17:32:20 CST)
  • AMBER: Please Disregard My Last E-mail: Missing 'yacc' command (Sat Oct 13 2007 - 18:04:11 CDT)
  • AMBER: Missing 'yacc' command (Sat Oct 13 2007 - 17:00:00 CDT)
  • RE: AMBER: Problems with 'make' (Fri Oct 05 2007 - 13:32:24 CDT)
  • AMBER: Problems with 'make' (Thu Oct 04 2007 - 14:07:42 CDT)
• Hu, Shaowen (JSC-SK)[USRA]
  • RE: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine (Tue Nov 13 2007 - 10:13:18 CST)
  • RE: AMBER: DNA base planarity restraint (Fri Sep 14 2007 - 13:29:13 CDT)
  • AMBER: DNA base planarity restraint (Fri Sep 14 2007 - 10:29:46 CDT)
  • RE: AMBER: Harmonic constraints (Mon Sep 10 2007 - 09:05:18 CDT)
  • AMBER: force field for irregulate DNA ends (Sat Aug 04 2007 - 13:20:42 CDT)
  • RE: AMBER: planarity restraints for NA (Thu Aug 02 2007 - 13:49:15 CDT)
  • RE: AMBER: Ionic strength in pbsa (Tue May 22 2007 - 15:29:02 CDT)
  • AMBER: Ionic strength in pbsa (Tue May 22 2007 - 09:59:01 CDT)
  • AMBER: Some questions on mm_pbsa (Fri May 18 2007 - 09:53:35 CDT)
  • AMBER: total energies during MM-PBSA (Wed May 16 2007 - 08:57:26 CDT)
  • AMBER: total energies during MM-PBSA (Tue May 15 2007 - 16:01:11 CDT)
  • RE: AMBER: nscm in simulation annealing (Tue Apr 17 2007 - 11:59:43 CDT)
  • RE: AMBER: nscm in simulation annealing (Tue Apr 17 2007 - 11:26:01 CDT)
  • RE: AMBER: nscm in simulation annealing (Tue Apr 17 2007 - 10:25:05 CDT)
  • RE: AMBER: nscm in simulation annealing (Fri Apr 13 2007 - 15:13:07 CDT)
  • RE: AMBER: nscm in simulation annealing (Fri Apr 13 2007 - 13:36:59 CDT)
  • RE: AMBER: nscm in simulation annealing (Fri Apr 13 2007 - 10:32:26 CDT)
  • RE: AMBER: nscm in simulation annealing (Thu Apr 12 2007 - 12:53:18 CDT)
  • AMBER: nscm in simulation annealing (Thu Apr 12 2007 - 09:38:09 CDT)
  • AMBER: dihedral angles restraint for DNA (Tue Apr 10 2007 - 12:51:13 CDT)
• Hu, Shaowen \(JSC-SK\)[USRA]
  • RE: AMBER: ntt=1 or ntt= 3? (Thu Mar 22 2007 - 15:40:09 CST)
  • RE: AMBER: ntt=1 or ntt= 3? (Thu Mar 22 2007 - 15:24:10 CST)
  • RE: AMBER: Is this system too large? (Fri Feb 23 2007 - 10:10:09 CST)
  • RE: AMBER: Is this system too large? (Thu Feb 22 2007 - 09:58:01 CST)
  • RE: AMBER: Is this system too large? (Wed Feb 21 2007 - 11:02:21 CST)
  • AMBER: Is this system too large? (Tue Feb 20 2007 - 22:17:41 CST)
• huzehan19870731_at_126.com
  • AMBER:How to calculate the free energy of a series of conformations (Mon Nov 19 2007 - 21:18:41 CST)
• Ichinkhorloo Erdenebaatar
  • AMBER: SANDER bug (Tue Feb 13 2007 - 19:19:21 CST)
• Idan Gabdank
  • Re: AMBER: Problems loading pdb file including Mg ions (Wed Oct 24 2007 - 08:05:46 CDT)
  • AMBER: Problems loading pdb file including Mg ions (Mon Oct 22 2007 - 10:53:12 CDT)
• Ignacio Faustino
  • AMBER: TI calculation: the perturbed charge is not integral (Wed Mar 21 2007 - 13:21:52 CST)
  • AMBER: xLeAP: TI calculation: the perturbed charge is not integral (Wed Mar 21 2007 - 13:17:12 CST)
• Ileana Stoica
  • AMBER: Internal dielectric and MMPBSA (Tue Jun 12 2007 - 06:32:17 CDT)
• Ilya Chorny
  • Re: AMBER: Re: Amber_ifort_x86_64 test error (Sun Dec 09 2007 - 20:42:45 CST)
  • Re: AMBER: Re: Amber_ifort_x86_64 test error (Sun Dec 09 2007 - 12:12:57 CST)
  • Re: AMBER: Re: Amber_ifort_x86_64 test error (Sun Dec 09 2007 - 12:11:52 CST)
  • Re: AMBER: Re: Amber_ifort_x86_64 test error (Sun Dec 09 2007 - 11:22:17 CST)
  • AMBER: Re: Amber_ifort_x86_64 test error (Sun Dec 09 2007 - 10:46:32 CST)
• Ilyas Yildirim
  • Re: AMBER: TI Approach - mass perturbation (Tue Dec 11 2007 - 01:47:52 CST)
  • AMBER: TI Approach - mass perturbation (Mon Dec 10 2007 - 12:20:49 CST)
  • RE: AMBER: Re: Amber_ifort_x86_64 test error (Sun Dec 09 2007 - 15:56:09 CST)
  • Re: AMBER: MD_model (Wed Dec 05 2007 - 17:54:50 CST)
  • Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault (Mon Dec 03 2007 - 16:42:54 CST)
  • Re: AMBER: angle between vectors (Fri Nov 30 2007 - 11:28:59 CST)
  • Re: AMBER: modifications to force field for Fe4S4 cubane (Tue Nov 27 2007 - 13:29:58 CST)
  • Re: AMBER: Xleap and Hydrogens (Tue Nov 27 2007 - 09:08:29 CST)
  • Re: AMBER: modifications to force field for Fe4S4 cubane (Tue Nov 27 2007 - 09:02:21 CST)
  • Re: AMBER: frcmod file and NONB for dummy atoms (Fri Nov 23 2007 - 20:26:37 CST)
  • Re: AMBER: RE: FF94 or FF99? (Fri Nov 23 2007 - 17:29:15 CST)
  • Re: AMBER: Fwd: About TER records (Fri Nov 23 2007 - 09:41:47 CST)
  • AMBER: frcmod file and NONB for dummy atoms (Thu Nov 22 2007 - 18:48:31 CST)
  • Re: AMBER: RE: FF94 or FF99? (Thu Nov 22 2007 - 18:29:08 CST)
  • Re: AMBER: thermodynamic integration (Thu Nov 08 2007 - 16:42:04 CST)
  • Re: AMBER: Antechamber (Tue Nov 06 2007 - 15:03:13 CST)
  • Re: AMBER: Antechamber (Tue Nov 06 2007 - 11:36:35 CST)
  • Re: AMBER: antechamber fails with large molecules (Sat Nov 03 2007 - 10:47:49 CST)
  • Re: AMBER: antechamber fails with large molecules (Sat Nov 03 2007 - 02:38:03 CST)
  • Re: AMBER: antechamber fails with large molecules (Fri Nov 02 2007 - 03:10:33 CST)
  • Re: AMBER: antechamber fails with large molecules (Fri Nov 02 2007 - 02:24:26 CST)
  • Re: AMBER: How to intergrate the area under a curve. (Mon Oct 22 2007 - 02:17:07 CDT)
  • AMBER: Re: using RESP (Tue Sep 25 2007 - 18:04:52 CDT)
  • RE: AMBER: Help WARNING: The unperturbed charge of the unit (Tue Sep 25 2007 - 13:56:19 CDT)
  • Re: AMBER: Help WARNING: The unperturbed charge of the unit (Mon Sep 24 2007 - 16:53:40 CDT)
  • Re: AMBER: TMD and "Current RMSD from reference" (Sun Sep 23 2007 - 13:14:48 CDT)
  • Re: AMBER: TMD and "Current RMSD from reference" (Sat Sep 22 2007 - 19:54:17 CDT)
  • Re: AMBER: TMD and "Current RMSD from reference" (Sat Sep 22 2007 - 15:49:26 CDT)
  • AMBER: TMD and "Current RMSD from reference" (Sat Sep 22 2007 - 05:40:05 CDT)
  • Re: AMBER: Targetted MD and ptraj analysis (Fri Sep 21 2007 - 14:40:36 CDT)
  • Re: AMBER: problem with Thermodynamic Integration (Wed Sep 19 2007 - 11:45:47 CDT)
  • AMBER: Targetted MD and ptraj analysis (Wed Sep 19 2007 - 00:47:19 CDT)
  • Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- (Mon Sep 17 2007 - 23:38:58 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Fri Sep 07 2007 - 19:39:04 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Fri Sep 07 2007 - 17:21:55 CDT)
  • Re: AMBER: Harmonic constraints (Fri Sep 07 2007 - 12:13:55 CDT)
  • Re: AMBER: command tleap is not normal (Tue Aug 21 2007 - 03:50:35 CDT)
  • Re: AMBER: Any experience on Dell two quad core system? (Mon Aug 13 2007 - 19:39:01 CDT)
  • RE: AMBER: Any experience on Dell two quad core system? (Mon Aug 13 2007 - 14:25:22 CDT)
  • Re: AMBER: Any experience on Dell two quad core system? (Fri Aug 03 2007 - 11:35:26 CDT)
  • Re: AMBER: Any experience on Dell two quad core system? (Thu Aug 02 2007 - 23:23:17 CDT)
  • AMBER: Any experience on Dell two quad core system? (Thu Aug 02 2007 - 19:33:40 CDT)
  • AMBER: Truncated Octahedron box volume (Sun Jul 22 2007 - 21:52:16 CDT)
  • Re: AMBER: xleap and amber7 (Wed Jul 04 2007 - 23:53:37 CDT)
  • AMBER: Does Chimera support AMBER file formats? (Tue Jun 26 2007 - 18:58:56 CDT)
  • AMBER: Energy outputs in TI Approach (Sat Jun 16 2007 - 00:03:26 CDT)
  • Re: AMBER: PDB problems (Fri Jun 15 2007 - 17:30:45 CDT)
  • Re: AMBER: .lib files (Fri Jun 15 2007 - 14:50:34 CDT)
  • Re: AMBER: Saving a structuring from trajectory (Fri Jun 15 2007 - 13:59:50 CDT)
  • Re: AMBER: Dihedral driver (Thu Jun 07 2007 - 15:16:15 CDT)
  • RE: AMBER: extracting starting structures from equilibration trajectory (Thu Jun 07 2007 - 14:58:19 CDT)
  • RE: AMBER: extracting starting structures from equilibration trajectory (Thu Jun 07 2007 - 14:54:06 CDT)
  • Re: AMBER: extracting starting structures from equilibration trajectory (Thu Jun 07 2007 - 13:14:18 CDT)
  • Re: AMBER: bad atom type errors in GB for halides? (Thu Apr 12 2007 - 14:57:13 CDT)
  • Re: AMBER: Combining RESP with AM1-BCC (Fri Mar 23 2007 - 18:27:07 CST)
  • AMBER: Combining RESP with AM1-BCC (Fri Mar 23 2007 - 15:41:04 CST)
  • AMBER: antechamber (Sun Mar 18 2007 - 11:56:00 CST)
  • AMBER: antechamber error (Sat Mar 17 2007 - 00:44:57 CST)
  • Re: AMBER: Topology file problem in TI ! (Wed Mar 07 2007 - 12:09:39 CST)
  • Re: AMBER: psi , phi angles (Tue Mar 06 2007 - 06:10:32 CST)
  • Re: Re: AMBER: crd to pdb conversion (Mon Feb 19 2007 - 11:12:43 CST)
  • Re: AMBER: crd to pdb conversion (Mon Feb 19 2007 - 07:35:16 CST)
  • Re: AMBER: Installing AMBER v9 in Linux (Sun Feb 18 2007 - 01:30:34 CST)
  • Re: AMBER: read the data (Fri Feb 16 2007 - 17:05:31 CST)
  • Re: AMBER: hi (Wed Feb 14 2007 - 16:14:11 CST)
  • Re: AMBER: Modified nucleotides (Tue Feb 13 2007 - 22:05:25 CST)
  • Re: AMBER: Modified nucleotides (Mon Feb 12 2007 - 22:58:50 CST)
  • Re: AMBER: extracting coordinates from crd file (Sat Feb 10 2007 - 02:59:04 CST)
  • AMBER: Heating the system prior to production run (Fri Feb 09 2007 - 15:28:08 CST)
  • Re: AMBER: equilibration in explicit solvent (Thu Feb 08 2007 - 14:16:10 CST)
  • Re: AMBER: side chain orientation (Wed Feb 07 2007 - 12:00:37 CST)
  • Re: AMBER: Link to Modified NA bases files (Mon Feb 05 2007 - 22:05:21 CST)
  • Re: AMBER: equilibration in explicit solvent (Sun Feb 04 2007 - 23:13:48 CST)
  • Re: AMBER: Charges in TI calculations and leap (Tue Jan 30 2007 - 13:48:00 CST)
  • Re: AMBER: Antechamber esp calculation (Tue Jan 23 2007 - 00:07:31 CST)
• In Hee Park
  • Re: AMBER: MPI Quiescence problem in REMD (Thu Aug 16 2007 - 17:56:37 CDT)
  • Re: AMBER: MPI Quiescence problem in REMD (Wed Jul 11 2007 - 11:41:47 CDT)
  • AMBER: MPI Quiescence problem in REMD (Tue Jul 10 2007 - 23:03:08 CDT)
  • AMBER: rst overflow for implicit REMD (Tue Jun 26 2007 - 09:37:45 CDT)
• Ingvar Lagerstedt
  • AMBER: 64-bit pgf90 revisited (Tue May 29 2007 - 03:39:07 CDT)
• Irene Newhouse
  • RE: AMBER: Problems with Carbohydrate Non-standard Residue (Wed Sep 12 2007 - 11:58:17 CDT)
  • RE: AMBER: modified leaprc for glycoproteins (Fri Aug 31 2007 - 20:14:32 CDT)
  • AMBER: modified leaprc for glycoproteins (Fri Aug 31 2007 - 15:53:05 CDT)
• j j
  • AMBER: GDP UNKNOWN ATOM TYPE: O3 warning (Sat Jul 21 2007 - 12:21:32 CDT)
  • Re: AMBER: Slight_error_on_Compiling_Replica_Exchange (Wed Jul 04 2007 - 05:13:22 CDT)
  • AMBER: Slight_error_on_Compiling_Replica_Exchange (Wed Jul 04 2007 - 03:57:28 CDT)
  • Re: AMBER: Re: Fwd: joshua (Wed Jun 20 2007 - 08:01:00 CDT)
  • AMBER: Re: Fwd: joshua (Wed Jun 20 2007 - 06:27:43 CDT)
  • Re: AMBER: ff99 vs ff99SB for RNA (Thu Jun 14 2007 - 10:30:21 CDT)
  • Re: AMBER: Trouble on wiki about GAFF (Fri Jun 08 2007 - 02:14:13 CDT)
  • AMBER: Trouble on wiki about GAFF (Thu Jun 07 2007 - 18:29:37 CDT)
  • Re: AMBER: pdb flie format (Mon Jun 04 2007 - 16:10:32 CDT)
  • Re: AMBER: adding polar hydrogens (Thu May 24 2007 - 08:00:12 CDT)
  • Re: AMBER: adding polar hydrogens (Thu May 24 2007 - 06:09:04 CDT)
  • Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj (Wed May 16 2007 - 06:39:48 CDT)
  • Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj (Wed May 16 2007 - 04:01:24 CDT)
  • Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj (Wed May 16 2007 - 03:56:54 CDT)
  • Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj (Tue May 15 2007 - 13:32:30 CDT)
  • AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj (Tue May 15 2007 - 12:55:40 CDT)
  • Re: AMBER: Problem using Ptraj (Mon Apr 23 2007 - 11:47:50 CDT)
  • Re: AMBER: mol2 format (Mon Apr 23 2007 - 04:04:53 CDT)
  • Re: AMBER: NTX=7 ?............lastist= ?...........lastrst= ????? (Mon Apr 09 2007 - 09:18:58 CDT)
  • Re: AMBER: The ring number exceeds MAXRING, increase MAXRING and recompile the programs, exit (Tue Mar 27 2007 - 12:43:49 CST)
  • AMBER: The ring number exceeds MAXRING, increase MAXRING and recompile the programs, exit (Tue Mar 27 2007 - 08:04:48 CST)
  • Re: AMBER: Restart from restart file obtained from ptraj with added velocities (Thu Mar 01 2007 - 11:43:13 CST)
  • AMBER: Restart from restart file obtained from ptraj with added velocities (Thu Mar 01 2007 - 10:17:41 CST)
  • Re: AMBER: Box problems in vacuum minimization with sander.serial 8 (Tue Feb 13 2007 - 13:43:34 CST)
  • AMBER: Box problems in vacuum minimization with sander.serial 8 (Tue Feb 13 2007 - 13:05:16 CST)
• jacopo.sgrignani_at_unifi.it
  • AMBER: ptraj hbond (Sat Feb 03 2007 - 10:28:20 CST)
• James W
  • AMBER: Can I set harmonic constraints in SMD simulations ? (Fri Sep 14 2007 - 21:50:35 CDT)
  • Re: AMBER: Steered MD & Jarzynski's equality (Wed May 02 2007 - 04:44:28 CDT)
  • AMBER: Steered MD & Jarzynski's equality (Wed May 02 2007 - 01:44:20 CDT)
• janavi raghavan
  • AMBER: sander bomb (Tue Apr 03 2007 - 09:28:39 CDT)
  • Re: AMBER: Problem related simulation of dimer (Thu Mar 15 2007 - 11:28:32 CST)
  • Re: AMBER: Problem related simulation of dimer (Thu Mar 15 2007 - 11:24:23 CST)
  • Re: AMBER: solvate shell (Thu Mar 15 2007 - 11:27:42 CST)
  • AMBER: solvate shell (Thu Mar 15 2007 - 10:33:13 CST)
• jantonioms J. A. Mondragon S
  • Re: AMBER: Pre-ABMER Installation Prob w/ MPICH2 (Fri Nov 23 2007 - 11:36:12 CST)
• Jardas sucuriba
  • RE: AMBER: umbrella sampling (Sun Nov 25 2007 - 13:32:28 CST)
  • AMBER: dihedral angles (Tue Oct 30 2007 - 18:43:10 CST)
  • RE: AMBER: dihedral parameters (Tue Jun 12 2007 - 21:18:12 CDT)
  • AMBER: dihedral parameters (Mon Jun 11 2007 - 17:13:36 CDT)
  • RE: AMBER: NAD parameters (Wed Apr 25 2007 - 17:46:17 CDT)
  • AMBER: NAD parameters (Tue Apr 24 2007 - 13:02:56 CDT)
  • AMBER: mol2 format (Sun Apr 22 2007 - 17:57:12 CDT)
  • AMBER: mm_pbsa problems (Tue Jan 30 2007 - 09:55:00 CST)
  • AMBER: fluctuations (Tue Jan 02 2007 - 09:21:22 CST)
• Jarrod Smith
  • RE: AMBER: Problems with QMMM tests on Altix (Fri Feb 23 2007 - 13:34:53 CST)
  • AMBER: Problems with QMMM tests on Altix (Thu Feb 22 2007 - 16:03:14 CST)
• Jason Brown
  • AMBER: Unexpected Failure in XLeap (Tue Jun 26 2007 - 13:45:14 CDT)
• Jason DeChancie
  • AMBER: QM/MM Umbrella sampling (Fri Apr 27 2007 - 15:53:08 CDT)
• Jason K
  • Re: AMBER: REMD error (Thu May 24 2007 - 10:31:17 CDT)
  • Re: AMBER: REMD error (Tue May 22 2007 - 14:02:22 CDT)
  • AMBER: REMD error (Mon May 21 2007 - 10:20:12 CDT)
  • Re: AMBER: Gas-phase energies (and more) (Fri Jan 26 2007 - 15:36:25 CST)
  • AMBER: Gas-phase energies (and more) (Thu Jan 25 2007 - 17:04:16 CST)
• Jason Whitte
  • AMBER: incoherent intermediate scattering function (Tue Jul 17 2007 - 17:59:21 CDT)
• JAVIER PEREZ
  • AMBER: gibbs problems (Wed Oct 31 2007 - 05:48:22 CST)
• Jed W Pitera
  • Re: AMBER: Installing amber9 in IBM P5? (Wed Jun 13 2007 - 10:04:31 CDT)
• Jena M
  • AMBER: Umbrella sampling (Fri Oct 26 2007 - 08:48:26 CDT)
  • AMBER: how to simulate a ligand bound to a residue (Thu Oct 18 2007 - 08:49:55 CDT)
  • AMBER: neutral terminals (Wed Aug 01 2007 - 19:15:46 CDT)
  • AMBER: methods to approach two atoms (Thu Jul 26 2007 - 08:53:09 CDT)
  • AMBER: offending restraint (Sat Jul 21 2007 - 19:15:42 CDT)
  • AMBER: convergence criterion not reached (Mon Jul 02 2007 - 18:53:22 CDT)
  • AMBER: PMF calculation (Mon Jun 25 2007 - 14:59:02 CDT)
• Jennie Thomas
  • Re: AMBER: Rotations about center of mass of an isolated system (Mon May 14 2007 - 18:55:44 CDT)
  • Re: AMBER: Rotations about center of mass of an isolated system (Mon May 14 2007 - 14:50:30 CDT)
  • AMBER: Rotations about center of mass of an isolated system (Thu May 10 2007 - 20:08:06 CDT)
  • AMBER: NH3 potential (Wed Jan 03 2007 - 15:00:28 CST)
• Jeremy Weedon
  • Re: AMBER: Hardware recommendations please (Thu Jun 07 2007 - 10:24:54 CDT)
  • AMBER: Hardware recommendations please (Wed Jun 06 2007 - 11:15:16 CDT)
• Jerome.GOLEBIOWSKI_at_unice.fr
  • Re: AMBER: RE: FF94 or FF99? (Thu Nov 22 2007 - 09:57:33 CST)
  • Re: AMBER: Umbrella sampling (Fri Oct 26 2007 - 12:08:09 CDT)
  • Re: AMBER: Potential of mean force: how to extract the min structure? (Tue Sep 18 2007 - 03:09:29 CDT)
  • Re: AMBER: How to fix two angle but do umberlla sampling for distance? (Thu Jun 07 2007 - 10:38:26 CDT)
  • Re: AMBER: Reg restraint value obtained during umbrella sampling (Thu May 31 2007 - 13:02:45 CDT)
  • Re: AMBER: umbrella sampling: distance restraint (Thu May 10 2007 - 07:19:35 CDT)
  • Re: AMBER: Potential of mean force, how to calculate rate of dissociation? (Fri May 04 2007 - 03:06:17 CDT)
  • Re: AMBER: Potential of mean force, how to calculate rate of dissociation? (Thu May 03 2007 - 08:57:32 CDT)
  • Re: AMBER: QM/MM Umbrella sampling (Sat Apr 28 2007 - 02:55:49 CDT)
  • Re: AMBER: Minimization (Wed Mar 28 2007 - 02:48:35 CST)
  • Re: AMBER: Disulfide Bonds (Wed Feb 28 2007 - 07:27:23 CST)
  • Re: AMBER: Umbrella sampling (Mon Feb 12 2007 - 03:33:18 CST)
• Jesper Soerensen
  • Re: AMBER: RED-vIII fails (Mon Nov 05 2007 - 10:01:21 CST)
  • Re: AMBER: RED-vIII fails (Tue Oct 30 2007 - 03:16:36 CST)
  • AMBER: RED-vIII fails (Mon Oct 29 2007 - 08:51:56 CST)
  • AMBER: Protonation/deprotonation of terminal residues (Wed Apr 18 2007 - 07:56:26 CDT)
• Jesus Angulo
  • AMBER: Compiling parallel Amber9 on Linux cluster (Wed May 09 2007 - 05:27:23 CDT)
  • RE: AMBER: DHAS_10_12 compilation aborted for egb.f (Tue Mar 06 2007 - 11:41:37 CST)
  • AMBER: DHAS_10_12 compilation aborted for egb.f (Tue Mar 06 2007 - 08:31:28 CST)
• Ji-Lai Li
  • AMBER: replica exchange simulation (Sat Sep 15 2007 - 19:58:06 CDT)
  • AMBER: How to modify the velocity of a water molecule? (Thu Feb 15 2007 - 20:15:45 CST)
  • Re: AMBER: pmemd install error (Sun Jan 28 2007 - 21:18:05 CST)
  • AMBER: evaluate expression (Wed Jan 24 2007 - 22:14:11 CST)
  • Re: AMBER: calcium parameter for GB (Tue Jan 23 2007 - 20:07:21 CST)
  • AMBER: Re: pmemd install error (Tue Jan 23 2007 - 01:03:33 CST)
  • AMBER: pmemd install error (Tue Jan 23 2007 - 00:59:27 CST)
  • Re: AMBER: calcium parameter for GB (Wed Jan 17 2007 - 19:25:20 CST)
  • Re: AMBER: calcium parameter for GB (Wed Jan 17 2007 - 02:19:09 CST)
  • AMBER: explicit implicit solvent (Wed Jan 10 2007 - 08:24:20 CST)
• jialei
  • RE: AMBER: Free energy for part of the system (Tue Dec 04 2007 - 19:10:18 CST)
  • RE: AMBER: Free energy for part of the system (Tue Dec 04 2007 - 12:21:03 CST)
  • AMBER: Free energy for part of the system (Mon Dec 03 2007 - 13:12:47 CST)
• Jianmin Feng
  • Re: AMBER: Installation Question (Mon Jun 04 2007 - 09:33:20 CDT)
• Jianyin Shao
  • Re: AMBER: ptraj: RMS per residues and per time (Fri Jul 06 2007 - 02:54:06 CDT)
  • Re: AMBER: intra-molecular h-bonds in ptraj (Thu Jan 04 2007 - 14:11:36 CST)
  • Re: AMBER: H-bond in ptraj (Thu Jan 04 2007 - 13:49:38 CST)
• Jiapu.Zhang_at_csiro.au
  • AMBER: FORTRAN code for calculating ENERGY of all the four terms (bonds, angles, dihedrals, nonbanded pairs) of Amber8's sander (Thu Oct 18 2007 - 18:15:05 CDT)
  • RE: AMBER: Why there is a gap or jump if continue ntt=3 or ntt=1 (Mon Jan 29 2007 - 16:08:26 CST)
  • AMBER: Why there is a gap or jump if continue ntt=3 or ntt=1 (Mon Jan 29 2007 - 00:04:34 CST)
• Jimmy Heimdal
  • AMBER: EVB Calculations (Mon Oct 22 2007 - 01:30:48 CDT)
• Jin-Soo Kim
  • Re: AMBER: Problem while creating structure in xLeap (Sat Mar 24 2007 - 05:53:29 CST)
  • AMBER: Does Sander.MPI support coupling effect between different molecules at the same area at the same temperature in the mixture? (Sat Mar 24 2007 - 05:40:26 CST)
  • Re: AMBER: sander/topology problem (Sat Mar 24 2007 - 05:17:51 CST)
  • Re: AMBER: sander/topology problem (Fri Mar 23 2007 - 08:31:00 CST)
• Jingyuan Luke
  • AMBER: Sander Bomb in subroutine nonbond_list (Mon Apr 09 2007 - 21:34:51 CDT)
• Jiri Sponer
  • Re: AMBER: RE: FF94 or FF99? (Sat Nov 24 2007 - 04:53:24 CST)
  • Re: AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ? (Sun Nov 04 2007 - 07:01:02 CST)
  • Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- (Tue Sep 18 2007 - 03:11:19 CDT)
  • Re: AMBER: Harmonic constraints (Sat Sep 08 2007 - 01:07:23 CDT)
  • Re: AMBER: Force field for RNA with U-turn motif (Wed Aug 22 2007 - 11:33:46 CDT)
  • Re: AMBER: Pi-pi interactions (Tue May 22 2007 - 05:14:36 CDT)
  • Re: AMBER: Pi-pi interactions (Mon May 21 2007 - 10:34:37 CDT)
  • Re: AMBER: Pi-pi interactions (Mon May 21 2007 - 08:28:22 CDT)
  • Re: AMBER: Pi-pi interactions (Mon May 21 2007 - 08:09:08 CDT)
  • Re: AMBER: CHARMM vs. AMBER ff literature (Thu Apr 12 2007 - 07:58:32 CDT)
  • Re: AMBER: MMPBSA with water molecule in active site (Sun Mar 18 2007 - 12:21:17 CST)
  • Re: AMBER: Essential ions and water molecules in MMPBSA computations (Mon Mar 12 2007 - 08:44:08 CST)
  • Re: AMBER: Essential ions and water molecules in MMPBSA computations (Mon Mar 12 2007 - 07:05:49 CST)
  • Re: AMBER: denaturing salt conditions (Sat Mar 03 2007 - 18:28:28 CST)
  • AMBER: DNA and RNA computations (Mon Feb 19 2007 - 12:16:53 CST)
  • Re: AMBER: DNA structure analysis (Wed Jan 17 2007 - 04:39:36 CST)
• Jiten
  • Re: AMBER: bugfix for impropers in parmchk (Thu Aug 02 2007 - 01:23:20 CDT)
  • Re: AMBER: bugfix for impropers in parmchk (Wed Aug 01 2007 - 23:02:24 CDT)
  • AMBER: Re: amber mm-pbsa problem (Mon Apr 16 2007 - 20:39:26 CDT)
  • Re: AMBER: Amber:PBSA&Extract_coords problem (Needed help) (Sat Apr 14 2007 - 08:51:58 CDT)
• jitrayut jitonnom
  • Re: AMBER: protonation of His residue! (Thu Aug 23 2007 - 22:52:51 CDT)
  • Re: AMBER: Error in MMPBSA Calculation (Tue Aug 21 2007 - 02:11:52 CDT)
  • AMBER: MM-GBSA: pairwise decompose energy calculation can't read snapshot_com.all.out (Sun Jun 03 2007 - 11:08:16 CDT)
  • Fwd: AMBER: MM-PBSA: Can't finish the binding energy process (Wed May 09 2007 - 23:12:55 CDT)
  • AMBER: Binding free energy errors: Grid setting fail (Sun Apr 29 2007 - 08:48:17 CDT)
  • AMBER: MM-PBSA: Can't finish the binding energy process (Mon Apr 23 2007 - 07:34:48 CDT)
  • AMBER: MM-PBSA: decompose energy error (Mon Apr 23 2007 - 06:31:43 CDT)
  • AMBER: MM-PBSA: decompose energy error (Mon Apr 23 2007 - 06:31:43 CDT)
  • AMBER: Can't run decompose energy in MM-PBSA (Mon Jan 22 2007 - 08:20:51 CST)
  • Fwd: AMBER: Can't run Normal Mode Analysis !!! (Mon Jan 22 2007 - 06:58:24 CST)
  • AMBER: MM-PBSA problem: Why (Sun Jan 21 2007 - 23:20:38 CST)
  • AMBER: Can't run Normal Mode Analysis !!! (Sun Jan 21 2007 - 23:09:48 CST)
• jlalonde
  • AMBER: amber9 possible failure tgtmd (Fri Feb 09 2007 - 10:19:19 CST)
• JM Beames
  • Re: AMBER: nmode ntrun=2 (Thu Dec 13 2007 - 09:29:54 CST)
  • Re: AMBER: nmode ntrun=2 (Thu Dec 06 2007 - 05:48:43 CST)
  • AMBER: nmode ntrun=2 (Wed Dec 05 2007 - 04:03:24 CST)
• Joachim Hein
  • AMBER: Re: divcon on AIX using xlf 10.1 (Mon Dec 03 2007 - 10:43:19 CST)
  • AMBER: divcon on AIX using xlf 10.1 (Wed Nov 07 2007 - 10:23:14 CST)
• Joe Nolan
  • AMBER: Parallel test error with shared libraries (Mon Nov 05 2007 - 15:05:27 CST)
  • AMBER: Amber9 parallel installation error (retry) (Tue Oct 30 2007 - 12:25:35 CST)
  • Re: AMBER: Amber9 parallel installation error (with openMPI) (Mon Oct 29 2007 - 16:30:25 CST)
  • Re: AMBER: Amber9 parallel installation error (with openMPI) (Mon Oct 29 2007 - 15:55:43 CST)
  • AMBER: Amber9 parallel installation error (with openMPI) (Mon Oct 29 2007 - 15:02:10 CST)
  • AMBER: Amber9 installation error on Mandriva 2007 linux (Mon Oct 08 2007 - 12:07:58 CDT)
  • Re: AMBER: Amber Installation Error (Mon Jun 18 2007 - 14:08:48 CDT)
  • Re: AMBER: Amber Installation Error (Mon Jun 18 2007 - 10:52:16 CDT)
  • RE: AMBER: Amber Installation Error (Mon Jun 18 2007 - 09:34:12 CDT)
  • AMBER: Amber Installation Error (Fri Jun 15 2007 - 10:58:00 CDT)
• Johan Qvist
  • AMBER: Harmonic constraints (Fri Sep 07 2007 - 09:43:57 CDT)
• john chen
  • AMBER: calcium ion force-fields (Fri Sep 14 2007 - 10:35:29 CDT)
  • AMBER: heme force-field (2) (Tue Sep 11 2007 - 10:08:05 CDT)
  • AMBER: heme forcefield atom types (Tue Sep 11 2007 - 09:09:45 CDT)
  • AMBER: implementation of GB model in AMBER (Sun Jun 17 2007 - 07:49:24 CDT)
  • AMBER: problems using TIP4PBOX (Wed Jun 13 2007 - 05:53:30 CDT)
• John E. Kerrigan
  • Re: AMBER: PDBs (Tue Apr 17 2007 - 07:40:54 CDT)
• Johnson Agbo
  • AMBER: Saving (.)prepin file (Mon Jul 09 2007 - 13:22:40 CDT)
  • AMBER: Saving (.)prepin file (Mon Jul 02 2007 - 15:35:00 CDT)
• Jojart Balazs
  • Re: AMBER: [chirality.c] Atom did not match (Fri Nov 16 2007 - 11:48:51 CST)
  • AMBER: MM-PBSA POPC/TIP3P/GPCR/LIGAND (Sat Jun 30 2007 - 13:25:49 CDT)
• Jonathan Suever
  • AMBER: Use of Counter Ions in binding energy calculations (Thu Dec 20 2007 - 12:42:15 CST)
  • AMBER: Slow Processor Loads when Using PMEMD (Mon Jul 02 2007 - 19:28:48 CDT)
• Jones de Andrade
  • Re: AMBER: Resp: "Statistics of the Fitting" (Wed Oct 10 2007 - 11:05:09 CDT)
  • AMBER: adding extra points to amber - how to? (Mon Oct 08 2007 - 11:44:42 CDT)
  • AMBER: Resp: "Statistics of the Fitting" (Sun Oct 07 2007 - 13:40:04 CDT)
  • Re: AMBER: cyclohexane and decalin on amber (Tue Oct 02 2007 - 22:12:48 CDT)
  • Re: AMBER: cyclohexane and decalin on amber (Mon Oct 01 2007 - 00:46:44 CDT)
  • AMBER: cyclohexane and decalin on amber (Sat Sep 29 2007 - 10:26:02 CDT)
  • AMBER: Performance of polarizable model simulations (Wed Aug 22 2007 - 23:17:52 CDT)
• Jordi Camps
  • Re: AMBER: Problems simulating a big system (Tue Jul 17 2007 - 04:57:13 CDT)
  • AMBER: Problems simulating a big system (Mon Jul 16 2007 - 06:55:55 CDT)
• Jose Gallego
  • AMBER: short 2'OH-OP contacts in RNA (Fri Aug 10 2007 - 11:22:35 CDT)
• Joseph Maxwell
  • AMBER: Pre-ABMER Installation Prob w/ MPICH2 (Thu Nov 22 2007 - 13:55:18 CST)
  • AMBER: Simulated Annealing (Mon Jun 25 2007 - 18:28:14 CDT)
• Julien Michel
  • Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI (Sun Jul 01 2007 - 17:42:53 CDT)
  • Re: AMBER: equilibrium constants via MMPBSA (Fri Jun 01 2007 - 11:48:55 CDT)
  • Re: AMBER: cutoff & speed-up of GBSA (Thu May 31 2007 - 16:24:11 CDT)
• Jun Liu
  • AMBER: A question related with periodic boundary condition (Wed Sep 19 2007 - 13:42:25 CDT)
  • Re: AMBER: A question related with periodic boundary condition (Wed Sep 19 2007 - 13:10:54 CDT)
  • AMBER: A question related with periodic boundary condition (Tue Sep 18 2007 - 20:48:22 CDT)
• Junmei Wang
  • Re: AMBER: antechamber: read in charges (Wed Nov 28 2007 - 14:58:36 CST)
  • Re: AMBER: antechamber: read in charges (Tue Nov 27 2007 - 11:50:11 CST)
  • AMBER: Re: antechamber problem (Tue Nov 27 2007 - 11:38:17 CST)
  • Re: AMBER:antechamber fails with large molecules (Fri Nov 02 2007 - 00:29:11 CST)
  • Re: AMBER: antechamber fails with large molecules (Fri Nov 02 2007 - 00:16:41 CST)
  • Re: AMBER: antechamber fails with large molecules (Wed Oct 31 2007 - 22:43:49 CST)
  • Re: AMBER: Prepin error (?) in xleap (Thu Sep 06 2007 - 23:44:50 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Fri Aug 31 2007 - 15:22:07 CDT)
  • Re: AMBER: antechamber question (Fri Aug 31 2007 - 15:07:09 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Mon Aug 27 2007 - 17:17:53 CDT)
  • Re: AMBER: Parallelizin antechamber? (Wed Aug 15 2007 - 08:41:45 CDT)
  • Re: AMBER: antechamber, how does it work (Wed Aug 15 2007 - 08:33:36 CDT)
  • RE: AMBER: antechamber question (Tue May 22 2007 - 10:08:18 CDT)
  • RE: AMBER: missing impropers for nitros? (Mon May 21 2007 - 12:48:58 CDT)
  • RE: AMBER: Antechamber (Thu Apr 19 2007 - 08:58:14 CDT)
  • RE: AMBER: AM1-bcc (Tue Feb 27 2007 - 20:57:23 CST)
  • RE: AMBER: Antechamber Charge Calculation Method (Mon Jan 29 2007 - 20:48:17 CST)
  • RE: AMBER: gaussian output to prepin problem (Mon Jan 29 2007 - 20:43:56 CST)
• Kailee
  • AMBER: compile amber8 with mpich2 (Tue Aug 07 2007 - 08:18:14 CDT)
  • Re: AMBER: question about iwrap (Thu Jul 12 2007 - 08:55:06 CDT)
  • Re: AMBER: question about iwrap (Thu Jul 12 2007 - 08:17:32 CDT)
  • Re: AMBER: question about iwrap (Thu Jul 12 2007 - 05:55:28 CDT)
  • AMBER: question about iwrap (Wed Jul 11 2007 - 08:17:29 CDT)
  • Re: AMBER: How to reimage the trajectories of LES calculations? (Wed Mar 21 2007 - 11:32:34 CST)
  • AMBER: How to reimage the trajectories of LES calculations? (Wed Mar 21 2007 - 07:35:06 CST)
  • AMBER: questions about analysing LES results (Tue Jan 30 2007 - 11:00:40 CST)
  • Re: AMBER: error when compiling Moilview (Thu Jan 25 2007 - 10:12:09 CST)
  • Re: AMBER: error when compiling Moilview (Thu Jan 25 2007 - 07:03:07 CST)
  • AMBER: error when compiling Moilview (Thu Jan 25 2007 - 05:31:24 CST)
  • AMBER: error when using sander.LES: exceeded MAXLES (Thu Jan 18 2007 - 10:33:18 CST)
• kanon gemini
  • AMBER: (Fri Sep 21 2007 - 10:35:11 CDT)
• Kara Di Giorgio
  • AMBER: Question about Boron (Wed Mar 14 2007 - 11:15:22 CST)
  • Re: AMBER: Example needed for addAtomType command (Thu Feb 01 2007 - 17:02:39 CST)
  • AMBER: Example needed for addAtomType command (Thu Feb 01 2007 - 15:26:12 CST)
• Karen Callahan
  • AMBER: Energy calculations. (Thu Oct 18 2007 - 14:15:29 CDT)
  • AMBER: hybridization in Amber, pertaining to resonant structures, ions (Mon Aug 06 2007 - 23:13:27 CDT)
  • AMBER: polarizable water models. (Sat May 05 2007 - 01:38:34 CDT)
• Karl Kirschner
  • Re: AMBER: calculating charges to modified 4GA unit (Wed Nov 07 2007 - 07:37:42 CST)
  • Re: AMBER: Re: how to create an O linked N-acetylglucosamine in a protein (Tue Jul 17 2007 - 08:39:43 CDT)
• Karol Kaszuba
  • AMBER: running_RED-III (Wed Jul 18 2007 - 14:02:10 CDT)
  • Re: AMBER: RESP_compilation_IT_WORKS (Tue Jul 17 2007 - 03:32:59 CDT)
  • AMBER: RESP_compilation (Mon Jul 16 2007 - 14:14:32 CDT)
• Kateryna Miroshnychenko
  • Re: AMBER: hbond ptraj pls help. (Wed May 23 2007 - 06:22:18 CDT)
  • Re: AMBER: hbond ptraj pls help. (Wed May 23 2007 - 04:01:03 CDT)
  • AMBER: RE: dihedral term charge dependence (Tue Apr 03 2007 - 08:59:08 CDT)
  • Re:AMBER: Problem while running Antechamber (Wed Mar 21 2007 - 05:06:15 CST)
• Katrina Lexa
  • AMBER: Squished dimer during transition from NVT to NPT (Thu Aug 30 2007 - 16:02:20 CDT)
• kepa koldo burusco
  • AMBER: Dipolar and Inertia Moments (Thu Mar 15 2007 - 05:46:17 CST)
  • AMBER: about coordinates ****** and diffusion (Sun Jan 28 2007 - 11:15:57 CST)
  • AMBER: coordinates ****** (Tue Jan 23 2007 - 10:19:54 CST)
• Kevin Cahill
  • AMBER: problem compiling Amber 7 (Sun Jan 14 2007 - 20:35:00 CST)
• Kevin Davies
  • AMBER: Amber 9 - bugfix.40 fails (Wed Dec 05 2007 - 11:27:27 CST)
• Kevin Kelliher
  • AMBER: Is there a pmemd machine file for OSX Intel (Fri Jan 26 2007 - 15:50:29 CST)
  • Re: AMBER: G5 OSX serial compile error (Fri Jan 05 2007 - 12:58:56 CST)
• Khatcharin Siriwong
  • Re: AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out" (Sat Apr 21 2007 - 22:57:18 CDT)
  • AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out" (Sat Apr 21 2007 - 02:42:14 CDT)
  • Re: AMBER: amber9: running parallel error (Wed Apr 18 2007 - 02:03:13 CDT)
  • RE: AMBER: amber9: running parallel error (Wed Apr 18 2007 - 02:00:29 CDT)
  • RE: AMBER: amber9: running parallel error (Wed Apr 11 2007 - 22:40:27 CDT)
  • AMBER: amber9: running parallel error (Wed Apr 11 2007 - 03:08:16 CDT)
• khn _
  • AMBER: radial distribution function in ptraj (Fri Jun 22 2007 - 20:25:05 CDT)
  • Re: AMBER: pair distribution function (Sun Jun 17 2007 - 03:25:56 CDT)
  • AMBER: pair distribution function (Thu Jun 14 2007 - 18:20:47 CDT)
  • AMBER: g(r) (Wed Jun 13 2007 - 11:43:25 CDT)
  • AMBER: nonpolar solvation energy (Wed Jan 31 2007 - 10:33:55 CST)
  • AMBER: ptraj (Wed Jan 31 2007 - 10:26:00 CST)
  • AMBER: convert pdb files to restart files (Tue Jan 16 2007 - 04:50:47 CST)
  • AMBER: output (Sat Jan 13 2007 - 22:24:11 CST)
• Kijeong Kwac
  • AMBER: performance with implicit solvent (Fri Jun 15 2007 - 15:02:49 CDT)
  • AMBER: RE: RE: AMBER: QMMM with printcharges (Thu Apr 19 2007 - 10:42:38 CDT)
  • AMBER: QMMM with printcharges (Fri Apr 13 2007 - 19:37:45 CDT)
  • AMBER: Simulation of a charged system (Fri Jan 05 2007 - 17:08:42 CST)
• kkirschn_at_hamilton.edu
  • AMBER: Amber9's sander.MPI on x86_64 (Mon Jun 04 2007 - 12:13:51 CDT)
  • Re: AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8 (Wed May 30 2007 - 15:28:55 CDT)
  • Re: AMBER: using glycam04 parameters (Wed Apr 25 2007 - 15:02:49 CDT)
  • Re: AMBER: using glycam04 parameters (Thu Apr 19 2007 - 12:53:37 CDT)
  • Re: AMBER: Trimannoside Problem (Thu Mar 08 2007 - 07:37:27 CST)
  • Re: AMBER: Trimannoside Problem (Tue Mar 06 2007 - 12:13:43 CST)
  • Re: AMBER: Glycam (Tue Feb 06 2007 - 08:44:52 CST)
• Kliman, Michal
  • AMBER: Connecting two ethanes in LEaP (Thu Aug 30 2007 - 15:53:46 CDT)
  • AMBER: single phospholipid molecule in vacuo (Thu May 10 2007 - 15:02:55 CDT)
• Knut Langsetmo
  • AMBER: Amber 9 compile on OS X (Wed May 09 2007 - 16:29:44 CDT)
  • Re: AMBER: solaris 10 and compilers on X86_64 hardware (Wed Jan 17 2007 - 10:03:33 CST)
• Kresimir Sikic
  • AMBER: Normal Mode Analysis (Mon Aug 13 2007 - 10:12:59 CDT)
• Kristina Furse
  • Re: AMBER: Attaching capping groups (Wed Apr 11 2007 - 21:30:30 CDT)
  • RE: AMBER: Disulfide Problem (Thu Mar 01 2007 - 10:19:17 CST)
  • Re: AMBER: IFVARI parameter (Tue Feb 27 2007 - 15:50:45 CST)
• Kyle Brown
  • Re: AMBER: ANGVE/TORAVE (Thu Oct 25 2007 - 13:33:52 CDT)
• Kyle L. Brown
  • AMBER: DISAVE value1 (Wed Mar 28 2007 - 15:42:16 CST)
  • AMBER: DNA Flat Angle Restraints (Mon Mar 26 2007 - 11:04:09 CST)
• L. W. Yang
  • Re: AMBER: heme forcefield atom types (Wed Oct 24 2007 - 11:18:31 CDT)
• Lachele Foley (Lists)
  • AMBER: Amber 9 TI Details (Tue Mar 27 2007 - 15:03:20 CST)
• Lalit Dubey
  • Re: AMBER: POPS Lipid Bilayer: Full Parameter/Topology File (Fri Dec 07 2007 - 00:45:59 CST)
  • AMBER: POPS Lipid Bilayer: Full Parameter/Topology File (Tue Dec 04 2007 - 18:39:29 CST)
• Lars Skjærven
  • Re: AMBER: PME and counter ions (Thu Dec 20 2007 - 09:12:53 CST)
  • Re: AMBER: PME and counter ions (Wed Dec 19 2007 - 19:52:11 CST)
  • Re: AMBER: PME and counter ions (Tue Dec 18 2007 - 20:34:26 CST)
  • AMBER: PME and counter ions (Tue Dec 18 2007 - 10:04:12 CST)
  • AMBER: ptraj hbond mask (Mon Nov 05 2007 - 10:00:03 CST)
  • Re: AMBER: PMEMD configuration and scaling (Tue Oct 09 2007 - 08:56:09 CDT)
• Lars.Skjarven_at_biomed.uib.no
  • AMBER: PMEMD configuration and scaling (Tue Oct 09 2007 - 05:05:37 CDT)
  • AMBER: PMEMD configuration and scaling (Sun Oct 07 2007 - 05:40:00 CDT)
  • AMBER: PMEMD configuration and scaling (Sat Oct 06 2007 - 06:35:03 CDT)
• Laura McDriscoll
  • AMBER: Segmentation Fault when saving prmtop and inpcrd files in xleap (Thu Mar 15 2007 - 23:59:33 CST)
• Laurent Chiche
  • Re: AMBER: Charge not integral. Head-to-tail cyclic peptides (Mon Jun 18 2007 - 09:37:53 CDT)
• Lei Jia
  • AMBER: Temperature fluctuation in NPT and NVE ensemble (Wed Oct 17 2007 - 18:46:29 CDT)
  • AMBER: Calcium parameters (Fri Mar 02 2007 - 13:58:27 CST)
• Li Su
  • Re: AMBER: Does amber use water density around 1 at room temperature (Wed Jan 24 2007 - 16:44:40 CST)
  • AMBER: Does amber use water density around 1 at room temperature (Tue Jan 23 2007 - 16:07:20 CST)
  • AMBER: How are water molecules at cutoff being treated? (Tue Jan 16 2007 - 16:48:47 CST)
  • AMBER: How to get a periodic box of modified water molecules (Wed Jan 03 2007 - 11:25:11 CST)
• Liang, Lei
  • Re: AMBER: Problem about prepare the model when running antechamber (Mon Jun 04 2007 - 16:03:45 CDT)
  • Re: AMBER: Problem about prepare the model when running antechamber (Mon Jun 04 2007 - 16:02:04 CDT)
  • AMBER: Problem about prepare the model when running antechamber (Mon Jun 04 2007 - 15:04:36 CDT)
  • Re: AMBER: Problems during compilation and test. (Mon Apr 09 2007 - 12:21:39 CDT)
  • AMBER: Problems during compilation and test. (Thu Apr 05 2007 - 15:43:23 CDT)
  • AMBER: Some problems during the testing of Amber. (Fri Mar 30 2007 - 12:12:50 CST)
• Lili Peng
  • AMBER: Making movies in VMD (Wed Dec 05 2007 - 18:57:08 CST)
  • Re: [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] (Thu Nov 15 2007 - 16:38:57 CST)
  • AMBER: Applying bugfixes in Amber (Thu Oct 04 2007 - 16:28:29 CDT)
  • Re: AMBER: Torsion terms in xleap (Wed Sep 19 2007 - 13:41:14 CDT)
  • Re: AMBER: Torsion terms in xleap (Mon Sep 17 2007 - 18:42:12 CDT)
  • AMBER: Torsion terms in xleap (Fri Sep 14 2007 - 17:35:23 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Sat Sep 08 2007 - 16:54:15 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Fri Sep 07 2007 - 18:33:24 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Fri Sep 07 2007 - 16:54:23 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Fri Sep 07 2007 - 16:22:42 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Thu Sep 06 2007 - 17:32:48 CDT)
  • Re: AMBER: Using ntr=1 in xleap (Tue Sep 04 2007 - 17:23:59 CDT)
  • AMBER: Using ntr=1 in xleap (Fri Aug 31 2007 - 16:27:44 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Thu Aug 30 2007 - 15:48:34 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Mon Aug 27 2007 - 16:38:30 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Fri Aug 24 2007 - 14:26:17 CDT)
  • Re: AMBER: Prepin error (?) in xleap (Fri Aug 24 2007 - 14:19:07 CDT)
  • Re: AMBER: articles (Fri Aug 24 2007 - 14:10:12 CDT)
  • AMBER: Prepin error (?) in xleap (Thu Aug 23 2007 - 16:04:03 CDT)
  • AMBER: Running Gaussian to get .out files (Wed Aug 22 2007 - 15:27:25 CDT)
  • Re: AMBER: xLeap "Could not find type" error (Tue Aug 21 2007 - 20:17:44 CDT)
  • AMBER: xLeap "Could not find type" error (Tue Aug 21 2007 - 14:28:46 CDT)
  • Re: AMBER: What is the best computer for running AMBER simulations? (Thu Aug 16 2007 - 23:50:42 CDT)
  • AMBER: What is the best computer for running AMBER simulations? (Thu Aug 16 2007 - 16:37:03 CDT)
  • Re: AMBER: Cygwin error (Thu Aug 09 2007 - 14:16:20 CDT)
  • Re: AMBER: Cygwin error (Thu Aug 09 2007 - 14:06:03 CDT)
  • Re: AMBER: Cygwin error (Thu Aug 09 2007 - 13:13:27 CDT)
  • Re: AMBER: Cygwin error (Wed Aug 08 2007 - 18:04:31 CDT)
  • Re: AMBER: Cygwin error (Wed Aug 08 2007 - 17:13:54 CDT)
  • Re: AMBER: Cygwin error (Wed Aug 08 2007 - 16:56:00 CDT)
  • AMBER: Cygwin error (Wed Aug 08 2007 - 16:33:22 CDT)
  • Re: AMBER: Problem generating .prepin file in Antechamber (Thu Aug 02 2007 - 14:15:41 CDT)
  • AMBER: Problem generating .prepin file in Antechamber (Thu Aug 02 2007 - 14:07:11 CDT)
  • AMBER: adding organic molecule to polypeptide residue (Thu Jul 26 2007 - 17:36:29 CDT)
  • Re: AMBER: MD simulation error (Wed Jul 25 2007 - 13:21:24 CDT)
  • Re: AMBER: MD simulation error (Wed Jul 25 2007 - 12:38:10 CDT)
  • AMBER: MD simulation error (Tue Jul 24 2007 - 18:53:59 CDT)
  • Re: AMBER: potential energy calculation (Wed Jul 18 2007 - 15:47:57 CDT)
  • AMBER: General AMBER questions (Tue Jul 17 2007 - 17:51:32 CDT)
  • Re: AMBER: potential energy calculation (Tue Jul 17 2007 - 17:46:55 CDT)
  • Re: AMBER: refc error (Tue Jul 17 2007 - 17:40:26 CDT)
  • Re: AMBER: refc error (Tue Jul 17 2007 - 13:35:06 CDT)
  • Re: AMBER: refc error (Mon Jul 16 2007 - 19:08:18 CDT)
  • AMBER: potential energy calculation (Mon Jul 16 2007 - 19:03:55 CDT)
  • AMBER: refc error (Mon Jul 16 2007 - 18:56:11 CDT)
  • AMBER: Basic AMBER question (Wed Jul 11 2007 - 14:15:48 CDT)
  • Re: AMBER: Problem with running Sander (Tue Jul 10 2007 - 18:01:11 CDT)
  • Re: AMBER: Problem with running Sander (Tue Jul 10 2007 - 17:58:22 CDT)
  • Re: AMBER: Problem with running Sander (Tue Jul 10 2007 - 16:50:45 CDT)
  • AMBER: Problem with running Sander (Sat Jul 07 2007 - 18:10:06 CDT)
  • Re: AMBER: Generating structure of polyethylene glycol in AMBER (Thu Mar 22 2007 - 16:17:22 CST)
  • AMBER: Generating structure of polyethylene glycol in AMBER (Thu Mar 22 2007 - 15:35:07 CST)
• Lillian chong
  • AMBER: effective step period for constant pH simulations (Mon Sep 24 2007 - 13:22:50 CDT)
  • Re: AMBER: setting dimensions of truncated octahedron (Sun Aug 05 2007 - 08:25:01 CDT)
  • AMBER: setting dimensions of truncated octahedron (Sat Aug 04 2007 - 15:34:59 CDT)
  • AMBER: poor performance of sander on a quad-core linux machine (Tue Mar 13 2007 - 11:27:31 CST)
• lily ferreira
  • Re : AMBER: intra-molecular h-bonds in ptraj (Fri Jan 05 2007 - 07:37:52 CST)
  • AMBER: intra-molecular h-bonds in ptraj (Thu Jan 04 2007 - 09:17:37 CST)
• Linda Prengaman
  • AMBER: Problem with anisotropic pressure scaling (Fri Mar 16 2007 - 08:23:30 CST)
• linfu
  • Re: AMBER: LINMIN Failure vs Parallelization (Thu Sep 13 2007 - 05:24:10 CDT)
  • Re: Re: AMBER: about shake (Wed Aug 08 2007 - 20:10:05 CDT)
  • Re: AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA (Wed Aug 08 2007 - 08:33:58 CDT)
  • AMBER: about shake (Tue Aug 07 2007 - 20:36:59 CDT)
• Lishan Yao
  • AMBER: Ne van del waals potential (Fri Jul 13 2007 - 11:09:37 CDT)
  • AMBER: dihedral simulation (Sun Jun 03 2007 - 10:49:33 CDT)
  • Re: AMBER: electric field calculation (Thu May 31 2007 - 08:33:20 CDT)
  • AMBER: electric field calculation (Wed May 30 2007 - 07:25:16 CDT)
  • AMBER: improper dihedral (Fri Jan 26 2007 - 08:42:15 CST)
• liu junjun
  • Re: AMBER: implicit solvent simulations (Tue Dec 11 2007 - 21:49:57 CST)
• Lorenzo Gontrani
  • Re: AMBER: energy minimization parameter (Wed Aug 29 2007 - 02:54:58 CDT)
  • AMBER: H-bond ptraj dilemma (Fri Feb 16 2007 - 09:46:54 CST)
• luckyang_at_gmail.com
  • Re: AMBER: Generating structure of polyethylene glycol in AMBER (Thu Mar 22 2007 - 16:38:02 CST)
• Luis Gracia
  • Re: AMBER: Problems with QMMM tests on Altix (Thu Feb 22 2007 - 16:35:14 CST)
• Lycourgos Chiniadis
  • AMBER: Information about Amber 9 (Fri Aug 03 2007 - 00:11:17 CDT)
• M kutty
  • RE: AMBER: Steered MD (Sun Dec 23 2007 - 23:04:41 CST)
  • AMBER: Steered MD (Fri Dec 21 2007 - 00:03:29 CST)
• M. L. Dodson
  • Re: AMBER: Steered MD (Fri Dec 21 2007 - 10:00:58 CST)
  • Re: AMBER: Steered MD (Fri Dec 21 2007 - 09:52:30 CST)
  • Re: AMBER: [SOLVED] Problem with LEaP generating topology and coord files after double bond creation (Wed Nov 28 2007 - 12:33:38 CST)
  • Re: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated (Wed Nov 28 2007 - 11:31:04 CST)
  • Re: AMBER: [SOLVED] Problem with LEaP generating topology and coord files after double bond creation (Tue Nov 27 2007 - 15:45:44 CST)
  • AMBER: Problem with LEaP generating topology and coord files after double bond creation (Wed Nov 21 2007 - 14:45:17 CST)
  • Re: [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] (Thu Nov 15 2007 - 11:28:28 CST)
  • [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] (Wed Nov 14 2007 - 12:51:35 CST)
  • AMBER: xleap patch for xorg-7.3 ?? (Thu Nov 08 2007 - 13:04:05 CST)
  • Re: AMBER: Criteria for classical md being OK to move to QM-MM (Wed Aug 29 2007 - 13:24:43 CDT)
  • Re: AMBER: Criteria for classical md being OK to move to QM-MM (Wed Aug 29 2007 - 12:11:29 CDT)
  • Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB (Sun Aug 26 2007 - 10:42:14 CDT)
  • Re: AMBER: solvateCap minin and mdin for qm-mm dftb (Fri Aug 24 2007 - 15:59:04 CDT)
  • Re: AMBER: solvateCap minin and mdin for qm-mm dftb (Fri Aug 24 2007 - 11:17:37 CDT)
  • Re: AMBER: solvateCap minin and mdin for qm-mm dftb (Fri Aug 24 2007 - 08:11:06 CDT)
  • Re: AMBER: Parallelizin antechamber? (Tue Aug 14 2007 - 09:29:16 CDT)
  • Re: AMBER: Any experience on Dell two quad core system? (Mon Aug 13 2007 - 12:37:47 CDT)
  • Re: AMBER: Any experience on Dell two quad core system? (Mon Aug 13 2007 - 10:59:11 CDT)
  • Re: AMBER: Fwd: QM region + cutoff larger that box (Mon Aug 06 2007 - 10:29:43 CDT)
  • Re: AMBER: Fwd: QM region + cutoff larger that box (Mon Aug 06 2007 - 07:58:56 CDT)
  • Re: AMBER: Fwd: QM region + cutoff larger that box (Sat Aug 04 2007 - 09:51:22 CDT)
  • Re: AMBER: Fwd: QM region + cutoff larger that box (Sat Aug 04 2007 - 09:32:17 CDT)
  • Re: AMBER: QMMM to follow reaction involving water (Tue Jul 31 2007 - 10:14:57 CDT)
  • AMBER: QMMM to follow reaction involving water (Mon Jul 30 2007 - 13:23:14 CDT)
  • Re: AMBER: Could not find cntrl namelist (Tue Jul 10 2007 - 17:25:17 CDT)
  • Re: AMBER: antechamber (Mon Jul 09 2007 - 19:08:27 CDT)
  • Re: AMBER: Could not find cntrl namelist (Mon Jul 09 2007 - 16:09:06 CDT)
  • Re: AMBER: Could not find cntrl namelist (Mon Jul 09 2007 - 12:10:58 CDT)
  • Re: AMBER: adding water molecules in lipid bilayer model (Mon Jul 09 2007 - 07:59:01 CDT)
  • Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH (Sun Jul 01 2007 - 10:57:05 CDT)
  • Re: Fwd: Re: AMBER: make test serial (Sat Jun 30 2007 - 11:30:05 CDT)
  • Re: AMBER: make serial failure for xleap (Fri Jun 29 2007 - 17:33:37 CDT)
  • Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH (Fri Jun 29 2007 - 08:34:08 CDT)
  • Re: AMBER: bugfix.all (Wed Jun 27 2007 - 15:52:07 CDT)
  • Re: AMBER: set up system solution with 3 different components, each with multiple copies (Tue Jun 26 2007 - 10:27:41 CDT)
  • Re: AMBER: box size bomb in QMMM calculation (Wed Jun 13 2007 - 04:43:52 CDT)
  • Re: AMBER: box size bomb in QMMM calculation (Tue Jun 12 2007 - 18:23:50 CDT)
  • AMBER: box size bomb in QMMM calculation (Tue Jun 12 2007 - 14:46:00 CDT)
  • Re: AMBER: (no subject) (Wed May 30 2007 - 12:54:04 CDT)
  • Re: AMBER: Small scale compute environments (Mon May 14 2007 - 13:32:36 CDT)
  • AMBER: Small scale compute environments (Sat May 12 2007 - 14:13:59 CDT)
  • Re: AMBER: Complexes (Tue May 08 2007 - 14:26:11 CDT)
  • Re: AMBER: Complexes (Tue May 08 2007 - 14:14:59 CDT)
  • Re: AMBER: Problem with SCC-DFTB parameter files (Wed May 02 2007 - 09:59:02 CDT)
  • Re: AMBER: psi , phi angles (Mon Mar 05 2007 - 11:42:13 CST)
  • Re: AMBER: Solvate box (Tue Feb 13 2007 - 21:33:49 CST)
  • AMBER: solaris 10 and compilers on X86_64 hardware (Wed Jan 17 2007 - 09:45:27 CST)
• M. Maeda
  • Re: AMBER: Machine environment to install AMBER 8 (Wed Aug 15 2007 - 00:17:03 CDT)
  • Re: AMBER: Machine environment to install AMBER 8 (Tue Aug 14 2007 - 04:45:53 CDT)
  • Re: AMBER: Machine environment to install AMBER 8 (Tue Aug 14 2007 - 04:19:37 CDT)
  • Re: AMBER: Machine environment to install AMBER 8 (Tue Aug 14 2007 - 03:54:03 CDT)
  • AMBER: Machine environment to install AMBER 8 (Tue Aug 14 2007 - 01:03:07 CDT)
  • Re: AMBER: program bug? (Wed Aug 08 2007 - 21:37:13 CDT)
  • Re: AMBER: program bug? (Thu Jul 12 2007 - 06:29:03 CDT)
  • Re: AMBER: program bug? (Wed Jul 11 2007 - 23:41:34 CDT)
  • Re: AMBER: program bug? (Wed Jul 11 2007 - 23:47:19 CDT)
  • AMBER: program bug? (Sun Jul 08 2007 - 21:24:58 CDT)
• Maciej Dlugosz
  • AMBER: constant-pH MD with replica exchange (Thu Oct 11 2007 - 01:38:49 CDT)
• Madjid Taghdir
  • Re: AMBER: calcium and zinc parameter (Tue Dec 11 2007 - 01:21:37 CST)
  • AMBER: calcium and zinc parameter (Wed Dec 05 2007 - 05:07:17 CST)
  • AMBER: (no subject) (Wed Dec 05 2007 - 03:18:11 CST)
  • Re: AMBER: amber9 installation problem (Mon Nov 12 2007 - 02:38:57 CST)
  • AMBER: amber9 installation problem (Tue Oct 16 2007 - 03:46:05 CDT)
• Mag. rer. nat. Hannes Wallnöfer
  • AMBER: angle between vectors (Fri Nov 30 2007 - 06:45:02 CST)
• Mag. rer. nat. Hannes Wallnöfer
  • Re: AMBER: angle between vectors (Mon Dec 03 2007 - 01:55:51 CST)
• Magne Olufsen
  • AMBER: how is the standard deviations calculated in mm-pbsa? (Tue Mar 06 2007 - 06:58:17 CST)
• mahdi fathi
  • AMBER: (no subject) (Thu Jan 18 2007 - 04:10:24 CST)
• Marc Baaden
  • AMBER: Interactive Molecular Dynamics with Amber? (Sat Oct 20 2007 - 17:10:23 CDT)
  • AMBER: Citation for Langevin thermostat? (Sat Aug 11 2007 - 02:13:28 CDT)
  • Re: AMBER: NMR vs. X-ray structures (Tue Jun 12 2007 - 00:51:21 CDT)
• Marcelo Puiatti
  • Re: AMBER: heme force field (Mon Jul 30 2007 - 08:08:52 CDT)
• Margaret Doll
  • Re: AMBER: Troubles installing amber (Fri Dec 07 2007 - 16:22:22 CST)
  • Re: AMBER: Troubles installing amber (Fri Dec 07 2007 - 15:36:36 CST)
  • AMBER: Troubles installing amber (Fri Dec 07 2007 - 13:47:26 CST)
• Marie Brut
  • AMBER: antechamber (Mon Jul 09 2007 - 06:56:19 CDT)
  • AMBER: rms in nmode (Fri Jun 01 2007 - 02:22:22 CDT)
  • Re: AMBER: nmode (Tue Apr 03 2007 - 10:42:17 CDT)
  • AMBER: nmode (Tue Apr 03 2007 - 05:17:39 CDT)
  • AMBER: units in hessian matrix (Thu Feb 15 2007 - 10:52:01 CST)
• Marius Retegan
  • Re: AMBER: Xleap and Hydrogens (Tue Nov 27 2007 - 09:43:36 CST)
  • AMBER: entropy with ptraj (Mon Oct 08 2007 - 07:24:36 CDT)
• Mark Williamson
  • Re: AMBER: installation (Sat Dec 29 2007 - 11:23:15 CST)
  • Re: AMBER: Compiling single programs (Fri Nov 02 2007 - 11:58:32 CST)
  • Re: AMBER: Amber9 installation error on Mandriva 2007 linux (Mon Oct 08 2007 - 12:31:39 CDT)
  • Re: AMBER: MPI (Fri Aug 17 2007 - 07:58:00 CDT)
  • Re: AMBER: Cygwin error (Wed Aug 08 2007 - 17:02:15 CDT)
  • Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 17:20:37 CDT)
  • Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 14:19:29 CDT)
  • Re: AMBER: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 10:28:06 CDT)
  • Re: AMBER: Amber9 parallel compilation openmpi issues (Wed Jul 25 2007 - 08:33:35 CDT)
  • Re: AMBER: problem in compiling amber9 and running amber9 (Sat Jul 21 2007 - 09:21:18 CDT)
  • Re: SV: AMBER: Atoms in contact to a specific atoms during MD (Mon Jul 16 2007 - 10:18:00 CDT)
  • Re: AMBER: Atoms in contact to a specific atoms during MD (Mon Jul 16 2007 - 09:52:39 CDT)
  • Re: AMBER: Improving pmemd parallel scaling (Thu Jun 28 2007 - 11:19:06 CDT)
  • Re: AMBER: Amber Installation Error (Mon Jun 18 2007 - 13:19:27 CDT)
  • Re: AMBER: Amber Installation Error (Mon Jun 18 2007 - 10:35:18 CDT)
  • Re: AMBER: amber9 compile problem (Mon Jun 11 2007 - 08:28:30 CDT)
  • Re: AMBER: amber9 compile problem (Sun Jun 10 2007 - 11:03:28 CDT)
  • Re: AMBER: AMBER8 compiler with intel 9.1 compiler (Fri May 18 2007 - 07:19:37 CDT)
  • AMBER: B or E Dihedral Labels in RDPARM output (Fri May 04 2007 - 09:04:17 CDT)
  • Re: AMBER: AMBER9 installation error on dual core AMD Opteron(tm) processor 275 (Fri Apr 13 2007 - 07:51:54 CDT)
  • Re: AMBER: basis set for RESP calculation (Wed Mar 21 2007 - 11:36:40 CST)
  • Re: AMBER: Help!! I cannot perform the ambpdb (Wed Feb 07 2007 - 14:25:19 CST)
  • Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) (Wed Feb 07 2007 - 11:45:29 CST)
  • Re: AMBER: Strange behavior on g95 compile. (Wed Feb 07 2007 - 10:18:16 CST)
  • Re: AMBER: Help!! I cannot perform the ambpdb (Wed Feb 07 2007 - 10:08:41 CST)
  • Re: AMBER: question about the testing of AMBER9 (Mon Jan 08 2007 - 15:10:53 CST)
  • Re: AMBER: question about the testing of AMBER9 (Mon Jan 08 2007 - 03:36:55 CST)
  • Re: AMBER: question about the testing of AMBER9 (Sun Jan 07 2007 - 17:36:28 CST)
• Markus Weingarth
  • AMBER: Calculate force constants (Sun Feb 04 2007 - 16:13:28 CST)
• Martin Klefas-Stennett
  • Re: AMBER: invalid digit '*' in the input file (Mon Nov 12 2007 - 08:31:08 CST)
  • Re: AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler (Wed Sep 19 2007 - 13:16:49 CDT)
  • Re: AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler (Wed Sep 19 2007 - 11:30:50 CDT)
• Martin Stennett
  • AMBER: problem with Thermodynamic Integration (Wed Sep 19 2007 - 06:46:30 CDT)
  • AMBER: Dihedrals in Sander (Thu Aug 30 2007 - 03:36:17 CDT)
  • Re: AMBER: TEST_FAILURES (Mon Aug 20 2007 - 07:56:36 CDT)
  • Re: AMBER: Problem with Sander restart file. (Wed Apr 11 2007 - 06:45:03 CDT)
  • AMBER: Problem with Sander restart file. (Wed Apr 11 2007 - 05:56:37 CDT)
  • Re: AMBER: Sander slower on 16 processors than 8 (Thu Feb 22 2007 - 15:58:57 CST)
  • Re: AMBER: Sander slower on 16 processors than 8 (Thu Feb 22 2007 - 15:10:40 CST)
  • AMBER: Strange behavior on g95 compile. (Wed Feb 07 2007 - 10:00:23 CST)
  • AMBER: Problem with paralell installation (Fri Feb 02 2007 - 02:22:25 CST)
• MARY O'CONNOR
  • AMBER: Force fields for iron (Mon Feb 05 2007 - 10:19:52 CST)
  • AMBER: How do I make and enter new ff parameters into AMBER (Fri Feb 02 2007 - 13:35:20 CST)
• mathew k varghese
  • AMBER: water count (Mon May 28 2007 - 01:41:50 CDT)
  • AMBER: grid output: bulk water density (Fri May 25 2007 - 05:19:30 CDT)
  • Re: AMBER: RESP calculation of modified nucleotides (Fri Mar 02 2007 - 05:35:41 CST)
  • Re: AMBER: RESP calculation of modified nucleotides (Thu Mar 01 2007 - 21:22:43 CST)
  • Re: AMBER: RESP calculation of modified nucleotides (Thu Mar 01 2007 - 08:33:00 CST)
  • Re: AMBER: RESP calculation of modified nucleotides (Wed Feb 28 2007 - 02:55:58 CST)
  • AMBER: Modified nucleotides-ATOM TYPES (Mon Feb 26 2007 - 03:13:59 CST)
  • Re: AMBER: RESP calculation of modified nucleotides (Sun Feb 25 2007 - 21:17:34 CST)
  • AMBER: RESP calculation of modified nucleotides (Sat Feb 24 2007 - 00:50:23 CST)
  • AMBER: Water density calculation (Mon Feb 19 2007 - 00:51:57 CST)
  • Re: AMBER: Modified nucleotides (Wed Feb 14 2007 - 23:09:56 CST)
  • Re: AMBER: Modified nucleotides (Tue Feb 13 2007 - 21:47:08 CST)
  • AMBER: Modified nucleotides (Mon Feb 12 2007 - 22:44:31 CST)
  • RE: AMBER: MM-PBSA doubt (Mon Jan 29 2007 - 22:22:50 CST)
  • AMBER: MM-PBSA doubt (Mon Jan 29 2007 - 20:12:44 CST)
  • AMBER: Antechamber esp calculation (Mon Jan 22 2007 - 22:44:42 CST)
• Mathy Froeyen
  • Re: AMBER: Nucleic acid : nonplanarity (Wed Jul 04 2007 - 08:57:08 CDT)
• Matthew Danielson
  • AMBER: MMPBSA-nmode .top question (Fri Jun 15 2007 - 16:11:52 CDT)
• Mattia Mori - CERM
  • Re: AMBER: calcium and zinc parameter (Tue Dec 11 2007 - 07:07:31 CST)
  • Re: AMBER: calcium and zinc parameter (Thu Dec 06 2007 - 07:21:10 CST)
  • Re: AMBER: calcium and zinc parameter (Wed Dec 05 2007 - 05:15:08 CST)
  • Re: AMBER: Zinc-Histidine force field (Thu Nov 22 2007 - 13:12:43 CST)
  • Re: AMBER: Zinc-Histidine force field (Thu Nov 22 2007 - 06:06:20 CST)
  • AMBER: Zinc-Histidine force field (Wed Nov 21 2007 - 10:54:02 CST)
  • Re: AMBER: problems visualizing mdcrd in VMD (Wed Oct 31 2007 - 06:59:24 CST)
  • AMBER: problems visualizing mdcrd in VMD (Wed Oct 31 2007 - 05:17:21 CST)
  • AMBER: amber with periodic condition (Mon Oct 29 2007 - 11:16:14 CST)
  • AMBER: calcium parameters (Mon Sep 24 2007 - 10:25:20 CDT)
• Mattias Blomberg
  • AMBER: modelling substrate binding (Mon Jul 16 2007 - 08:53:15 CDT)
  • AMBER: prepin for metal centre (Mon Jun 25 2007 - 13:17:02 CDT)
• mbrut_at_laas.fr
  • AMBER: total energy in sander and nmode (Tue Sep 25 2007 - 07:55:48 CDT)
  • AMBER: Hbonds (Thu Jun 14 2007 - 02:45:25 CDT)
  • AMBER: Hbonds (Wed Jun 13 2007 - 07:54:52 CDT)
• McElheny, Dan
  • AMBER: (Wed Nov 21 2007 - 16:04:26 CST)
  • AMBER: chem shift format (Fri Nov 16 2007 - 15:46:57 CST)
  • AMBER: &shf setup (Thu Nov 15 2007 - 17:39:42 CST)
  • Re: AMBER: remd/rdc's (Mon Jun 25 2007 - 11:12:20 CDT)
  • Re: AMBER: remd/rdc's (Mon Jun 25 2007 - 11:12:20 CDT)
  • AMBER: remd/rdc's (Fri Jun 22 2007 - 13:04:59 CDT)
• mchen2_at_mailer.fsu.edu
  • AMBER: NOC 3.0 is released (Wed May 16 2007 - 15:03:30 CDT)
• Mehmet Serkan Apaydin
  • AMBER: newby question on converting xyz format to pdb format after energy minimization (Tue Nov 20 2007 - 15:02:42 CST)
• Melinda Layten
  • Re: AMBER: (Fri Aug 31 2007 - 12:19:21 CDT)
  • Re: AMBER: Basic AMBER question (Wed Jul 11 2007 - 15:05:11 CDT)
  • Re: AMBER: TIP4P MD simulations (Mon Jul 09 2007 - 13:05:39 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Wed Jun 27 2007 - 11:01:00 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Tue Jun 26 2007 - 15:02:12 CDT)
  • Re: AMBER: Charge not integral. Head-to-tail cyclic peptides (Mon Jun 18 2007 - 09:28:57 CDT)
  • Re: AMBER: Atom types (Tue Jun 12 2007 - 13:16:34 CDT)
  • Re: AMBER: Request for addition of a useful command in ptraj module of AMBER #2 (Mon Apr 23 2007 - 16:52:26 CDT)
• Mengjuei Hsieh
  • Re: AMBER: problems compiling amber on mac OSX (Sat Oct 27 2007 - 14:41:26 CDT)
  • Re: AMBER: problems compiling amber on mac OSX (Sat Oct 27 2007 - 04:31:04 CDT)
  • Re: AMBER: G5 OSX serial compile error (Mon Jan 08 2007 - 18:26:26 CST)
  • Re: AMBER: G5 OSX serial compile error (Mon Jan 01 2007 - 04:16:12 CST)
• merc mertens
  • AMBER: mm_pbsa: missing values in ras-raf tutorials (Fri Oct 19 2007 - 03:28:09 CDT)
• mernst_at_tricity.wsu.edu
  • Re: AMBER: HF/6-31G* ESP Charges do not match with ff02 charges (Fri Jan 19 2007 - 12:59:52 CST)
  • Re: AMBER: HF/6-31G* ESP Charges do not match with ff02 charges (Fri Jan 19 2007 - 01:02:10 CST)
• Michael Lerner
  • AMBER: ptraj hydrogen bonding defaults (Fri Aug 17 2007 - 17:26:09 CDT)
  • Re: AMBER: How to couple only one residue to the temperature bath? (Fri Aug 10 2007 - 16:35:38 CDT)
  • AMBER: How to couple only one residue to the temperature bath? (Fri Aug 10 2007 - 09:45:10 CDT)
• Michel Becker
  • AMBER: basis set for RESP calculation (Tue Mar 20 2007 - 14:43:10 CST)
  • AMBER: NMR violations increase in explicite water (Wed Feb 14 2007 - 14:15:14 CST)
  • AMBER: RESP charges for charged species (Tue Jan 16 2007 - 15:44:26 CST)
  • AMBER: How many steps should be used for a MD calculation? (Tue Jan 09 2007 - 03:12:55 CST)
• Miguel Ferreira
  • AMBER: distance scan (Sat Jun 16 2007 - 05:25:59 CDT)
  • AMBER: distance scan (Sat Jun 16 2007 - 05:16:15 CDT)
  • AMBER: interior dielectric constant (Tue Feb 20 2007 - 11:22:31 CST)
  • AMBER: trajectory problem (Tue Feb 06 2007 - 22:52:25 CST)
• Miguel Ortiz-Lombardía
  • Re: AMBER: paper request (Mon Nov 05 2007 - 04:14:09 CST)
  • AMBER: paper request (Mon Nov 05 2007 - 03:01:08 CST)
  • Re: AMBER: fragment parametrization tutorial? (Sun Sep 30 2007 - 05:37:56 CDT)
  • AMBER: fragment parametrization tutorial? (Sat Sep 29 2007 - 13:53:05 CDT)
• Mike Hanby
  • RE: AMBER: Blue Gene, compile Amber9? (Fri Apr 20 2007 - 14:33:39 CDT)
  • RE: AMBER: Blue Gene, compile Amber9? (Thu Apr 19 2007 - 09:34:46 CDT)
  • RE: AMBER: Blue Gene, compile Amber9? (Tue Apr 10 2007 - 10:13:11 CDT)
  • RE: AMBER: Blue Gene, compile Amber9? (Tue Apr 10 2007 - 09:04:13 CDT)
  • AMBER: Blue Gene, compile Amber9? (Fri Apr 06 2007 - 12:22:57 CDT)
  • AMBER: Compile Amber9 for MVAPICH (Tue Feb 06 2007 - 13:51:18 CST)
  • AMBER: Preprocessor Error: _qmmm_module.f "Extra Characters..." (Wed Jan 03 2007 - 16:53:43 CST)
• Mike Summers
  • Re: AMBER: coordinate changes using ptraj (Sat Mar 03 2007 - 19:39:28 CST)
  • AMBER: coordinate changes using ptraj (Sat Mar 03 2007 - 18:34:24 CST)
  • Re: AMBER: OpenMPI on MacBook Pro -- problems (Sat Mar 03 2007 - 10:07:28 CST)
  • Re: AMBER: OpenMPI on MacBook Pro -- problems (Fri Mar 02 2007 - 14:36:07 CST)
  • Re: AMBER: OpenMPI on MacBook Pro -- problems (Fri Mar 02 2007 - 14:04:17 CST)
  • AMBER: OpenMPI on MacBook Pro -- problems (Fri Mar 02 2007 - 10:48:49 CST)
  • AMBER: Pseudo-CSA in Amber? (Mon Feb 19 2007 - 08:30:13 CST)
  • Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) (Tue Feb 06 2007 - 20:30:22 CST)
  • Re: AMBER: Tutorial for chemical shift calculation? (Tue Feb 06 2007 - 12:36:05 CST)
  • AMBER: Tutorial for chemical shift calculation? (Mon Feb 05 2007 - 19:04:48 CST)
  • Re: AMBER: MPI is slower than single processor with water (Tue Jan 16 2007 - 11:32:53 CST)
  • AMBER: MPI is slower than single processor with water (Tue Jan 16 2007 - 10:30:18 CST)
  • Re: AMBER: torsion angle penalty calculationy (Wed Jan 03 2007 - 12:13:24 CST)
  • AMBER: torsion angle penalty calculation (Wed Jan 03 2007 - 09:18:34 CST)
• Mike Wykes
  • AMBER: Free Energy Calculations (Wed Dec 12 2007 - 12:08:20 CST)
  • AMBER: Solvation free energy (Mon Nov 19 2007 - 12:08:23 CST)
• Mikyung
  • Re: AMBER: extract protein energy from MD trajectory (Wed Jul 11 2007 - 01:58:31 CDT)
  • AMBER: extract protein energy from MD trajectory (Tue Jul 10 2007 - 16:47:53 CDT)
  • Re: AMBER: surface area over the trajectory (Tue Jul 10 2007 - 11:20:12 CDT)
• ming hui
  • AMBER: Continuing an amber 8 simulation with amber 9 (Sat Dec 08 2007 - 01:03:55 CST)
  • Re: AMBER: Error when doing a TI simulation: "vlimit exceeded (Thu Nov 15 2007 - 19:26:43 CST)
  • Re: AMBER: Error when doing a TI simulation: "vlimit exceeded (Thu Nov 15 2007 - 18:48:05 CST)
  • AMBER: Error when doing a TI simulation: "vlimit exceeded (Wed Nov 14 2007 - 19:10:07 CST)
  • AMBER: Can a simulation run on AMBER 9 be compared with another from AMBER 8? (Tue Nov 06 2007 - 02:30:17 CST)
  • Re: AMBER: Problem encountered during thermodynamic integration (Wed Sep 19 2007 - 12:30:14 CDT)
  • AMBER: Problem encountered during thermodynamic integration (Sat Sep 15 2007 - 03:18:59 CDT)
  • AMBER: Thermodynamic Integration for a CHARGED molecule (Fri Aug 17 2007 - 04:12:38 CDT)
  • AMBER: Re: how to create an O linked N-acetylglucosamine in a protein (Mon Jul 16 2007 - 22:44:08 CDT)
  • AMBER: how to create an O linked N-acetylglucosamine in a protein (Mon Jul 16 2007 - 22:41:40 CDT)
• Mingfeng Yang
  • Re: AMBER: amber md movie using Chimera (Wed Sep 05 2007 - 13:04:57 CDT)
  • Re: AMBER: Does Chimera support AMBER file formats? (Tue Jun 26 2007 - 19:12:53 CDT)
  • Re: AMBER: Chemical shift: simulation vs. experiment (Fri May 04 2007 - 02:52:48 CDT)
  • Re: AMBER: Chemical shift: simulation vs. experiment (Fri May 04 2007 - 02:17:04 CDT)
  • Re: AMBER: Chemical shift: simulation vs. experiment (Fri May 04 2007 - 00:16:30 CDT)
  • AMBER: Chemical shift: simulation vs. experiment (Thu May 03 2007 - 20:07:05 CDT)
  • Re: AMBER: problem regarding water handling in explicit simu (Fri Mar 30 2007 - 13:50:00 CST)
  • AMBER: rms and rmsf in ptraj (Wed Mar 28 2007 - 15:06:02 CST)
• Miyeegombo Enkhbold
  • AMBER: yet another SANDER bug? (Sat Jan 27 2007 - 21:11:22 CST)
• mkseo
  • Re: AMBER: surface area over the trajectory (Mon Jul 09 2007 - 17:55:18 CDT)
  • AMBER: surface area over the trajectory (Mon Jul 09 2007 - 16:52:32 CDT)
• Monaghan, Martin (Cont, ARL/CISD)
  • AMBER: Amber 9 source code permissions (UNCLASSIFIED) (Mon Oct 29 2007 - 15:30:30 CST)
• Moruz Luminita
  • AMBER: Problems with Carbohydrate Non-standard Residue (Wed Sep 12 2007 - 05:30:09 CDT)
• Mostafa Sadighi
  • AMBER: Statictical significance of differences in energy mean values between different simulations (Sat May 19 2007 - 10:54:40 CDT)
  • AMBER: The parallel test fails while sander.MPI seems to be installed correctly (Mon Mar 12 2007 - 05:43:14 CST)
• Mr Defang Ouyang
  • AMBER: pdb flie format (Sun Jun 03 2007 - 07:53:08 CDT)
• msubhamoy_at_ibab.ac.in
  • AMBER: Abnormality in MM-PBSA result (Fri Oct 19 2007 - 10:01:16 CDT)
  • AMBER: creating topology files for RNA DNA hybrid.molecule (Mon Sep 03 2007 - 18:00:25 CDT)
  • AMBER: Error in MMPBSA Calculation (Tue Aug 21 2007 - 00:53:17 CDT)
  • AMBER: mmpbsa calculation (Mon Aug 20 2007 - 04:53:42 CDT)
  • AMBER: MMPBSA NOT Getting results (Tue Aug 14 2007 - 03:26:57 CDT)
  • AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA (Wed Aug 08 2007 - 08:08:04 CDT)
  • AMBER: (Wed Aug 08 2007 - 08:01:00 CDT)
• Muhammad Naim Mohmad Rouyan
  • AMBER: Fatal error: Command failed for target `test.sander.no_lmod' (Tue Jan 23 2007 - 19:26:45 CST)
  • AMBER: Fatal error: Command failed for target `test.sander.no_lmod' (Tue Jan 23 2007 - 03:50:58 CST)
• Myunggi Yi
  • Re: AMBER: pmemd with openmpi (Mon Nov 19 2007 - 15:40:41 CST)
  • AMBER: pmemd with openmpi (Mon Nov 19 2007 - 13:25:48 CST)
  • AMBER: Bug report: iwrap failure in PMEMD with netCDF (Wed Nov 14 2007 - 13:18:18 CST)
  • Re: AMBER: binary restart file (Sun Oct 07 2007 - 18:39:44 CDT)
  • AMBER: binary restart file (Thu Oct 04 2007 - 09:49:28 CDT)
  • Re: AMBER: Work with constand pH (Fri Apr 27 2007 - 20:42:32 CDT)
  • Re: AMBER: Work with constand pH (Wed Apr 25 2007 - 08:49:59 CDT)
  • Re: AMBER: ptraj and quasi harmonic analysis (Wed Apr 18 2007 - 11:46:22 CDT)
• n.buis_at_soton.ac.uk
  • AMBER: (no subject) (Thu Jul 19 2007 - 03:58:06 CDT)
• Nadia Vahdati
  • AMBER: sander and pmemd (Mon Dec 03 2007 - 07:20:17 CST)
• nadiav_at_soton.ac.uk
  • AMBER: NAB normal mode output (Thu May 24 2007 - 12:27:59 CDT)
• nag raj
  • AMBER: closest water molecules with 8 angstroms (Wed Dec 19 2007 - 00:52:45 CST)
  • Re: AMBER: calculating charges to modified 4GA unit (Wed Nov 07 2007 - 21:04:53 CST)
  • Re: AMBER: calculating charges to modified 4GA unit (Wed Nov 07 2007 - 21:04:53 CST)
  • AMBER: calculating charges to modified 4GA unit (Wed Nov 07 2007 - 05:26:51 CST)
  • AMBER: How to fix the distance between two atoms. (Tue Sep 18 2007 - 23:36:29 CDT)
  • AMBER: Regarding free energy calculation and covalent bond (Mon Aug 20 2007 - 23:07:04 CDT)
  • AMBER: Regarding conversion of CHARMM force field parameters to AMBER parameters. (Wed Jun 13 2007 - 22:58:22 CDT)
  • Re: AMBER: membrane simulation (Thu Apr 19 2007 - 07:51:56 CDT)
  • Re: AMBER: membrane simulation (Wed Apr 18 2007 - 21:53:27 CDT)
  • AMBER: Lipid bilayer (Wed Mar 14 2007 - 21:51:19 CST)
  • AMBER: H-bond in each fram (Sun Jan 07 2007 - 23:49:57 CST)
  • Re: AMBER: H-bond in ptraj (Sat Jan 06 2007 - 01:22:10 CST)
  • Re: AMBER: H-bond in ptraj (Thu Jan 04 2007 - 22:34:59 CST)
  • AMBER: H-acceptors problem in ptraj (Wed Jan 03 2007 - 23:20:09 CST)
  • AMBER: H-bond in ptraj (Wed Jan 03 2007 - 06:17:51 CST)
• Narayanan Veeraraghavan
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Tue Jul 17 2007 - 17:01:10 CDT)
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Mon Jul 16 2007 - 16:35:53 CDT)
  • Re: AMBER: Specific/Non-specific dihedral issue in Amber (Mon Jul 09 2007 - 13:02:38 CDT)
  • AMBER: Specific/Non-specific dihedral issue in Amber (Mon Jul 09 2007 - 09:30:44 CDT)
• Navnit Kumar Mishra
  • Re: AMBER: MM-PBSA: Can't finish the binding energy process (Mon Apr 23 2007 - 09:04:12 CDT)
  • Re: AMBER: Problem with Sander restart file. (Wed Apr 11 2007 - 06:19:20 CDT)
  • Re: AMBER: xleap (Tue Jan 30 2007 - 05:53:11 CST)
• Neelanjana Sengupta
  • Re: AMBER: Known residue, unknown error in teLeap (Tue Jul 17 2007 - 13:58:12 CDT)
  • Re: AMBER: Known residue, unknown error in teLeap (Tue Jul 17 2007 - 13:53:16 CDT)
  • Re: AMBER: Known residue, unknown error in teLeap (Tue Jul 17 2007 - 11:33:39 CDT)
  • AMBER: Known residue, unknown error in teLeap (Mon Jul 16 2007 - 14:19:07 CDT)
  • AMBER: Input required for RESP (Tue Jul 10 2007 - 13:03:54 CDT)
  • AMBER: RESP charge generation (Sat Jul 07 2007 - 18:08:07 CDT)
  • Re: AMBER: antechamber: mopac charges (Thu Jul 05 2007 - 14:26:30 CDT)
  • AMBER: antechamber: mopac charges (Wed Jul 04 2007 - 18:21:02 CDT)
  • Re: AMBER: divcon missing in Antechamber 1.27 (Mon May 28 2007 - 21:18:08 CDT)
  • AMBER: Re: divcon missing in Antechamber 1.27 (Mon May 28 2007 - 19:56:55 CDT)
  • AMBER: divcon missing in Antechamber 1.27 (Mon May 28 2007 - 19:54:18 CDT)
  • AMBER: command line alternatives for teLeap (Wed May 02 2007 - 23:21:07 CDT)
  • AMBER: Error in protonating (Fri Apr 27 2007 - 06:31:52 CDT)
  • AMBER: .prmtop entries (Mon Apr 23 2007 - 00:53:46 CDT)
  • Re: AMBER: Attaching capping groups (Thu Apr 12 2007 - 21:54:30 CDT)
  • AMBER: Attaching capping groups (Wed Apr 11 2007 - 20:28:33 CDT)
  • AMBER: Fails to load libraries present in /leap/lib/ (Mon Apr 09 2007 - 04:33:29 CDT)
  • AMBER: PDB file format for AMBER (Fri Apr 06 2007 - 21:41:43 CDT)
  • AMBER: Parameter file for Dipeptide (Mon Mar 26 2007 - 23:23:32 CST)
• neetu_at_imtech.res.in
  • Re: AMBER: manganese ion (Tue Jul 10 2007 - 23:03:54 CDT)
  • AMBER: query regarding parameter files for manganese (Thu May 10 2007 - 07:43:44 CDT)
  • AMBER: query regarding parameter files for manganese and mercuric ions (Tue May 08 2007 - 06:40:56 CDT)
• Neha Gandhi
  • AMBER: Parse charges for small molecules (Wed Aug 22 2007 - 23:50:38 CDT)
  • Re: AMBER: charges in PBSA calculation (Sun Aug 19 2007 - 18:01:47 CDT)
  • AMBER: charges in PBSA calculation (Sat Aug 18 2007 - 21:20:16 CDT)
• neva_at_mmb.pcb.ub.es
  • AMBER: Bad residue/molecule data in prmtop (Wed Jul 25 2007 - 08:03:19 CDT)
• neville forlemu
  • Re: AMBER: bug in nonbond_list.f (nee ew_setup.f) (Wed Aug 08 2007 - 13:35:51 CDT)
  • Re: AMBER: Cutoff list exceeds largest sphere in unit cell (Sat Jul 14 2007 - 21:09:36 CDT)
• Nevin Gerek
  • AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) (Tue Feb 06 2007 - 17:08:08 CST)
  • AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) (Tue Feb 06 2007 - 17:08:08 CST)
• Nicolas Lux Fawzi
  • Re: AMBER: predictive NOE generation (Tue Nov 27 2007 - 12:26:48 CST)
  • AMBER: ff99SB and the N- and C- charged terminal residues (Wed Oct 10 2007 - 11:03:09 CDT)
  • Re: AMBER: Solvation net forces (Tue Sep 25 2007 - 16:24:05 CDT)
  • Re: AMBER: Amber9 analyze timecorr manual ambigous (Thu Jul 12 2007 - 17:11:30 CDT)
  • AMBER: Amber9 analyze timecorr manual ambigous (Thu Jul 12 2007 - 14:26:19 CDT)
  • Re: AMBER: set up system solution with 3 different components, each with multiple copies (Tue Jun 26 2007 - 10:16:54 CDT)
  • AMBER: ptray segfault: vector out (Thu Jun 21 2007 - 14:19:49 CDT)
  • AMBER: set up system solution with 3 different components, each with multiple copies (Thu Jun 21 2007 - 10:56:57 CDT)
  • AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? 2nd try (Tue Apr 17 2007 - 16:50:07 CDT)
  • AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? (Tue Apr 17 2007 - 14:00:18 CDT)
  • AMBER: ptraj bug? -- doesn't like restart files from REMD (Thu Feb 22 2007 - 15:33:58 CST)
• Nikola Trbovic
  • Re: AMBER: NVE energy and temperature drift (Sat Aug 11 2007 - 16:33:09 CDT)
  • Re: AMBER: imin=5 and inptraj (Sat Aug 11 2007 - 16:31:40 CDT)
  • AMBER: imin=5 and inptraj (Sat Aug 11 2007 - 15:11:08 CDT)
  • RE: AMBER: NVE energy and temperature drift (Thu Aug 09 2007 - 19:11:07 CDT)
  • Re: AMBER: NVE energy and temperature drift (Thu Aug 09 2007 - 17:50:45 CDT)
  • AMBER: NVE energy and temperature drift (Thu Aug 09 2007 - 15:24:11 CDT)
  • RE: AMBER: extracting starting structures from equilibration trajectory (Thu Jun 07 2007 - 15:07:48 CDT)
  • RE: AMBER: extracting starting structures from equilibration trajectory (Thu Jun 07 2007 - 14:54:35 CDT)
  • RE: AMBER: extracting starting structures from equilibration trajectory (Thu Jun 07 2007 - 14:33:35 CDT)
  • AMBER: extracting starting structures from equilibration trajectory (Thu Jun 07 2007 - 13:06:15 CDT)
  • RE: AMBER: problem running parallel jobs (Thu Jun 07 2007 - 09:58:47 CDT)
  • RE: AMBER: problem running parallel jobs (Wed Jun 06 2007 - 13:43:14 CDT)
  • RE: AMBER: problem running parallel jobs (Wed Jun 06 2007 - 12:31:16 CDT)
  • AMBER: problem running parallel jobs (Tue Jun 05 2007 - 15:43:02 CDT)
• Nitin Bhardwaj
  • AMBER: Hydrogen in a phosphate ion (Fri Jan 05 2007 - 16:00:09 CST)
  • Fwd: AMBER: Atoms overlapping (Thu Jan 04 2007 - 18:58:26 CST)
  • Re: AMBER: The unperturbed charge of the unit: -20.999999 is not zero. (Thu Jan 04 2007 - 09:54:39 CST)
• Nursultan Bogatov
  • AMBER: another sander bug? (Fri Jan 26 2007 - 00:43:13 CST)
  • AMBER: sander bug? (Thu Jan 25 2007 - 20:28:53 CST)
• odde
  • AMBER: Re: MM-PBSA amber script problem (Tue Apr 17 2007 - 13:45:06 CDT)
  • Re: AMBER: Re: amber mm-pbsa problem (Tue Apr 17 2007 - 08:57:37 CDT)
  • AMBER: MM-PBSA_binding energy script error (Mon Apr 16 2007 - 18:33:14 CDT)
  • AMBER: Amber:PBSA&Extract_coords problem (Needed help) (Fri Apr 13 2007 - 14:06:42 CDT)
• Ozlem Demir
  • AMBER: electron density difference (Thu Sep 06 2007 - 08:36:29 CDT)
• Pablo Englebienne
  • Re: AMBER: PME and counter ions (Wed Dec 19 2007 - 13:05:30 CST)
  • Re: AMBER: divcon (Thu Nov 08 2007 - 11:50:25 CST)
  • Re: AMBER: MD simulations with Pt atom - how to keep square planar geometry? (Thu Nov 08 2007 - 11:44:43 CST)
  • AMBER: MD simulations with Pt atom - how to keep square planar geometry? (Wed Nov 07 2007 - 20:21:21 CST)
• Pan, Yongmei
  • AMBER: unsubscribe (Mon Aug 13 2007 - 12:35:12 CDT)
• Pankaj Daga
  • Re: AMBER: MM_PBSA with complex plus Ion (Sun Sep 23 2007 - 10:50:21 CDT)
• Pankaj R. Daga
  • AMBER: help in QM/MM simulation (Thu Dec 13 2007 - 15:02:17 CST)
  • AMBER: QMMM simulations (Tue Nov 27 2007 - 17:20:51 CST)
  • AMBER: decomposition energy (Tue Sep 04 2007 - 09:31:25 CDT)
  • AMBER: Molsurf error (Fri Aug 17 2007 - 12:46:54 CDT)
  • AMBER: PBSA Error (Tue Jun 26 2007 - 09:03:41 CDT)
  • Re: AMBER: deeper problem with the energetics (Thu May 17 2007 - 11:50:11 CDT)
  • AMBER: deeper problem with the energetics (Thu May 17 2007 - 08:46:33 CDT)
  • Re: AMBER: signal SIGSEGV(11) (Tue Apr 24 2007 - 09:55:14 CDT)
  • Re: AMBER: signal SIGSEGV(11) (Wed Apr 18 2007 - 14:16:48 CDT)
  • AMBER: signal SIGSEGV(11) (Wed Apr 18 2007 - 10:25:55 CDT)
  • AMBER: Sander error : Coordinate resetting (SHAKE) cannot be accomplished (Thu Mar 29 2007 - 21:59:08 CST)
  • AMBER: abnormal termination of tleap (Fri Mar 09 2007 - 16:24:37 CST)
  • Re: AMBER: problems with bonding disulfide linkages (Mon Feb 19 2007 - 16:54:24 CST)
• Parish, Carol
  • RE: AMBER: request for hardware recommendations (Sat Oct 06 2007 - 12:20:13 CDT)
  • AMBER: request for hardware recommendations (Sat Oct 06 2007 - 10:59:01 CDT)
• Patel, Bhavesh H
  • AMBER: RE: FF94 or FF99? (Thu Nov 22 2007 - 08:34:55 CST)
• Patrick McCarren
  • Re: AMBER: AIX 5 test failures: -NaNQ (Wed Apr 25 2007 - 18:44:15 CDT)
  • Re: AMBER: AIX 5 test failures: -NaNQ (Mon Apr 23 2007 - 16:51:46 CDT)
  • Re: AMBER: AIX 5 test failures: -NaNQ (Fri Apr 20 2007 - 18:01:53 CDT)
  • Re: AMBER: process and plot matrix data (Fri Apr 20 2007 - 05:02:15 CDT)
  • AMBER: AIX 5 test failures: -NaNQ (Thu Apr 19 2007 - 18:30:35 CDT)
• paula lario
  • AMBER: amber94 parameters for cholesterol (Thu Jun 07 2007 - 17:57:38 CDT)
• Pavan G
  • Re: AMBER: Group input for restrained atoms (Fri Nov 30 2007 - 10:43:23 CST)
  • Re: AMBER: Re: Calculating Energies with imin=5 (Fri Nov 30 2007 - 10:35:02 CST)
  • Re: AMBER: Re: Calculating Energies with imin=5 (Fri Nov 30 2007 - 06:55:14 CST)
  • AMBER: Re: Calculating Energies with imin=5 (Fri Nov 30 2007 - 06:24:18 CST)
  • AMBER: Improper torsion terms (Thu Nov 01 2007 - 18:24:46 CST)
  • AMBER: Re: ff02 and ff03 parameters (Mon Jun 25 2007 - 14:34:30 CDT)
  • Re: AMBER: Re: Strange shape in my MD simulations (Tue Jun 19 2007 - 13:37:18 CDT)
  • Re: AMBER: Re: Strange shape in my MD simulations (Tue Jun 19 2007 - 09:34:45 CDT)
  • Re: AMBER: Re: Strange shape in my MD simulations (Tue Jun 19 2007 - 09:09:48 CDT)
  • AMBER: Re: Strange shape in my MD simulations (Tue Jun 19 2007 - 07:47:58 CDT)
  • Re: AMBER: Ptraj: watershell and distance (Tue Jan 30 2007 - 16:01:07 CST)
  • Fwd: AMBER: Improper angle by Antechamber (Tue Jan 30 2007 - 12:46:34 CST)
  • AMBER: Improper angle by Antechamber (Sun Jan 28 2007 - 11:28:29 CST)
  • Re: AMBER: HF/6-31G* ESP Charges do not match with ff02 charges (Sun Jan 28 2007 - 09:45:32 CST)
  • AMBER: HF/6-31G* ESP Charges do not match with ff02 charges (Fri Jan 19 2007 - 00:19:19 CST)
• Peljidiyn Genden
  • AMBER: mdfil.f (Sat Apr 14 2007 - 02:43:27 CDT)
• Perdita Barran
  • AMBER: unsubscribe (Sun Jan 07 2007 - 12:13:40 CST)
• Peter Gannett
  • Re: AMBER: Would amber work with Linspire 6.0? (Tue Nov 27 2007 - 21:20:19 CST)
  • RE: AMBER: Installing AMBER v9 in Linux (Mon Feb 19 2007 - 06:27:44 CST)
• Peter Varnai
  • AMBER: replica exchange problems with ifort >10.0.023 (Sat Nov 10 2007 - 10:44:30 CST)
  • AMBER: addles (Sat Nov 10 2007 - 10:40:21 CST)
  • Re: AMBER: Problems loading pdb file including Mg ions (Tue Oct 23 2007 - 05:38:53 CDT)
• Peter Z. Qin
  • Re: AMBER: AMBER8 compiler with intel 9.1 compiler (Fri May 25 2007 - 11:49:13 CDT)
  • Re: AMBER: AMBER8 compiler with intel 9.1 compiler (Wed May 23 2007 - 00:39:18 CDT)
  • Re: AMBER: AMBER8 compiler with intel 9.1 compiler (Fri May 18 2007 - 19:53:29 CDT)
  • Re: AMBER: AMBER8 compiler with intel 9.1 compiler (Thu May 17 2007 - 18:17:29 CDT)
  • Re: AMBER: AMBER8 compiler with intel 9.1 compiler (Thu May 17 2007 - 17:49:39 CDT)
  • Re: AMBER: AMBER8 compiler with intel 9.1 compiler (Wed May 16 2007 - 15:37:53 CDT)
  • AMBER: AMBER8 compiler with intel 9.1 compiler (Tue May 15 2007 - 20:37:22 CDT)
• Petr Kulhanek
  • Re: AMBER: image command (Wed Jan 10 2007 - 02:45:45 CST)
• Phineus Markwick
  • Re: AMBER: Sander Error (Fri Jun 29 2007 - 10:48:04 CDT)
  • Re: AMBER: Sander Error (Fri Jun 29 2007 - 10:45:18 CDT)
• pig5678
  • Re:Re: AMBER: ????pig5678?????? (Thu Jul 12 2007 - 20:36:10 CDT)
  • Re:Re: AMBER: ????pig5678?????? (Tue Jul 10 2007 - 22:27:55 CDT)
  • AMBER: À´×Ôpig5678µÄÓʼþ (Tue Jul 10 2007 - 01:59:22 CDT)
• Piotr Cieplak
  • Re: AMBER: THF parameters (Wed Dec 05 2007 - 13:33:42 CST)
  • Re: AMBER: unres (Mon Jun 18 2007 - 19:00:47 CDT)
  • Re: AMBER: psi , phi angles (Mon Mar 05 2007 - 13:27:13 CST)
  • Re: AMBER: psi , phi angles (Mon Mar 05 2007 - 12:30:46 CST)
  • Re: AMBER: psi , phi angles (Mon Mar 05 2007 - 11:29:30 CST)
• Pradipta Bandyopadhyay
  • AMBER: Fe bonds in HEME ! (Mon Nov 05 2007 - 05:50:58 CST)
  • AMBER: Heme and CYS !! (Fri Oct 26 2007 - 05:49:47 CDT)
  • AMBER: Reproducing constant pH results !! (Thu Sep 27 2007 - 00:16:49 CDT)
  • AMBER: ff02 + POL3 - polar interactions !! (Wed Apr 18 2007 - 11:04:22 CDT)
  • Re: AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? 2nd try (Tue Apr 17 2007 - 23:33:52 CDT)
  • Re: AMBER: Topology file problem in TI ! (Thu Mar 08 2007 - 10:18:58 CST)
  • Re: AMBER: Topology file problem in TI ! (Wed Mar 07 2007 - 23:55:26 CST)
  • AMBER: Topology file problem in TI ! (Wed Mar 07 2007 - 05:08:39 CST)
• Prashanth Athri
  • AMBER: TIP5P questions (Tue Sep 11 2007 - 16:26:56 CDT)
  • Re: AMBER: Force Field Parameters (Thu Aug 02 2007 - 12:39:10 CDT)
  • Re: AMBER: DNA denatures during MD simulation (Mon Jul 23 2007 - 17:51:32 CDT)
  • AMBER: DNA denatures during MD simulation (Mon Jul 23 2007 - 14:38:12 CDT)
• Praveena Gopal
  • AMBER: Amber: Number density profile, pucker..reg (Tue Jun 12 2007 - 01:17:37 CDT)
• Prem
  • Re: AMBER: angle between vectors (Tue Dec 04 2007 - 15:59:29 CST)
• Prem Prakash Pathak
  • Re: AMBER: make test.parallel not complete (Thu Dec 20 2007 - 03:59:03 CST)
  • AMBER: make test.parallel not complete (Thu Dec 13 2007 - 02:10:16 CST)
  • Re: AMBER: for NMR restrains files (Fri Sep 07 2007 - 23:36:11 CDT)
  • Re: AMBER: refinement of NMR struture using AMBER (Wed Sep 05 2007 - 09:01:41 CDT)
  • AMBER: refinement of NMR struture using AMBER (Wed Aug 29 2007 - 05:57:11 CDT)
  • Re: AMBER: What is the best computer for running AMBER simulations? (Sat Aug 18 2007 - 04:36:00 CDT)
  • AMBER: force field for hydrogels (Fri Aug 03 2007 - 01:03:48 CDT)
  • Re: AMBER: not getting topology and restraint file (Wed Jul 25 2007 - 08:45:57 CDT)
  • Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap (Tue Jul 24 2007 - 23:12:48 CDT)
  • Re: AMBER: not getting topology and restraint file (Tue Jul 24 2007 - 23:11:00 CDT)
  • AMBER: not getting topology and restraint file (Tue Jul 24 2007 - 09:09:40 CDT)
  • Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap (Tue Jul 24 2007 - 07:30:31 CDT)
  • AMBER: problem in compiling amber with suse 9.1 i686, finally in leap (Mon Jul 23 2007 - 10:39:21 CDT)
  • AMBER: using amber to minimize structure obatined from cyana (Mon Jul 23 2007 - 02:27:26 CDT)
  • AMBER: problem in compiling amber9 and running amber9 (Sat Jul 21 2007 - 07:27:18 CDT)
• priya priya
  • Re: AMBER: Parallel scaling (Tue Nov 13 2007 - 05:26:23 CST)
  • AMBER: Parallel scaling (Tue Nov 13 2007 - 04:35:20 CST)
  • AMBER: segmentation fault occured doing MD (Fri Oct 26 2007 - 06:51:31 CDT)
  • Re: AMBER: multi chain simulations (Thu Oct 04 2007 - 07:44:56 CDT)
  • Re: AMBER: multi chain simulations (Thu Oct 04 2007 - 06:07:44 CDT)
  • AMBER: multi chain simulations (Thu Oct 04 2007 - 05:30:27 CDT)
  • AMBER: multichain simulations (Tue Oct 02 2007 - 04:31:26 CDT)
  • AMBER: multichain simulations (Tue Oct 02 2007 - 04:31:26 CDT)
  • AMBER: ow to split MDCRD file using ptraj (Fri Aug 24 2007 - 02:34:27 CDT)
  • AMBER: Unable to open MDCRD file using vmd (Thu Aug 23 2007 - 10:04:19 CDT)
  • Re: AMBER: setbox command error (Tue Aug 14 2007 - 03:58:40 CDT)
  • Re: AMBER: setbox command error (Tue Aug 14 2007 - 01:42:45 CDT)
  • AMBER: setbox command error (Mon Aug 13 2007 - 11:18:16 CDT)
  • Re: AMBER: heical content in simulations (Tue Aug 07 2007 - 03:41:16 CDT)
  • AMBER: heical content in simulations (Tue Aug 07 2007 - 02:58:12 CDT)
  • AMBER: Specific heat graph is a straight line (Mon Aug 06 2007 - 08:33:52 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 10:00:30 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 09:23:08 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 08:36:12 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 08:13:32 CDT)
  • Re: AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 07:11:17 CDT)
  • AMBER: temperature fluctuation in REMD (Fri Jul 20 2007 - 05:58:48 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 11:41:05 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 08:43:13 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 08:27:27 CDT)
  • Re: AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 07:41:22 CDT)
  • AMBER: Stirp command in ptraj (Fri Jul 06 2007 - 07:33:11 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Fri Jul 06 2007 - 07:25:02 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Fri Jul 06 2007 - 05:39:58 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Fri Jul 06 2007 - 01:58:28 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 11:40:41 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 10:57:59 CDT)
  • Re: AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 10:10:23 CDT)
  • AMBER: How to extract energy of molecule from the system with explicit water molecules (Thu Jul 05 2007 - 09:31:03 CDT)
  • Re: AMBER: radius of gyration (Fri Jun 29 2007 - 08:14:49 CDT)
  • Re: AMBER: radius of gyration (Fri Jun 29 2007 - 04:16:24 CDT)
  • Re: AMBER: problems in adding ACE and NME group (Mon Jun 25 2007 - 09:01:52 CDT)
  • AMBER: how to calculate energy of the peptide (Mon Jun 25 2007 - 08:56:54 CDT)
  • Re: AMBER: radius of gyration (Mon Jun 25 2007 - 07:57:39 CDT)
  • Re: AMBER: radius of gyration (Mon Jun 25 2007 - 07:59:39 CDT)
  • Re: AMBER: radius of gyration (Fri Jun 22 2007 - 10:23:03 CDT)
  • AMBER: radius of gyration (Fri Jun 22 2007 - 10:10:36 CDT)
  • Re: AMBER: problem with running rem on amber9 (Mon Jun 18 2007 - 10:25:37 CDT)
  • Re: AMBER: problem with running rem on amber9 (Mon Jun 18 2007 - 10:02:55 CDT)
  • Re: AMBER: problem with running rem on amber9 (Mon Jun 18 2007 - 07:59:38 CDT)
  • AMBER: problem with running rem on amber9 (Mon Jun 18 2007 - 07:41:02 CDT)
  • AMBER: Using position restraints during constant pressure equilibration (Tue Jun 12 2007 - 08:17:44 CDT)
  • RE: AMBER: problem with starting REM on amber9 (Wed Jun 06 2007 - 02:07:14 CDT)
  • Re: AMBER: problem with starting REM on amber9 (Tue Jun 05 2007 - 09:21:12 CDT)
  • AMBER: problem with starting REM on amber9 (Tue Jun 05 2007 - 08:32:50 CDT)
  • Re: AMBER: Problem related simulation of dimer (Mon Mar 19 2007 - 04:38:59 CST)
  • Re: AMBER: Problem related simulation of dimer (Sun Mar 18 2007 - 23:35:42 CST)
  • AMBER: Problem related simulation of dimer (Thu Mar 15 2007 - 05:23:31 CST)
• puneet kacker
  • Re: AMBER: problem while analysing result (Wed Mar 14 2007 - 00:46:22 CST)
  • Re: AMBER: problem while analysing result (Tue Mar 13 2007 - 23:59:20 CST)
  • AMBER: Drug Leads interaction with ds and Triplex DNA (Wed Jan 24 2007 - 23:28:41 CST)
• Qiang Zhong
  • Re:AMBER: AMBER parametrization (??) for OAA and Mg++ (Tue Sep 11 2007 - 02:32:17 CDT)
  • AMBER: energy minimization parameter (Wed Aug 29 2007 - 02:54:12 CDT)
  • RE: AMBER: QM/MM in reaction pathways? (Tue Aug 28 2007 - 19:52:21 CDT)
  • AMBER: QM/MM in reaction pathways? (Tue Aug 28 2007 - 02:51:30 CDT)
  • Re: AMBER: SMD simulation (Sat Aug 25 2007 - 04:49:09 CDT)
  • Re: AMBER: SMD simulation (Sat Aug 25 2007 - 04:49:09 CDT)
  • AMBER: SMD simulation (Fri Aug 24 2007 - 05:33:41 CDT)
  • AMBER: QM/MM in reaction pathways? (Fri Aug 24 2007 - 03:00:50 CDT)
  • AMBER: protonation of His residue! (Thu Aug 23 2007 - 21:39:51 CDT)
  • AMBER: Ca(2+) parameter (Thu Aug 23 2007 - 06:01:24 CDT)
  • AMBER: How to use AMBER Parameter Database ? (Wed Aug 22 2007 - 03:53:04 CDT)
  • AMBER: Tutorial of document about QM/MM in reaction pathways? (Tue Aug 21 2007 - 09:06:53 CDT)
  • AMBER: How to use AMBER Parameter Database ? (Tue Aug 21 2007 - 07:36:46 CDT)
  • AMBER: command tleap is not normal (Tue Aug 21 2007 - 03:12:44 CDT)
  • AMBER: $tleap is not normal (Mon Aug 20 2007 - 20:34:00 CDT)
  • Re: AMBER: TEST_FAILURES (Mon Aug 20 2007 - 19:43:23 CDT)
  • AMBER: TEST_FAILURES (Mon Aug 20 2007 - 07:59:28 CDT)
  • AMBER: Tutorial about SMD? (Tue Aug 14 2007 - 05:19:09 CDT)
• Qing Zhang
  • Re: AMBER: Calcium parameters (Fri Mar 02 2007 - 17:10:24 CST)
  • Re: AMBER: calcium parameter for GB (Wed Jan 24 2007 - 11:33:24 CST)
  • Re: AMBER: calcium parameter for GB (Tue Jan 23 2007 - 12:49:54 CST)
  • Re: AMBER: calcium parameter for GB (Wed Jan 17 2007 - 11:06:36 CST)
• Qizhi Cui
  • Re: AMBER: Ionic strength in pbsa (Tue May 22 2007 - 15:21:27 CDT)
• Quantum Mechanics
  • AMBER: MacOSX installation help (Mon Sep 24 2007 - 04:39:46 CDT)
• r. a.
  • AMBER: distance calculation! (Mon Mar 05 2007 - 02:43:45 CST)
  • AMBER: native contact analysis! (Wed Feb 21 2007 - 20:52:37 CST)
• Rachel
  • Re: AMBER: about wrap the trajectory (Fri Jul 27 2007 - 09:52:50 CDT)
  • Re: AMBER: about wrap the trajectory (Fri Jul 27 2007 - 09:38:12 CDT)
  • Re: AMBER: about wrap the trajectory (Fri Jul 27 2007 - 09:08:23 CDT)
  • Re: AMBER: about wrap the trajectory (Thu Jul 26 2007 - 11:43:48 CDT)
  • AMBER: about wrap the trajectory (Thu Jul 26 2007 - 11:18:32 CDT)
  • AMBER: how to solvate the protein with different solvents (Fri May 11 2007 - 08:01:07 CDT)
• Rafi Ahmad
  • RE: AMBER: MMPBSA NOT Getting results (Tue Aug 14 2007 - 03:34:35 CDT)
  • SV: AMBER: Atoms in contact to a specific atoms during MD (Mon Jul 16 2007 - 10:04:46 CDT)
  • AMBER: Atoms in conatct to a specific atoms during MD (Mon Jul 16 2007 - 08:23:38 CDT)
  • AMBER: Regarding counter ions (Wed Mar 14 2007 - 14:00:59 CST)
  • RE: AMBER: hi.. (Tue Mar 13 2007 - 06:32:18 CST)
  • RE: AMBER: hi.. (Tue Mar 13 2007 - 06:20:28 CST)
  • RE: AMBER: Best Force field for protein, DNA, and organic compounds? (Wed Feb 14 2007 - 07:35:28 CST)
  • RE: AMBER: atomicfluct (Mon Feb 12 2007 - 02:32:37 CST)
  • RE: AMBER: atomicfluct (Mon Feb 12 2007 - 02:32:37 CST)
• Rajendra P. OJHA
  • AMBER: Transformation table (Sun Oct 07 2007 - 05:12:37 CDT)
  • RE: AMBER: Building parallel Amber 9.0 (Wed Aug 15 2007 - 10:44:10 CDT)
  • RE: AMBER: Building parallel Amber 9.0 (Wed Aug 15 2007 - 10:41:25 CDT)
  • Re: AMBER: potential energy calculation (Wed Jul 18 2007 - 01:03:55 CDT)
• Rama krishnan
  • AMBER: Request reg parameter for vitamin e (Tue Nov 06 2007 - 01:13:51 CST)
  • AMBER: Request reg parameter for vitamin e (Tue Nov 06 2007 - 01:11:47 CST)
• Ranjib Dey
  • Re: AMBER: tleap crashing (Wed Dec 12 2007 - 01:04:55 CST)
  • AMBER: tleap crashing (Tue Dec 11 2007 - 13:12:20 CST)
• Raviprasad Aduri
  • Re: AMBER: Force Field Parameters (Thu Aug 02 2007 - 14:49:37 CDT)
  • Re: AMBER: RESP calculation of modified nucleotides (Fri Mar 02 2007 - 11:16:39 CST)
  • Re: AMBER: RESP calculation of modified nucleotides (Thu Mar 01 2007 - 12:12:54 CST)
  • Re: AMBER: RESP calculation of modified nucleotides (Wed Feb 28 2007 - 15:11:34 CST)
  • Re: AMBER: RESP calculation of modified nucleotides (Mon Feb 26 2007 - 10:56:47 CST)
  • Re: AMBER: Modified nucleotides (Wed Feb 14 2007 - 18:58:39 CST)
  • Re: AMBER: Modified nucleotides (Tue Feb 13 2007 - 11:23:15 CST)
• ravishk kumar
  • AMBER: PCA with ptraj (Sat Jul 28 2007 - 07:02:13 CDT)
  • AMBER: rmsd residue wise (Thu Jul 26 2007 - 08:02:20 CDT)
• Ray Luo
  • RE: AMBER: Zinc-Histidine force field (Thu Nov 22 2007 - 13:01:30 CST)
  • RE: AMBER: Zinc-Histidine force field (Wed Nov 21 2007 - 11:30:21 CST)
  • Re: AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua (Fri Oct 26 2007 - 12:31:03 CDT)
  • RE: AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua (Thu Oct 25 2007 - 13:20:14 CDT)
  • Re: AMBER: charges in PBSA calculation (Sun Aug 19 2007 - 08:32:19 CDT)
  • RE: AMBER: correlation between PBTOT and GBTOT values in a MD trajectory (Fri May 11 2007 - 11:54:21 CDT)
  • RE: AMBER: bug in reprocessing with PB? (Thu May 10 2007 - 16:04:42 CDT)
  • RE: AMBER: bug in reprocessing with PB? (Thu May 10 2007 - 13:52:37 CDT)
  • RE: AMBER: nonpolar solvation energy (Wed Jan 31 2007 - 13:37:34 CST)
  • RE: AMBER: MM-PBSA doubt (Mon Jan 29 2007 - 23:29:01 CST)
  • RE: AMBER: MM-PBSA doubt (Mon Jan 29 2007 - 22:04:52 CST)
  • RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f (Tue Jan 23 2007 - 12:43:23 CST)
  • RE: RE: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f (Mon Jan 22 2007 - 20:35:06 CST)
  • RE: AMBER: Can't run decompose energy in MM-PBSA (Mon Jan 22 2007 - 11:27:03 CST)
  • RE: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f (Sat Jan 20 2007 - 12:45:36 CST)
  • RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f (Fri Jan 19 2007 - 11:50:19 CST)
  • RE: AMBER: CYX residue missing from Amber 9 ff03ua (?) (Thu Jan 11 2007 - 16:59:29 CST)
• rdauria_at_uci.edu
  • Re: AMBER: Making movies in VMD (Wed Dec 05 2007 - 23:20:12 CST)
  • AMBER: pressure tensor in a slab configuration (Mon Apr 30 2007 - 21:16:08 CDT)
• rebeca_at_mmb.pcb.ub.es
  • Re: AMBER: invalid digit '*' in the input file (Mon Nov 12 2007 - 08:56:26 CST)
  • AMBER: invalid digit '*' in the input file (Mon Nov 12 2007 - 08:06:16 CST)
  • AMBER: using amber for cyclic peptides (Mon Oct 15 2007 - 12:23:50 CDT)
  • AMBER: contacts in ptraj (Amber 9) (Wed Feb 21 2007 - 12:56:50 CST)
  • AMBER: Amber/ANAL and psf files (Wed Feb 21 2007 - 10:24:33 CST)
  • AMBER: experimental phi-values as restraints (Wed Jan 10 2007 - 10:06:11 CST)
• Rene Salmon
  • AMBER: Amber 9 make parallel fails with mpich (Fri Mar 02 2007 - 11:45:37 CST)
• Rima Chaudhuri
  • AMBER: Water cap MD error (Mon Oct 15 2007 - 17:17:07 CDT)
  • Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa (Wed Feb 28 2007 - 16:25:54 CST)
  • AMBER: MD temperature and MM_pbsa temperature (Fri Feb 23 2007 - 15:22:30 CST)
  • Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa (Sat Feb 17 2007 - 14:10:38 CST)
  • AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa (Fri Feb 16 2007 - 16:17:49 CST)
  • AMBER: Positive binding free energy! (Tue Feb 13 2007 - 16:53:05 CST)
  • AMBER: Missing values for MM ELE (MM-PBSA)..help!! (Wed Feb 07 2007 - 10:21:38 CST