AMBER Archive (2008) - Aug 2008 By Author

Starting: Fri Aug 01 2008 - 01:59:00 CDT
Ending: Sun Aug 31 2008 - 16:30:08 CDT

• Abdul Hameed, MohamedDiwanMo
  • AMBER: Silicon parameters (Wed Aug 20 2008 - 11:15:56 CDT)
• Adrian Roitberg
  • Re: AMBER: Is there a way to cluster frames of a trajectory? (Wed Aug 27 2008 - 19:56:08 CDT)
• Adrien Delmont
  • Re: AMBER: united atom force field (Fri Aug 22 2008 - 14:17:10 CDT)
  • AMBER: united atom force field (Fri Aug 22 2008 - 07:35:06 CDT)
• Alan
  • Re: AMBER: to understand how frcmod.ff99SB works (Fri Aug 29 2008 - 04:00:01 CDT)
  • Re: AMBER: to understand how frcmod.ff99SB works (Thu Aug 28 2008 - 13:36:55 CDT)
  • AMBER: to understand how frcmod.ff99SB works (Thu Aug 28 2008 - 05:29:18 CDT)
  • Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro (Mon Aug 18 2008 - 04:34:03 CDT)
  • Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro (Mon Aug 18 2008 - 02:42:35 CDT)
  • AMBER: value of Pi in Amber (Fri Aug 08 2008 - 05:36:06 CDT)
• Alessandro Nascimento
  • Re: AMBER: interaction energies (Fri Aug 15 2008 - 11:18:05 CDT)
  • Re: AMBER: empty frcmod file but missing parameters (Tue Aug 12 2008 - 17:02:01 CDT)
• Alex Spasic
  • Re: AMBER: Problem with setting the NMR restraints (Mon Aug 04 2008 - 14:35:20 CDT)
  • Re: AMBER: Problem with setting the NMR restraints (Mon Aug 04 2008 - 11:58:17 CDT)
  • AMBER: Problem with setting the NMR restraints (Mon Aug 04 2008 - 09:15:25 CDT)
• Andreas Svrcek-Seiler
  • Re: AMBER: Error when compiling and testing AmberTools (Fri Aug 22 2008 - 04:11:14 CDT)
  • RE: AMBER: NAB conjgrad returns error? (Fri Aug 08 2008 - 10:48:28 CDT)
  • Re: AMBER: NAB conjgrad returns error? (Thu Aug 07 2008 - 10:33:28 CDT)
• aneesh cna
  • AMBER: RDF output file format (Mon Aug 18 2008 - 04:48:45 CDT)
  • AMBER: problem with prep file generation (Wed Aug 13 2008 - 07:05:58 CDT)
• Anna Karawajczyk
  • AMBER: mol2, xleap, Segmentation fault (Mon Aug 25 2008 - 08:01:31 CDT)
  • AMBER: bacteriochlorophyll ff (Fri Aug 01 2008 - 05:04:44 CDT)
• Arturas Ziemys
  • AMBER: wrapping w/ ptraj (Fri Aug 29 2008 - 16:57:52 CDT)
  • AMBER: interaction energies (Thu Aug 14 2008 - 10:21:34 CDT)
  • Re: AMBER: mm-pbsa / sander.MPI ? (Thu Aug 14 2008 - 09:42:02 CDT)
  • AMBER: mm-pbsa / sander.MPI ? (Wed Aug 13 2008 - 17:26:56 CDT)
  • AMBER: glycoprotein setup (Tue Aug 12 2008 - 22:35:35 CDT)
• Ben Roberts
  • AMBER: Error when compiling and testing AmberTools (Thu Aug 21 2008 - 16:46:43 CDT)
• Bertrand P. S. Russell
  • Re: AMBER: RDF output file format (Mon Aug 18 2008 - 05:26:08 CDT)
• Bill Ross
  • Re: AMBER: Source FIles of SANDER (Tue Aug 26 2008 - 14:28:34 CDT)
  • Re: AMBER: Problems with sleap and amoeba (Tue Aug 19 2008 - 18:51:18 CDT)
• Brent Krueger
  • Re: AMBER: Trans proline (Sat Aug 02 2008 - 22:47:16 CDT)
• Carlos Simmerling
  • Re: AMBER: Critical patch for pmemd 10 extra points code (Sun Aug 31 2008 - 08:54:33 CDT)
  • Re: AMBER: Is there a way to cluster frames of a trajectory? (Wed Aug 27 2008 - 19:58:27 CDT)
  • Re: AMBER: Re: Dell 2 Quad Core System Performance (Wed Aug 27 2008 - 17:15:42 CDT)
  • Re: AMBER: pmemd iwrap trouble (Wed Aug 27 2008 - 08:26:54 CDT)
  • Re: AMBER: Querry (Wed Aug 27 2008 - 08:20:55 CDT)
  • Re: AMBER: Source FIles of SANDER (Tue Aug 26 2008 - 18:21:31 CDT)
  • Re: AMBER: molecular structure (Tue Aug 26 2008 - 17:32:51 CDT)
  • Re: AMBER: Source FIles of SANDER (Tue Aug 26 2008 - 14:20:40 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 11:57:28 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 09:26:53 CDT)
  • Re: AMBER: Querry (Tue Aug 26 2008 - 09:09:25 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 11:35:53 CDT)
  • Re: AMBER: MOIL-View is for SGI. How do we analyze LES trajectories? (Sat Aug 23 2008 - 07:39:16 CDT)
  • Re: AMBER: vdw 6-9 potential (Sat Aug 23 2008 - 05:51:24 CDT)
  • Re: AMBER: vdw 6-9 potential (Fri Aug 22 2008 - 16:02:48 CDT)
  • Re: AMBER: Error runing Addles (Fri Aug 22 2008 - 07:48:07 CDT)
  • Re: AMBER: Force field equation (Thu Aug 21 2008 - 07:21:55 CDT)
  • Re: AMBER: MOIL-View: is there a command line version? (Wed Aug 20 2008 - 13:46:12 CDT)
  • Re: AMBER: Force field equation (Wed Aug 20 2008 - 12:53:03 CDT)
  • Re: AMBER: NMR average structure (Wed Aug 20 2008 - 12:50:28 CDT)
  • Re: AMBER: Questions about Locally enhanced sampling (LES) and Replica exchange (Wed Aug 20 2008 - 12:47:12 CDT)
  • Re: AMBER: amber9 hangas after job submission (Thu Aug 14 2008 - 05:45:14 CDT)
  • Re: AMBER: aggregation or cluster detection (Thu Aug 07 2008 - 10:38:52 CDT)
  • Re: AMBER: problem with minimization (Thu Aug 07 2008 - 10:29:10 CDT)
  • Re: AMBER: addles (Tue Aug 05 2008 - 06:02:47 CDT)
  • Re: AMBER: Problem with setting the NMR restraints (Mon Aug 04 2008 - 13:28:36 CDT)
  • Re: AMBER: Bonds getting shorter in sander (Fri Aug 01 2008 - 08:18:36 CDT)
• Carra, Claudio (JSC-SK)[USRA]
  • AMBER: MM-PBSA multiple trajectory problem (Wed Aug 27 2008 - 09:16:38 CDT)
  • RE: AMBER: NAB conjgrad returns error? (Mon Aug 11 2008 - 17:44:09 CDT)
  • RE: AMBER: NAB conjgrad returns error? (Mon Aug 11 2008 - 16:14:12 CDT)
  • RE: AMBER: NAB conjgrad returns error? (Thu Aug 07 2008 - 11:19:52 CDT)
  • AMBER: NAB conjgrad returns error? (Thu Aug 07 2008 - 10:04:38 CDT)
• Cenk \(Jenk\) Andac
  • Re: AMBER: installation amber on suse11.0 (Tue Aug 26 2008 - 09:40:30 CDT)
  • Re: AMBER: mol2, xleap, Segmentation fault (Mon Aug 25 2008 - 09:38:28 CDT)
• cgji
  • Re: AMBER: all & united atoms force field (Thu Aug 21 2008 - 17:28:49 CDT)
  • AMBER: Is G_disp calculated in MM_PBSA now? (Sat Aug 09 2008 - 07:51:55 CDT)
• Charles Letner, Ph.D.
  • AMBER: AMBER under cygwin on 64 bit Vista (Sun Aug 31 2008 - 16:30:08 CDT)
• Chih-Ying Lin
  • AMBER: molecular structure (Tue Aug 26 2008 - 17:24:29 CDT)
  • AMBER: pdb file ?? (Thu Aug 21 2008 - 01:21:47 CDT)
  • Re: AMBER: Force field equation (Thu Aug 21 2008 - 00:16:42 CDT)
  • AMBER: Force field equation (Wed Aug 20 2008 - 11:05:39 CDT)
• Daniel Cappel
  • Re: AMBER: modified parmtop file from ptraj? (Wed Aug 13 2008 - 08:37:19 CDT)
• David A. Case
  • Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! (Fri Aug 22 2008 - 22:11:14 CDT)
  • Re: AMBER: trying ff99SP (Wed Aug 20 2008 - 13:31:22 CDT)
  • Re: AMBER: Problem loading the leaprc.amoeba force field file in Amber 10. (Wed Aug 20 2008 - 12:24:17 CDT)
  • Re: AMBER: impropers over bonds between sidechains (Wed Aug 20 2008 - 12:14:03 CDT)
  • Re: AMBER: Proton Parameters (Wed Aug 20 2008 - 12:12:02 CDT)
  • Re: AMBER: MD with NMR restraints (Wed Aug 20 2008 - 12:07:15 CDT)
  • Re: AMBER: questions about previous posts (Sat Aug 16 2008 - 10:00:38 CDT)
  • Re: AMBER: Using RDCs for structure refinement (Tue Aug 12 2008 - 11:36:24 CDT)
  • Re: AMBER: NAB conjgrad returns error? (Mon Aug 11 2008 - 16:40:49 CDT)
  • Re: AMBER: Compailation problum in Amber 10 (Fri Aug 08 2008 - 17:50:55 CDT)
  • Re: AMBER: NMR structure as initial structure (Tue Aug 05 2008 - 19:09:25 CDT)
  • Re: AMBER: Set 251 is corrupted, ptraj error... (Mon Aug 04 2008 - 10:31:28 CDT)
  • Re: AMBER: Problem with setting the NMR restraints (Mon Aug 04 2008 - 10:26:51 CDT)
  • Re: AMBER: error in parallel amber 9 test (Sun Aug 03 2008 - 23:28:45 CDT)
  • Re: AMBER: error in parallel amber 9 test (Sat Aug 02 2008 - 20:37:10 CDT)
  • Re: AMBER: Compailation problum in Amber 10 (Fri Aug 01 2008 - 14:48:55 CDT)
• David LeBard
  • Re: AMBER: Compile AMBER 9 on TACC Ranger super computer (Thu Aug 14 2008 - 14:43:52 CDT)
• David Witte
  • AMBER: Using RDCs for structure refinement (Tue Aug 12 2008 - 02:52:53 CDT)
• Deepangi Pandit
  • AMBER: Solvent Accesible Surface Area (SASA) - Confused (Fri Aug 29 2008 - 13:45:19 CDT)
• dipti lele
  • Re: AMBER: Querry (Wed Aug 27 2008 - 08:33:45 CDT)
  • AMBER: querry (Wed Aug 27 2008 - 04:07:52 CDT)
  • Re: AMBER: Querry (Wed Aug 27 2008 - 04:00:46 CDT)
  • AMBER: Querry (Tue Aug 26 2008 - 06:50:32 CDT)
  • AMBER: Glycoprotein once again.......... (Thu Aug 14 2008 - 07:10:10 CDT)
  • AMBER: Querry (Wed Aug 13 2008 - 07:15:11 CDT)
  • AMBER: Querry about simulating a glycopeptide (Tue Aug 12 2008 - 05:23:24 CDT)
  • AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) (Tue Aug 05 2008 - 05:03:10 CDT)
• E.M.
  • Re: AMBER: Minimization methods (Mon Aug 11 2008 - 07:22:25 CDT)
• fatima.chami_at_durham.ac.uk
  • Re: AMBER: output file format in SANDER.MPI & PMEMD (Thu Aug 28 2008 - 07:53:42 CDT)
  • AMBER: output file format in SANDER.MPI & PMEMD (Thu Aug 28 2008 - 05:47:17 CDT)
  • Re: AMBER: vdw 6-9 potential (Tue Aug 26 2008 - 11:03:55 CDT)
  • Re: AMBER: vdw 6-9 potential (Sat Aug 23 2008 - 05:34:57 CDT)
  • AMBER: vdw 6-9 potential (Fri Aug 22 2008 - 15:56:57 CDT)
  • Re: AMBER: all & united atoms force field (Fri Aug 22 2008 - 15:46:11 CDT)
  • Re: AMBER: all & united atoms force field (Fri Aug 22 2008 - 08:31:34 CDT)
  • AMBER: all & united atoms force field (Thu Aug 21 2008 - 17:05:12 CDT)
  • AMBER: aggregation or cluster detection (Thu Aug 07 2008 - 08:41:24 CDT)
• Fiona McRobb
  • RE: [!!!] - Re: AMBER: GPCR membrane simulation, setting surface tension - Message is from an unknown sender (Wed Aug 13 2008 - 00:09:49 CDT)
  • AMBER: GPCR membrane simulation, setting surface tension (Mon Aug 11 2008 - 20:42:47 CDT)
• Florian Haberl
  • Re: AMBER: modified parmtop file from ptraj? (Wed Aug 13 2008 - 07:47:21 CDT)
• Francesco Pietra
  • AMBER: Parameters for chloride ion in contact with a protein (Mon Aug 25 2008 - 09:25:13 CDT)
  • AMBER: Biased MD with Amber 10 (Mon Aug 04 2008 - 13:35:31 CDT)
  • AMBER: PDB files in Amber10 (Sat Aug 02 2008 - 02:21:58 CDT)
• FyD
  • Re: AMBER: xleap fails to savemol2 (Sat Aug 30 2008 - 01:58:21 CDT)
  • Re: AMBER: xleap fails to savemol2 (Fri Aug 29 2008 - 16:14:42 CDT)
  • Re: AMBER: Problem in calculation of resp charges using RED III (Fri Aug 29 2008 - 10:19:23 CDT)
  • Re: AMBER: Problem in calculation of resp charges using RED III (Fri Aug 29 2008 - 02:50:42 CDT)
  • Re: AMBER: xleap fails to savemol2 (Thu Aug 28 2008 - 23:58:08 CDT)
• Geoff Wood
  • AMBER: amber 9 on Intel Harpertown (Wed Aug 13 2008 - 04:45:36 CDT)
• Gigil Toton
  • AMBER: net charge (Wed Aug 27 2008 - 00:03:19 CDT)
  • AMBER: NMR average structure (Wed Aug 20 2008 - 12:42:08 CDT)
  • AMBER: general question (Wed Aug 13 2008 - 01:49:12 CDT)
• Grange Hermitage
  • AMBER: RESP charges fitting for polarizable force fields (Sat Aug 30 2008 - 23:48:37 CDT)
  • AMBER: new residues in AMOEBA (Thu Aug 21 2008 - 02:14:59 CDT)
  • Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro (Mon Aug 18 2008 - 19:30:25 CDT)
  • Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro (Mon Aug 18 2008 - 04:01:38 CDT)
  • AMBER: trying ff99SP (Mon Aug 18 2008 - 01:12:33 CDT)
  • Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro (Mon Aug 18 2008 - 00:04:18 CDT)
  • Re: AMBER: Prepgen (Sun Aug 17 2008 - 22:22:32 CDT)
  • AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro (Sun Aug 17 2008 - 21:28:17 CDT)
  • Re: AMBER: Prepgen (Fri Aug 15 2008 - 01:12:50 CDT)
  • Re: AMBER: impropers over bonds between sidechains (Thu Aug 14 2008 - 22:08:49 CDT)
  • AMBER: impropers over bonds between sidechains (Thu Aug 14 2008 - 20:12:05 CDT)
  • Re: AMBER: Prepgen (Mon Aug 11 2008 - 02:10:00 CDT)
  • AMBER: respgen -a charge groups function ineffective unless (Sat Aug 02 2008 - 00:00:29 CDT)
• Hakkim Boy
  • AMBER: solvent interaction in active site (Wed Aug 27 2008 - 21:41:24 CDT)
• Hannes Wallnoefer
  • AMBER: modified parmtop file from ptraj? (Wed Aug 13 2008 - 07:14:34 CDT)
  • AMBER: PBCAL in MM_PBSA (Fri Aug 08 2008 - 09:19:30 CDT)
  • AMBER: MM_PBSA snapshot statistic calc problem (Tue Aug 05 2008 - 07:45:48 CDT)
• Henrik Öberg
  • AMBER: coordinate change of pdb structure using xleap (Wed Aug 27 2008 - 01:26:42 CDT)
• Ilyas Yildirim
  • RE: AMBER: to understand how frcmod.ff99SB works (Thu Aug 28 2008 - 16:58:03 CDT)
  • AMBER: Re: Dell 2 Quad Core System Performance (Wed Aug 27 2008 - 16:04:14 CDT)
  • AMBER: Dell 2 Quad Core System Performance (Fri Aug 22 2008 - 20:16:49 CDT)
  • AMBER: Negative dihedral coefficients in amber99 - Possible? (Sun Aug 17 2008 - 21:33:16 CDT)
• In Hee Park
  • AMBER: IGB=10 in Amber10 (Tue Aug 19 2008 - 13:55:05 CDT)
• IN SUK JOUNG
  • AMBER: NAB: getseq_from_pdb() (Tue Aug 05 2008 - 19:00:21 CDT)
  • AMBER: divcon.rst ?? (Mon Aug 04 2008 - 19:06:43 CDT)
• Jaber Jahanbin Sardroodi
  • AMBER: help me for filling a nanotube with water?? (Mon Aug 04 2008 - 20:39:05 CDT)
  • Re: AMBER: error in parallel amber 9 test (Sun Aug 03 2008 - 03:15:19 CDT)
  • AMBER: error in parallel amber 9 test (Sat Aug 02 2008 - 16:12:07 CDT)
• Jacopo Sgrignani
  • AMBER: tan luo radii (Tue Aug 26 2008 - 04:06:39 CDT)
• Jeffrey
  • Re: Re: RE: AMBER: How to convert a CHARMM trajectory to AMBER format? (Thu Aug 21 2008 - 02:11:55 CDT)
  • Re: RE: AMBER: How to convert a CHARMM trajectory to AMBER format? (Tue Aug 19 2008 - 19:43:58 CDT)
  • AMBER: How to convert a CHARMM trajectory to AMBER format? (Tue Aug 19 2008 - 06:30:35 CDT)
• jialei
  • RE: AMBER: Compile AMBER 9 on TACC Ranger super computer (Fri Aug 15 2008 - 11:38:38 CDT)
  • RE: AMBER: Compile AMBER 9 on TACC Ranger super computer (Thu Aug 14 2008 - 19:15:39 CDT)
  • AMBER: Compile AMBER 9 on TACC Ranger super computer (Wed Aug 13 2008 - 17:26:07 CDT)
• Jianyin Shao
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Sat Aug 02 2008 - 21:23:53 CDT)
  • Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 (Fri Aug 01 2008 - 14:43:14 CDT)
• john smith
  • AMBER: compilation problem (Sat Aug 30 2008 - 06:51:07 CDT)
• Jose Borreguero
  • AMBER: conversion from crd to netcdf returns almost identical file! (Thu Aug 28 2008 - 15:38:50 CDT)
• Junmei Wang
  • Re: AMBER: respgen -a charge groups function ineffective unless (Wed Aug 27 2008 - 15:55:47 CDT)
  • AMBER: latest update on residuegen (Tue Aug 26 2008 - 08:55:09 CDT)
  • Re: AMBER: Silicon parameters (Fri Aug 22 2008 - 15:29:05 CDT)
  • Re: AMBER: Prepgen (Fri Aug 15 2008 - 08:52:27 CDT)
  • Re: AMBER: frcmod:attn needs revision (Wed Aug 13 2008 - 14:34:50 CDT)
  • Re: AMBER: problem with prep file generation (Wed Aug 13 2008 - 11:59:49 CDT)
  • Re: AMBER: frcmod:attn needs revision (Wed Aug 13 2008 - 11:45:11 CDT)
  • Re: AMBER: Prepgen (Tue Aug 12 2008 - 17:30:45 CDT)
  • Re: AMBER: Prepgen (Tue Aug 05 2008 - 10:50:00 CDT)
• khuram sb
  • AMBER: unsubscribe (Mon Aug 18 2008 - 03:56:36 CDT)
• Lachele Foley (Lists)
  • Re: AMBER: Glycoprotein once again.......... (Thu Aug 14 2008 - 08:28:30 CDT)
  • Re: AMBER: Querry (Wed Aug 13 2008 - 10:03:49 CDT)
  • Re: AMBER: Querry about simulating a glycopeptide (Tue Aug 12 2008 - 09:03:14 CDT)
  • Re: AMBER: aggregation or cluster detection (Thu Aug 07 2008 - 10:44:07 CDT)
  • Fwd: AMBER: prepare an initial structure in Amber (Fri Aug 01 2008 - 09:52:50 CDT)
• Lars Skjærven
  • Re: AMBER: pmemd iwrap trouble (Thu Aug 28 2008 - 05:38:02 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 13:36:06 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 11:23:31 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 17:03:14 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 09:58:01 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 08:32:26 CDT)
  • AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 05:25:09 CDT)
• luzhenw1_at_msu.edu
  • AMBER: generate topology file for alanine scanning (mmpbsa) (Thu Aug 14 2008 - 14:32:56 CDT)
  • AMBER: problem with minimization (Thu Aug 07 2008 - 10:13:17 CDT)
• M. L. Dodson
  • AMBER: DFTB QMMM parameters ambiguity in AMBER10 docs (Thu Aug 21 2008 - 12:56:38 CDT)
  • Re: AMBER: impropers over bonds between sidechains (Thu Aug 14 2008 - 21:29:54 CDT)
  • Re: AMBER: Help compiling Nab programs for AMBER tools (Thu Aug 14 2008 - 14:50:51 CDT)
  • Re: AMBER: Minimization methods (Mon Aug 11 2008 - 10:34:05 CDT)
• Maicon Sartin
  • Re: AMBER: Source FIles of SANDER (Wed Aug 27 2008 - 07:47:47 CDT)
  • Re: AMBER: Source FIles of SANDER (Tue Aug 26 2008 - 18:18:49 CDT)
  • AMBER: Source FIles of SANDER (Tue Aug 26 2008 - 14:17:39 CDT)
  • AMBER: Source FIles of SANDER (Tue Aug 26 2008 - 14:17:39 CDT)
  • Re: AMBER: installation amber on suse11.0 (Tue Aug 26 2008 - 09:52:01 CDT)
  • AMBER: SANDER Parallel (Thu Aug 21 2008 - 07:36:56 CDT)
  • AMBER: Fwd: Welcome to amber (Thu Aug 21 2008 - 07:33:08 CDT)
• Markus Kaukonen
  • Re: AMBER: help me for filling a nanotube with water?? (Wed Aug 13 2008 - 01:29:48 CDT)
• Matthew Tessier
  • RE: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) (Tue Aug 05 2008 - 10:07:22 CDT)
• Melinda Layten
  • Re: AMBER: to understand how frcmod.ff99SB works (Thu Aug 28 2008 - 09:55:40 CDT)
• Miguel Ortiz-Lombardía
  • Re: AMBER: mm-pbsa / sander.MPI ? (Thu Aug 14 2008 - 02:58:54 CDT)
• moitrayee_at_mbu.iisc.ernet.in
  • Re: AMBER: Problem in calculation of resp charges using RED III (Fri Aug 29 2008 - 06:41:21 CDT)
  • AMBER: Problem in calculation of resp charges using RED III (Fri Aug 29 2008 - 01:56:24 CDT)
  • Re: AMBER: frcmod:attn needs revision (Wed Aug 13 2008 - 23:51:50 CDT)
  • Re: AMBER: frcmod:attn needs revision (Wed Aug 13 2008 - 11:55:40 CDT)
  • Re: AMBER: empty frcmod file but missing parameters (Tue Aug 12 2008 - 17:10:03 CDT)
  • AMBER: frcmod:attn needs revision (Tue Aug 12 2008 - 17:18:02 CDT)
  • AMBER: empty frcmod file but missing parameters (Tue Aug 12 2008 - 16:20:19 CDT)
• Naser Alijabbari
  • AMBER: questions about previous posts (Mon Aug 11 2008 - 23:17:40 CDT)
• Neil J. Henson
  • Re: AMBER: Problems with sleap and amoeba (Tue Aug 19 2008 - 19:03:52 CDT)
  • AMBER: Problems with sleap and amoeba (Tue Aug 19 2008 - 18:16:17 CDT)
• NIEL MICHAEL HENRIKSEN
  • RE: AMBER: NAB conjgrad returns error? (Mon Aug 11 2008 - 18:07:27 CDT)
  • RE: AMBER: NAB conjgrad returns error? (Fri Aug 08 2008 - 14:31:13 CDT)
  • RE: AMBER: NAB conjgrad returns error? (Fri Aug 08 2008 - 08:50:05 CDT)
• Pablo Englebienne
  • Re: AMBER: Using Na+ ions as input to leap? - solved (Wed Aug 20 2008 - 14:25:25 CDT)
  • AMBER: Using Na+ ions as input to leap? (Wed Aug 20 2008 - 12:40:11 CDT)
• Peter Gannett
  • AMBER: Bonds getting shorter in sander (Fri Aug 01 2008 - 07:47:02 CDT)
• Peterson, Matthew W.
  • AMBER: MM-PBSA Issue in Amber 10 (Tue Aug 12 2008 - 12:44:29 CDT)
• Piyush Wanjari
  • Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! (Mon Aug 25 2008 - 17:00:33 CDT)
  • Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! (Mon Aug 25 2008 - 14:52:37 CDT)
  • AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! (Wed Aug 20 2008 - 23:36:20 CDT)
• priya priya
  • AMBER: Membrane simulations (Thu Aug 28 2008 - 03:31:57 CDT)
• Ragnarok sdf
  • AMBER: Help compiling Nab programs for AMBER tools (Thu Aug 14 2008 - 14:36:04 CDT)
• Ranga Swamy
  • RE: AMBER: Compailation problum in Amber 10 (Fri Aug 08 2008 - 03:12:56 CDT)
• Ray Luo
  • RE: AMBER: united atom force field (Tue Aug 26 2008 - 18:11:47 CDT)
  • RE: AMBER: tan luo radii (Tue Aug 26 2008 - 14:12:57 CDT)
  • Re: AMBER: all & united atoms force field (Fri Aug 22 2008 - 12:44:16 CDT)
  • Re: AMBER: united atom force field (Fri Aug 22 2008 - 12:37:38 CDT)
  • RE: AMBER: Is G_disp calculated in MM_PBSA now? (Mon Aug 11 2008 - 14:33:14 CDT)
  • RE: AMBER: PBCAL in MM_PBSA (Fri Aug 08 2008 - 13:27:17 CDT)
• rebeca_at_mmb.pcb.ub.es
  • AMBER: minimization stops or does not write anything (Thu Aug 14 2008 - 04:01:17 CDT)
  • AMBER: Not integral charge increasing with number of lipids (Thu Aug 07 2008 - 05:18:01 CDT)
  • AMBER: Problems with the charge (membrane simulation) (Wed Aug 06 2008 - 13:20:30 CDT)
• Robert Duke
  • Re: AMBER: Critical patch for pmemd 10 extra points code (Sun Aug 31 2008 - 11:48:56 CDT)
  • Re: AMBER: pmemd iwrap trouble (Thu Aug 28 2008 - 17:05:05 CDT)
  • AMBER: Critical patch for pmemd 10 extra points code (Thu Aug 28 2008 - 10:20:59 CDT)
  • Re: AMBER: output file format in SANDER.MPI & PMEMD (Thu Aug 28 2008 - 07:34:44 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 22:17:29 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 14:49:18 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 11:59:34 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 23:38:40 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 23:22:44 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 22:38:13 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 10:45:03 CDT)
  • Re: AMBER: pmemd iwrap trouble (Mon Aug 25 2008 - 07:40:03 CDT)
  • Re: AMBER: amber9 hangas after job submission (Thu Aug 14 2008 - 07:54:43 CDT)
  • Re: AMBER: minimization stops or does not write anything (Thu Aug 14 2008 - 07:39:01 CDT)
• Ross Walker
  • RE: AMBER: vlimit exceeded (Sat Aug 30 2008 - 13:41:02 CDT)
  • RE: AMBER: compilation problem (Sat Aug 30 2008 - 13:33:13 CDT)
  • RE: AMBER: to understand how frcmod.ff99SB works (Fri Aug 29 2008 - 10:17:27 CDT)
  • RE: AMBER: output file format in SANDER.MPI & PMEMD (Thu Aug 28 2008 - 12:09:38 CDT)
  • RE: AMBER: to understand how frcmod.ff99SB works (Thu Aug 28 2008 - 11:59:09 CDT)
  • AMBER: RE: Personal favor (Thu Aug 28 2008 - 11:39:59 CDT)
  • RE: AMBER: Re: Dell 2 Quad Core System Performance (Wed Aug 27 2008 - 18:01:59 CDT)
  • RE: AMBER: Source FIles of SANDER (Tue Aug 26 2008 - 18:57:55 CDT)
  • RE: AMBER: installation amber on suse11.0 (Tue Aug 26 2008 - 09:39:31 CDT)
  • RE: AMBER: How to convert a CHARMM trajectory to AMBER format? (Tue Aug 19 2008 - 09:26:25 CDT)
  • RE: AMBER: Initial structure from NMR structures (Tue Aug 19 2008 - 09:05:43 CDT)
  • RE: AMBER: Negative dihedral coefficients in amber99 - Possible? (Mon Aug 18 2008 - 00:15:45 CDT)
  • RE: AMBER: Compile AMBER 9 on TACC Ranger super computer (Fri Aug 15 2008 - 12:36:36 CDT)
  • RE: AMBER: Compile AMBER 9 on TACC Ranger super computer (Thu Aug 14 2008 - 19:38:30 CDT)
  • RE: AMBER: Compile AMBER 9 on TACC Ranger super computer (Thu Aug 14 2008 - 11:00:02 CDT)
  • RE: AMBER: Compile AMBER 9 on TACC Ranger super computer (Wed Aug 13 2008 - 22:39:47 CDT)
  • RE: AMBER: Querry (Wed Aug 13 2008 - 09:48:19 CDT)
  • RE: AMBER: amber 9 on Intel Harpertown (Wed Aug 13 2008 - 09:24:47 CDT)
  • RE: AMBER: questions about previous posts (Tue Aug 12 2008 - 01:18:49 CDT)
  • RE: AMBER: Minimization methods (Mon Aug 11 2008 - 09:43:47 CDT)
  • RE: AMBER: problem with minimization (Thu Aug 07 2008 - 10:40:46 CDT)
  • RE: AMBER: aggregation or cluster detection (Thu Aug 07 2008 - 10:29:28 CDT)
  • RE: AMBER: Not integral charge increasing with number of lipids (Thu Aug 07 2008 - 10:24:28 CDT)
  • RE: AMBER: Problems with the charge (membrane simulation) (Thu Aug 07 2008 - 10:18:12 CDT)
  • RE: AMBER: Compailation problum in Amber 10 (Wed Aug 06 2008 - 09:50:05 CDT)
• Ruchi Sachdeva
  • AMBER: how to choose the appropriate ensemble for a given problem (Wed Aug 13 2008 - 23:09:28 CDT)
• Sally Pias
  • AMBER: MD with NMR restraints (Wed Aug 13 2008 - 23:25:56 CDT)
• Sampath Koppole
  • AMBER: Trouble installing Amber 9 (Wed Aug 20 2008 - 05:28:58 CDT)
• Samuel Genheden (a03samge)
  • RE: AMBER: Bennett acceptance ratio with Amber10 (Wed Aug 27 2008 - 01:04:28 CDT)
  • AMBER: Bennett acceptance ratio with Amber10 (Tue Aug 26 2008 - 06:58:13 CDT)
• Sasha Buzko
  • Re: AMBER: Is there a way to cluster frames of a trajectory? (Wed Aug 27 2008 - 19:57:07 CDT)
  • AMBER: Is there a way to cluster frames of a trajectory? (Wed Aug 27 2008 - 19:45:01 CDT)
  • Re: AMBER: MOIL-View is for SGI. How do we analyze LES trajectories? (Sat Aug 23 2008 - 15:19:07 CDT)
  • AMBER: MOIL-View is for SGI. How do we analyze LES trajectories? (Wed Aug 20 2008 - 17:42:01 CDT)
  • Re: AMBER: MOIL-View: is there a command line version? (Wed Aug 20 2008 - 13:50:39 CDT)
  • AMBER: MOIL-View: is there a command line version? (Wed Aug 20 2008 - 13:35:24 CDT)
  • AMBER: Simulating protein conformational changes? (Fri Aug 01 2008 - 17:42:07 CDT)
• saurabh agrawal
  • Re: AMBER: coordinate change of pdb structure using xleap (Wed Aug 27 2008 - 02:23:09 CDT)
• Scott Brozell
  • Re: AMBER: value of Pi in Amber (Tue Aug 26 2008 - 17:07:49 CDT)
  • Re: AMBER: PDB files in Amber10 (Mon Aug 25 2008 - 16:32:16 CDT)
• selami ercan
  • Re: AMBER: installation amber on suse11.0 (Wed Aug 27 2008 - 13:50:13 CDT)
  • AMBER: installation amber on suse11.0 (Tue Aug 26 2008 - 05:57:12 CDT)
• shubhra srivastava
  • AMBER: constant ph (cpinutil file) (Wed Aug 27 2008 - 01:46:36 CDT)
  • AMBER: constph (Thu Aug 14 2008 - 06:54:57 CDT)
• Shultz, Jack
  • AMBER: Error runing Addles (Thu Aug 21 2008 - 22:25:17 CDT)
  • RE: AMBER: Amber compile (Tue Aug 19 2008 - 14:25:56 CDT)
  • AMBER: Amber compile (Tue Aug 19 2008 - 13:21:18 CDT)
  • AMBER: Compile Error (Tue Aug 19 2008 - 10:44:25 CDT)
  • AMBER: Proton Parameters (Thu Aug 14 2008 - 15:34:54 CDT)
• Siddharth Rastogi
  • AMBER: Initial structure from NMR structures (Tue Aug 19 2008 - 01:15:44 CDT)
  • AMBER: NMR structure as initial structure (Tue Aug 05 2008 - 01:40:54 CDT)
• srinivas sudani
  • AMBER: Compailation problum in Amber 10 (Wed Aug 06 2008 - 04:24:51 CDT)
  • Re: AMBER: Compailation problum in Amber 10 (Mon Aug 04 2008 - 00:41:13 CDT)
  • AMBER: Compailation problum in Amber 10 (Fri Aug 01 2008 - 01:59:00 CDT)
• steinbrt_at_scripps.edu
  • RE: AMBER: Bennett acceptance ratio with Amber10 (Wed Aug 27 2008 - 11:28:13 CDT)
  • Re: AMBER: Bennett acceptance ratio with Amber10 (Tue Aug 26 2008 - 08:45:55 CDT)
• Swarup Gupta
  • AMBER: Re: entropy of released water (Thu Aug 07 2008 - 07:40:26 CDT)
  • AMBER: entropy of released water (Thu Aug 07 2008 - 07:36:32 CDT)
• taufik.alsarraj_at_utoronto.ca
  • Re: AMBER: xleap fails to savemol2 (Fri Aug 29 2008 - 16:28:52 CDT)
  • AMBER: join two units in amber9 or amber10 (Fri Aug 29 2008 - 16:17:58 CDT)
  • Re: AMBER: xleap fails to savemol2 (Fri Aug 29 2008 - 12:28:33 CDT)
  • AMBER: xleap fails to savemol2 (Thu Aug 28 2008 - 17:43:07 CDT)
• teresa.ierano_at_unina.it
  • Re: AMBER: Minimization methods (Mon Aug 11 2008 - 11:39:30 CDT)
  • RE: AMBER: Minimization methods (Mon Aug 11 2008 - 11:30:50 CDT)
  • AMBER: Minimization methods (Mon Aug 11 2008 - 07:11:23 CDT)
• Thomas Cheatham
  • Re: AMBER: modified parmtop file from ptraj? (Wed Aug 13 2008 - 12:43:24 CDT)
• Thomas Cheatham III
  • Re: AMBER: pmemd iwrap trouble (Thu Aug 28 2008 - 16:47:51 CDT)
  • Re: AMBER: pmemd iwrap trouble (Tue Aug 26 2008 - 11:48:04 CDT)
• Thomas Leonard
  • AMBER: PBCAL in MM_PBSA (Mon Aug 11 2008 - 03:12:51 CDT)
  • AMBER: parameters (Fri Aug 08 2008 - 00:45:09 CDT)
• Thomas Steinbrecher
  • Re: AMBER: help me for filling a nanotube with water?? (Wed Aug 13 2008 - 11:40:22 CDT)
• Titus, Jamie (bairdje)
  • AMBER: Gohlke in-house iRED Simulated Order Parameter Script (Thu Aug 21 2008 - 07:53:09 CDT)
• Urszula Uciechowska
  • AMBER: LES trajectories (Mon Aug 25 2008 - 03:12:23 CDT)
  • AMBER: mmpbsa (Mon Aug 11 2008 - 03:43:17 CDT)
  • AMBER: LES (Fri Aug 08 2008 - 07:31:56 CDT)
  • AMBER: linear interaction energy (Thu Aug 07 2008 - 08:55:18 CDT)
  • AMBER: addles (Tue Aug 05 2008 - 03:30:20 CDT)
• Vijay Manickam Achari
  • AMBER: amber9 hangas after job submission (Thu Aug 14 2008 - 01:40:03 CDT)
• Vlad Cojocaru
  • Re: AMBER: GPCR membrane simulation, setting surface tension (Tue Aug 12 2008 - 03:45:08 CDT)
• Wang,Ying
  • RE: AMBER: vlimit exceeded (Sat Aug 30 2008 - 18:14:21 CDT)
  • AMBER: vlimit exceeded (Sat Aug 30 2008 - 10:49:03 CDT)
• Waqas Nasir
  • Re: AMBER: Set 251 is corrupted, ptraj error... (Tue Aug 05 2008 - 06:23:47 CDT)
  • AMBER: Set 251 is corrupted, ptraj error... (Mon Aug 04 2008 - 09:54:09 CDT)
• Wei Huang
  • Re: AMBER: How to convert a CHARMM trajectory to AMBER format? (Tue Aug 19 2008 - 09:02:22 CDT)
• Wenyong Tong
  • Re: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) (Tue Aug 05 2008 - 14:32:31 CDT)
  • Re: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) (Tue Aug 05 2008 - 09:51:31 CDT)
• xiaonan zhang
  • AMBER: Questions about Locally enhanced sampling (LES) and Replica exchange (Wed Aug 20 2008 - 02:25:43 CDT)
• Yong Duan
  • RE: AMBER: all & united atoms force field (Fri Aug 22 2008 - 19:39:23 CDT)
• Zhao, Zhen (zhaozh)
  • AMBER: Problem with the prmtop file generated by sleap and leaprc.amoeba in Amber 10. (Mon Aug 25 2008 - 10:04:34 CDT)
  • AMBER: Problem loading the leaprc.amoeba force field file in Amber 10. (Tue Aug 19 2008 - 15:20:00 CDT)
• ÕÅÓÂ
  • Re:AMBER: Compile AMBER 9 on TACC Ranger super computer (Thu Aug 14 2008 - 08:32:30 CDT)
  • Re:AMBER: Compile AMBER 9 on TACC Ranger super computer (Thu Aug 14 2008 - 08:32:30 CDT)

Last message date: Wed Dec 31 2008 - 22:47:27 CST
Archived on: Thu Jan 08 2009 - 16:01:48 CST