AMBER Archive (2007) - Mar 2007 By ThreadMost recent messages
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About this archive
Starting: Thu Mar 01 2007 - 06:10:55 CST
Ending: Sat Mar 31 2007 - 22:13:48 CST
- AMBER: Disulfide Problem Beale, John (Thu Mar 01 2007 - 07:49:22 CST)
- AMBER: Restart from restart file obtained from ptraj with added velocities j j (Thu Mar 01 2007 - 10:17:41 CST)
- AMBER: [rsachdeva@imtech.res.in: A query] David A. Case (Thu Mar 01 2007 - 11:02:27 CST)
- AMBER: qm/mm ti Ben Sattelle (Fri Mar 02 2007 - 07:54:53 CST)
- AMBER: Restart Files Steve Seibold (Fri Mar 02 2007 - 09:26:03 CST)
- AMBER: restraints during MD Seth Lilavivat (Fri Mar 02 2007 - 10:16:05 CST)
- AMBER: reproducibility between software Stern, Julie (Fri Mar 02 2007 - 10:34:32 CST)
- AMBER: Amber 9 make parallel fails with mpich Rene Salmon (Fri Mar 02 2007 - 11:45:37 CST)
- AMBER: ptraj average structure strip water Youyi Peng (Fri Mar 02 2007 - 13:52:02 CST)
- AMBER: Calcium parameters Lei Jia (Fri Mar 02 2007 - 13:58:27 CST)
- AMBER: Restraints on modified NA's Seth Lilavivat (Fri Mar 02 2007 - 15:56:07 CST)
- AMBER: calculate RMSD of only chain C ÕÔÑÇÑ© (Fri Mar 02 2007 - 20:21:33 CST)
- AMBER: TI calculation: charge is not zero in the perturbed state brmeher_at_iitg.ernet.in (Sat Mar 03 2007 - 14:32:02 CST)
- AMBER: denaturing salt conditions Sean Rathlef (Sat Mar 03 2007 - 16:35:45 CST)
- AMBER: Question about translational and rotational degree of freedom in MM-PBSA v9 computations Cenk Andac (Sun Mar 04 2007 - 06:06:22 CST)
- AMBER: prep file limit exceeding gurpreet singh (Mon Mar 05 2007 - 01:52:49 CST)
- AMBER: distance calculation! r. a. (Mon Mar 05 2007 - 02:43:45 CST)
- AMBER: psi , phi angles deepti nayar (Mon Mar 05 2007 - 05:07:41 CST)
- AMBER: pbsa installation problem bala (Mon Mar 05 2007 - 06:34:32 CST)
- AMBER: Beale, John (Mon Mar 05 2007 - 11:50:26 CST)
- AMBER: Beale, John (Mon Mar 05 2007 - 11:51:29 CST)
- AMBER: constraint pdb file Stern, Julie (Mon Mar 05 2007 - 15:06:47 CST)
- AMBER: mm_pbsa individual contributions of residues AYTUG TUNCEL (Mon Mar 05 2007 - 17:12:54 CST)
- AMBER: how to incorporate ismem =1 into mm_pbsa AYTUG TUNCEL (Mon Mar 05 2007 - 17:32:19 CST)
- AMBER: any general approach to create SiO2 wall Sisir Das (Mon Mar 05 2007 - 22:46:42 CST)
- AMBER: Trimannoside Problem Sandeep Kaushik (Tue Mar 06 2007 - 06:44:20 CST)
- AMBER: how is the standard deviations calculated in mm-pbsa? Magne Olufsen (Tue Mar 06 2007 - 06:58:17 CST)
- AMBER: DHAS_10_12 compilation aborted for egb.f Jesus Angulo (Tue Mar 06 2007 - 08:31:28 CST)
- AMBER: how to modify map.DG-AMBER file? Seth Lilavivat (Tue Mar 06 2007 - 14:55:40 CST)
- AMBER: addles segmentation fault deepti nayar (Wed Mar 07 2007 - 01:18:39 CST)
- AMBER: Topology file problem in TI ! Pradipta Bandyopadhyay (Wed Mar 07 2007 - 05:08:39 CST)
- Re: AMBER: Amber 9, sander imin = 5, -y flag S.Sundar Raman (Wed Mar 07 2007 - 12:05:19 CST)
- AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat? Chengwen Chen (Fri Mar 09 2007 - 02:04:00 CST)
- AMBER: problem with ptraj with calculating auto time correlation functions Terry Lang (Fri Mar 09 2007 - 12:36:14 CST)
- AMBER: abnormal termination of tleap Pankaj R. Daga (Fri Mar 09 2007 - 16:24:37 CST)
- AMBER: rmsd calculation in ptraj gurpreet singh (Sat Mar 10 2007 - 07:24:50 CST)
- AMBER: rmsd calculation in ptraj gurpreet singh (Sat Mar 10 2007 - 07:38:28 CST)
- AMBER: rmsd calculation in ptraj II gurpreet singh (Sat Mar 10 2007 - 22:37:10 CST)
- AMBER: unable to run test Anju Sharma (Sun Mar 11 2007 - 23:14:03 CST)
- AMBER: addles deepti nayar (Mon Mar 12 2007 - 00:29:37 CST)
- AMBER: Essential ions and water molecules in MMPBSA computations Cenk Andac (Mon Mar 12 2007 - 03:13:56 CST)
- AMBER: NEB tutorial deepti nayar (Mon Mar 12 2007 - 04:03:17 CST)
- AMBER: The parallel test fails while sander.MPI seems to be installed correctly Mostafa Sadighi (Mon Mar 12 2007 - 05:43:14 CST)
- AMBER: DNA Helicoïdal Plots over time Stéphane Téletchéa (Mon Mar 12 2007 - 06:31:02 CST)
- AMBER: Can I measure improper torsion by ptarj? Chengwen Chen (Mon Mar 12 2007 - 10:21:55 CST)
- AMBER: hi.. Anju Sharma (Tue Mar 13 2007 - 05:59:24 CST)
- AMBER: problem with mm_pbsa Yves Boulard (Tue Mar 13 2007 - 08:21:22 CST)
- AMBER: poor performance of sander on a quad-core linux machine Lillian chong (Tue Mar 13 2007 - 11:27:31 CST)
- AMBER: problem while running minimisation Anju Sharma (Tue Mar 13 2007 - 22:10:15 CST)
- AMBER: Problem Solved Anju Sharma (Tue Mar 13 2007 - 22:19:57 CST)
- AMBER: NEB tutorial and addles deepti nayar (Tue Mar 13 2007 - 22:28:20 CST)
- AMBER: problem while analysing result Anju Sharma (Tue Mar 13 2007 - 23:38:37 CST)
- AMBER: Need help in Analysis Anju Sharma (Wed Mar 14 2007 - 03:13:03 CST)
- AMBER: torsion angle deepti nayar (Wed Mar 14 2007 - 06:03:08 CST)
- AMBER: Question about Boron Kara Di Giorgio (Wed Mar 14 2007 - 11:15:22 CST)
- AMBER: mmpbsa free energy pairwise decomposition Gianluca Degliesposti (Wed Mar 14 2007 - 12:54:32 CST)
- AMBER: Regarding counter ions Rafi Ahmad (Wed Mar 14 2007 - 14:00:59 CST)
- AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) Eric Shamay (Wed Mar 14 2007 - 19:12:49 CST)
- AMBER: How to build organic compound in Amber Anju Sharma (Wed Mar 14 2007 - 22:24:09 CST)
- AMBER: hii Anju Sharma (Thu Mar 15 2007 - 03:28:47 CST)
- AMBER: Problem related simulation of dimer priya priya (Thu Mar 15 2007 - 05:23:31 CST)
- AMBER: Dipolar and Inertia Moments kepa koldo burusco (Thu Mar 15 2007 - 05:46:17 CST)
- AMBER: solvate shell janavi raghavan (Thu Mar 15 2007 - 10:33:13 CST)
- AMBER: van der waals parameters. Stefano Tonzani (Thu Mar 15 2007 - 11:52:09 CST)
- AMBER: Segmentation Fault when saving prmtop and inpcrd files in xleap Laura McDriscoll (Thu Mar 15 2007 - 23:59:33 CST)
- AMBER: hi Anju Sharma (Fri Mar 16 2007 - 04:50:44 CST)
- AMBER: vlimit error Amit Kumar (Fri Mar 16 2007 - 17:10:06 CST)
- AMBER: antechamber error Ilyas Yildirim (Sat Mar 17 2007 - 00:44:57 CST)
- AMBER: targeted MD problem gurpreet singh (Sat Mar 17 2007 - 06:17:27 CST)
- AMBER: targetedMD problem gurpreet singh (Sun Mar 18 2007 - 07:32:40 CST)
- AMBER: antechamber Ilyas Yildirim (Sun Mar 18 2007 - 11:56:00 CST)
- AMBER: hi Anju Sharma (Sun Mar 18 2007 - 21:56:22 CST)
- AMBER: Problem while creating structure in xLeap Anju Sharma (Sun Mar 18 2007 - 22:30:03 CST)
- AMBER: Problem!! Anju Sharma (Mon Mar 19 2007 - 00:38:15 CST)
- AMBER: MM-GBSA residues decomposition comparison Sergey Samsonov (Tue Mar 20 2007 - 08:17:26 CST)
- AMBER: basis set for RESP calculation Michel Becker (Tue Mar 20 2007 - 14:43:10 CST)
- AMBER: Problem while loading Pdb in xleap Anju Sharma (Tue Mar 20 2007 - 22:12:55 CST)
- AMBER: Problem while running Antechamber Anju Sharma (Wed Mar 21 2007 - 03:35:28 CST)
- AMBER: Modified Nucleic Acid Problem SHARAD gupta (Wed Mar 21 2007 - 07:22:10 CST)
- AMBER: How to reimage the trajectories of LES calculations? Kailee (Wed Mar 21 2007 - 07:35:06 CST)
- AMBER: ntt=1 or ntt= 3? Therese Malliavin (Wed Mar 21 2007 - 11:32:07 CST)
- AMBER: xLeAP: TI calculation: the perturbed charge is not integral Ignacio Faustino (Wed Mar 21 2007 - 13:17:12 CST)
- AMBER: TI calculation: the perturbed charge is not integral Ignacio Faustino (Wed Mar 21 2007 - 13:21:52 CST)
- AMBER: restraint in minimization deepti nayar (Thu Mar 22 2007 - 02:21:32 CST)
- AMBER: Holding NA Base syn during annealing Seth Lilavivat (Thu Mar 22 2007 - 09:23:20 CST)
- AMBER: Generating structure of polyethylene glycol in AMBER Lili Peng (Thu Mar 22 2007 - 15:35:07 CST)
- Re: AMBER: sander/topology problem Jin-Soo Kim (Fri Mar 23 2007 - 08:31:00 CST)
- AMBER: anneal algorthm Seth Lilavivat (Fri Mar 23 2007 - 13:33:42 CST)
- AMBER: Error - must define AMBERHOME environment variable bertrand russell (Fri Mar 23 2007 - 14:05:47 CST)
- AMBER: Combining RESP with AM1-BCC Ilyas Yildirim (Fri Mar 23 2007 - 15:41:04 CST)
- AMBER: water density Esther Brugger (Fri Mar 23 2007 - 16:47:33 CST)
- AMBER: amber 9 - output of forces Eric Shamay (Fri Mar 23 2007 - 17:00:39 CST)
- AMBER: Does Sander.MPI support coupling effect between different molecules at the same area at the same temperature in the mixture? Jin-Soo Kim (Sat Mar 24 2007 - 05:40:26 CST)
- AMBER: Please check the total charge and your -nc flag snoze pa (Sun Mar 25 2007 - 22:54:52 CST)
- AMBER: phe-phe simulation deepti nayar (Mon Mar 26 2007 - 01:25:19 CST)
- AMBER: pmemd segmentation fault Vlad Cojocaru (Mon Mar 26 2007 - 03:14:50 CST)
- AMBER: DNA Flat Angle Restraints Kyle L. Brown (Mon Mar 26 2007 - 11:04:09 CST)
- AMBER: pdb file produced by vmd Rita Cassia (Mon Mar 26 2007 - 10:04:19 CST)
- AMBER: distcovar in ptraj Zhenyu Lu (Mon Mar 26 2007 - 22:00:13 CST)
- AMBER: Parameter file for Dipeptide Neelanjana Sengupta (Mon Mar 26 2007 - 23:23:32 CST)
- AMBER: The ring number exceeds MAXRING, increase MAXRING and recompile the programs, exit j j (Tue Mar 27 2007 - 08:04:48 CST)
- AMBER: Question about loadMol2 David LeBard (Tue Mar 27 2007 - 12:31:56 CST)
- AMBER: amber 9 install: patch reject Stern, Julie (Tue Mar 27 2007 - 12:50:33 CST)
- AMBER: amber 9: fortran/test failures Stern, Julie (Tue Mar 27 2007 - 12:55:43 CST)
- AMBER: residue types for GLY/high pH Stern, Julie (Tue Mar 27 2007 - 14:19:47 CST)
- AMBER: Amber 9 TI Details Lachele Foley (Lists) (Tue Mar 27 2007 - 15:03:20 CST)
- AMBER: specifying psi and phi for a dipeptide deepti nayar (Wed Mar 28 2007 - 05:50:28 CST)
- AMBER: DISAVE value1 Kyle L. Brown (Wed Mar 28 2007 - 15:42:16 CST)
- AMBER: rms and rmsf in ptraj Mingfeng Yang (Wed Mar 28 2007 - 15:06:02 CST)
- AMBER: problem in implcit simulation gurpreet singh (Wed Mar 28 2007 - 22:25:53 CST)
- AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up) Vlad Cojocaru (Thu Mar 29 2007 - 03:50:29 CST)
- AMBER: minimization not running deepti nayar (Thu Mar 29 2007 - 03:57:15 CST)
- AMBER: minimization energy query deepti nayar (Thu Mar 29 2007 - 04:55:39 CST)
- AMBER: is possible to compile pmemd using scali MPI? Andrea Bortolato (Thu Mar 29 2007 - 10:17:05 CST)
- AMBER: Amber9 Sander Error A Box (Thu Mar 29 2007 - 20:26:21 CST)
- AMBER: Sander error : Coordinate resetting (SHAKE) cannot be accomplished Pankaj R. Daga (Thu Mar 29 2007 - 21:59:08 CST)
- AMBER: minimization + simulation deepti nayar (Fri Mar 30 2007 - 01:54:03 CST)
- AMBER: RST can not be opened deepti nayar (Fri Mar 30 2007 - 03:21:58 CST)
- AMBER: problem regarding water handling in explicit simu gurpreet singh (Fri Mar 30 2007 - 03:35:49 CST)
- AMBER: Some problems during the testing of Amber. Liang, Lei (Fri Mar 30 2007 - 12:12:50 CST)
- AMBER: A question about biomineral simulation, help!! WANG,YING (Fri Mar 30 2007 - 15:36:02 CST)
- AMBER: Distance restraint to centre of mass Evan Kelly (Fri Mar 30 2007 - 16:41:32 CST)
Last message date: Mon Dec 31 2007 - 15:27:41 CST
Archived on: Thu Jan 10 2008 - 17:13:08 CST
406 messages sorted by:
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