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AMBER Archive (2006) - Jun 2006 By Thread
Most recent messages358 messages sorted by: [ author ] [ date ] [ subject ]
About this archive
Starting: Thu Jun 01 2006 - 00:22:01 CDT
Ending: Fri Jun 30 2006 - 23:39:09 CDT
- Re: AMBER: Installation of Amber8 on Fedora Core 5. . Don.Bashford_at_stjude.org (Thu Jun 01 2006 - 11:23:11 CDT)
- AMBER: offset? Tonda March (Thu Jun 01 2006 - 01:12:19 CDT)
- AMBER: Bond Force Conctants in Amber Force Fields åÇÏÒÏ× ä.á. (Thu Jun 01 2006 - 00:22:01 CDT)
- AMBER: Another Installation Problem Seth Lilavivat (Thu Jun 01 2006 - 18:01:13 CDT)
- AMBER: compile error with pgf90 Evan Kelly (Fri Jun 02 2006 - 00:33:21 CDT)
- AMBER: some questions and problems about antechamber and divcon Zhihong Yu (Fri Jun 02 2006 - 02:11:22 CDT)
- AMBER: How to analyze the trajectory generated by LES simulation pang zhao (Fri Jun 02 2006 - 02:08:03 CDT)
- AMBER: attachments for my last mail Zhihong Yu (Fri Jun 02 2006 - 02:30:30 CDT)
- AMBER: Programes to calculate ligand RMSD nag raj (Fri Jun 02 2006 - 05:59:04 CDT)
- AMBER: individual torsion/bond energies from a minimization Thomas Pochapsky (Fri Jun 02 2006 - 08:25:33 CDT)
- AMBER: distance restraints Myunggi Yi (Fri Jun 02 2006 - 10:06:38 CDT)
- AMBER: bugfix for frcmod.ff03 in Amber 9 David A. Case (Fri Jun 02 2006 - 11:45:29 CDT)
- AMBER: NMR restraint Myunggi Yi (Fri Jun 02 2006 - 13:11:51 CDT)
- AMBER: trouble adding mdcrd files together Adam Pelzer (Fri Jun 02 2006 - 17:22:46 CDT)
- AMBER: manual docking mathew k varghese (Fri Jun 02 2006 - 22:50:03 CDT)
- AMBER: manual docking mathew k varghese (Fri Jun 02 2006 - 22:39:13 CDT)
- AMBER: How to use the prmtop and inpcrd files of ligand in a complex system? Zhihong Yu (Sat Jun 03 2006 - 02:00:23 CDT)
- Re: AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system? Zhihong Yu (Mon Jun 05 2006 - 03:57:44 CDT)
- AMBER: MM-PBSA and first solvation shell Andrea Bortolato (Mon Jun 05 2006 - 04:42:39 CDT)
- AMBER: process_mdout Navnit Kumar Mishra (Mon Jun 05 2006 - 07:00:40 CDT)
- AMBER: Amber: Segfault while running sander sethl_at_gatech.edu (Mon Jun 05 2006 - 13:19:33 CDT)
- AMBER: does the Amber8 or Amber9 contains Br,I and Sulfur parameter for MM-PBSA or MM-GBSA. linfu (Mon Jun 05 2006 - 21:24:17 CDT)
- AMBER: How to submit a job in cluster pkb bioinfo (Tue Jun 06 2006 - 03:46:21 CDT)
- AMBER: calculating box dimensions during MD Vlad Cojocaru (Tue Jun 06 2006 - 09:13:14 CDT)
- AMBER: antechamber and FMN David Mobley (Tue Jun 06 2006 - 12:47:03 CDT)
- AMBER: xleap problem Hashem Taha (Tue Jun 06 2006 - 13:29:31 CDT)
- AMBER: compiler error for Amber9 Weihua Li (Wed Jun 07 2006 - 09:34:49 CDT)
- AMBER: antechamber Steve Seibold (Wed Jun 07 2006 - 11:16:47 CDT)
- AMBER: RE: antechamber and FMN Junmei Wang (Wed Jun 07 2006 - 15:39:48 CDT)
- AMBER: pmemd_parallel_ins_prob pkmukher (Wed Jun 07 2006 - 16:00:20 CDT)
- AMBER: problem with amber 9 and igb=5 M. Scott Shell (Wed Jun 07 2006 - 20:06:02 CDT)
- Re: AMBER: problem with amber 9 and igb=5 Carlos Simmerling (Wed Jun 07 2006 - 21:02:34 CDT)
- Re: AMBER: problem with amber 9 and igb=5 John Mongan (Wed Jun 07 2006 - 21:04:59 CDT)
- Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Thu Jun 08 2006 - 10:55:36 CDT)
- Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Fri Jun 09 2006 - 00:15:56 CDT)
- Re: AMBER: problem with amber 9 and igb=5 David A. Case (Fri Jun 09 2006 - 16:58:02 CDT)
- Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Sat Jun 10 2006 - 13:40:05 CDT)
- RE: AMBER: problem with amber 9 and igb=5 Ross Walker (Sat Jun 10 2006 - 14:31:26 CDT)
- Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Thu Jun 08 2006 - 10:55:36 CDT)
- AMBER: How to build N-terminal of alanine : NH2 jitrayut jitonnom (Thu Jun 08 2006 - 02:59:34 CDT)
- AMBER: save coordinates during SANDER minimisation Hannes Barsch (Thu Jun 08 2006 - 04:34:51 CDT)
- AMBER: Ask for help in pbsa error in AMBER9 Cheng Luo, Ph.D. (Thu Jun 08 2006 - 11:08:10 CDT)
- AMBER: software to visualize normal modes Douali, Latifa (Thu Jun 08 2006 - 12:03:26 CDT)
- AMBER: AMD 64 Installation / configuration clarification sethl_at_gatech.edu (Thu Jun 08 2006 - 14:09:50 CDT)
- AMBER: COM khn _ (Thu Jun 08 2006 - 19:13:27 CDT)
- AMBER: Problem with Leap jitrayut jitonnom (Thu Jun 08 2006 - 23:40:52 CDT)
- AMBER: charmm force field in amber9 soo (Thu Jun 08 2006 - 23:23:26 CDT)
- AMBER: use ptraj and two differenct prmtop file to analyze LES trajectory pang zhao (Fri Jun 09 2006 - 03:56:57 CDT)
- AMBER: MMPBSA problem jitrayut jitonnom (Fri Jun 09 2006 - 04:48:50 CDT)
- AMBER: ptraj Marcela Madrid (Fri Jun 09 2006 - 16:19:54 CDT)
- AMBER: Why the result from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? Yongmei Pan (Fri Jun 09 2006 - 22:03:26 CDT)
- AMBER: Why the energy from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? Yongmei Pan (Fri Jun 09 2006 - 21:57:42 CDT)
- AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? linfu (Fri Jun 09 2006 - 22:25:24 CDT)
- AMBER: MD stopped Miguel Ferreira (Sat Jun 10 2006 - 04:33:05 CDT)
- AMBER: Umbrella sampling Atsutoshi Okabe (Sat Jun 10 2006 - 05:42:34 CDT)
- AMBER: parmchk error Evan Kelly (Sat Jun 10 2006 - 22:30:11 CDT)
- Re: Re: AMBER:it seems that The SAS in MMPBSA is SES , not SAS. ???? linfu (Sat Jun 10 2006 - 22:27:20 CDT)
- AMBER: mm_pbsa calculation for calcium Navnit Kumar Mishra (Mon Jun 12 2006 - 00:59:06 CDT)
- AMBER: switching function for electrostatic interactions Fabien Cailliez (Mon Jun 12 2006 - 06:38:22 CDT)
- AMBER: How to calculate the mmpbsa for explicit MD ? jitrayut jitonnom (Mon Jun 12 2006 - 11:41:52 CDT)
- Re: AMBER: How to calculate the mmpbsa for explicit MD ? Thomas Steinbrecher (Mon Jun 12 2006 - 11:58:33 CDT)
- Re: AMBER: How to calculate the mmpbsa for explicit MD ? Chris Moth (Mon Jun 12 2006 - 14:23:01 CDT)
- AMBER: How to strip waters in trajectorie ? jitrayut jitonnom (Mon Jun 12 2006 - 14:50:02 CDT)
- AMBER: Nmode memory allocation problem JunJun Liu (Mon Jun 12 2006 - 18:45:14 CDT)
- AMBER: SGI compiler problems Peter Gannett (Tue Jun 13 2006 - 07:46:18 CDT)
- AMBER: MMPBSA error jitrayut jitonnom (Tue Jun 13 2006 - 09:52:08 CDT)
- AMBER: Difficulty loading a pdb file Kara Di Giorgio (Tue Jun 13 2006 - 13:20:41 CDT)
- AMBER: LEaP Warning ... when do NH2-neutral fragment jitrayut jitonnom (Tue Jun 13 2006 - 13:40:47 CDT)
- AMBER: compiler requirement for SGI Fuel To install AMBER9 S.Sundar Raman (Wed Jun 14 2006 - 01:45:40 CDT)
- AMBER: How to simplify this big system rationally to perform MD studies Zhihong Yu (Wed Jun 14 2006 - 05:43:59 CDT)
- Fwd: Fwd: AMBER: MMPBSA error jitrayut jitonnom (Wed Jun 14 2006 - 06:27:51 CDT)
- AMBER: problems on mm_pbsa Giovanni (Wed Jun 14 2006 - 07:05:03 CDT)
- AMBER: saveamberparams error in Amber9 Weihua Li (Wed Jun 14 2006 - 08:28:43 CDT)
- AMBER: ptraj: rms per residue simon whitehead (Wed Jun 14 2006 - 09:14:28 CDT)
- AMBER: Fully QM periodic runs Steven Winfield (Wed Jun 14 2006 - 11:03:43 CDT)
- Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Kara Di Giorgio (Wed Jun 14 2006 - 12:20:40 CDT)
- AMBER: best way to customize linkages sethl_at_gatech.edu (Wed Jun 14 2006 - 15:25:07 CDT)
- AMBER: Re: Problem in compiling sander with MMTSB Scott Brozell (Wed Jun 14 2006 - 22:29:57 CDT)
- AMBER: RMS FLUCTUATIONS Jiang Jianwen (Thu Jun 15 2006 - 06:37:24 CDT)
- AMBER: GBSA of nonstandard cations Martin LEPSIK (Thu Jun 15 2006 - 17:46:16 CDT)
- AMBER: Re: Problem in compiling sander with MMTSB Scott Brozell (Thu Jun 15 2006 - 18:28:27 CDT)
- AMBER: repeat use of a trimer lib file Eric Hu (Thu Jun 15 2006 - 18:35:39 CDT)
- AMBER: MPICH and Sander Andrew Box (Thu Jun 15 2006 - 21:07:11 CDT)
- AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Fri Jun 16 2006 - 08:52:33 CDT)
- Fwd: Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Fri Jun 16 2006 - 12:28:08 CDT)
- AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand Christophe Guilbert (Fri Jun 16 2006 - 23:32:12 CDT)
- AMBER: Problems with restart file from pmemd sim. anna.schrey_at_gmx.de (Sat Jun 17 2006 - 07:30:56 CDT)
- AMBER: charge in LEaP step jitrayut jitonnom (Sat Jun 17 2006 - 13:14:24 CDT)
- AMBER: Non bond list overflow in amber8.0 program. nag raj (Sun Jun 18 2006 - 23:54:04 CDT)
- AMBER: Post-MD minimization sangeeta_at_bioinfo.ernet.in (Mon Jun 19 2006 - 06:33:58 CDT)
- Re: AMBER: Post-MD minimization Carlos Simmerling (Mon Jun 19 2006 - 09:27:37 CDT)
- RE: AMBER: Post-MD minimization Ross Walker (Mon Jun 19 2006 - 10:20:25 CDT)
- RE: AMBER: checkoverlap doubt [was: Post-MD minimization] sangeeta_at_bioinfo.ernet.in (Tue Jun 20 2006 - 08:21:11 CDT)
- RE: AMBER: Post-MD minimization sangeeta_at_bioinfo.ernet.in (Fri Jun 23 2006 - 01:09:31 CDT)
- RE: AMBER: Post-MD minimization Ross Walker (Fri Jun 23 2006 - 07:19:14 CDT)
- AMBER: Can we submit jobs in sequences to amber? a a (Mon Jun 26 2006 - 02:14:05 CDT)
- Re: AMBER: Can we submit jobs in sequences to amber? Ilyas Yildirim (Mon Jun 26 2006 - 02:22:00 CDT)
- AMBER: Minizsation strange error message! Please help. a a (Mon Jun 26 2006 - 05:38:35 CDT)
- Re: AMBER: Can we submit jobs in sequences to amber? Roberto Gomperts (Mon Jun 26 2006 - 05:25:03 CDT)
- AMBER: Amber7-CHARMM22-TRIPOS force fields opitz_at_che.udel.edu (Mon Jun 19 2006 - 10:37:24 CDT)
- AMBER: help with custom RNA molecule sethl_at_gatech.edu (Mon Jun 19 2006 - 13:55:59 CDT)
- AMBER: Antechamber poorly define atom angles of a five ring system which causes NH2 and C not to be planar as expected Christophe Guilbert (Mon Jun 19 2006 - 20:00:29 CDT)
- AMBER: ions+proteins Hannes Loeffler (Mon Jun 19 2006 - 20:45:57 CDT)
- AMBER: RE: Antechamber poorly define atom angles of a five ring system whichcauses NH2 and C not to be planar as expected Junmei Wang (Mon Jun 19 2006 - 22:08:56 CDT)
- AMBER: second derivative matrix Marie Brut (Tue Jun 20 2006 - 07:28:02 CDT)
- Re: AMBER: second derivative matrix David A. Case (Tue Jun 20 2006 - 16:37:01 CDT)
- AMBER: Tutorial 2: Production MD. a a (Wed Jun 21 2006 - 05:19:05 CDT)
- Re: AMBER: Tutorial 2: Production MD. Thomas Steinbrecher (Wed Jun 21 2006 - 10:37:51 CDT)
- AMBER: kill job command? a a (Thu Jun 22 2006 - 02:47:51 CDT)
- Re: AMBER: kill job command? JunJun Liu (Thu Jun 22 2006 - 08:13:04 CDT)
- AMBER: Tutorial 2: Minimise and equlibrium error NaN a a (Fri Jun 23 2006 - 05:05:05 CDT)
- RE: AMBER: Tutorial 2: Minimise and equlibrium error NaN Ross Walker (Fri Jun 23 2006 - 06:28:17 CDT)
- AMBER: Tutorial 2: Production MD. a a (Wed Jun 21 2006 - 05:19:05 CDT)
- Re: AMBER: second derivative matrix David A. Case (Tue Jun 20 2006 - 16:37:01 CDT)
- AMBER: why has "ELE " a large fluctuation in MMP BSA? yxiong99 (Tue Jun 20 2006 - 08:47:44 CDT)
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 16:37:52 CDT)
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 18:10:48 CDT)
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Thomas Cheatham (Tue Jun 20 2006 - 18:48:54 CDT)
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 17:55:09 CDT)
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 19:18:21 CDT)
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 19:19:10 CDT)
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 18:45:52 CDT)
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 20:54:51 CDT)
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 20:08:32 CDT)
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 18:10:48 CDT)
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 16:37:52 CDT)
- AMBER: why has "ELE " a large fluctuation in MMPBSA? JunJun Liu (Tue Jun 20 2006 - 08:56:25 CDT)
- AMBER: ptraj vector Myunggi Yi (Tue Jun 20 2006 - 11:13:54 CDT)
- AMBER: amber9 hostfile snoze pa (Tue Jun 20 2006 - 19:12:50 CDT)
- AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test David McGiven (Wed Jun 21 2006 - 05:46:40 CDT)
- AMBER: MMTSB: phi-pdi-based clustering sangeeta_at_bioinfo.ernet.in (Wed Jun 21 2006 - 07:37:39 CDT)
- AMBER: terms in mm-pbsa Lwin, ThuZar (Wed Jun 21 2006 - 10:48:37 CDT)
- AMBER: openmpi snoze pa (Wed Jun 21 2006 - 12:28:28 CDT)
- AMBER: problems with cpinutil.pl Abhilash Mohan (Wed Jun 21 2006 - 16:06:05 CDT)
- AMBER: What's the meaning of NTYPES? JunJun Liu (Wed Jun 21 2006 - 15:27:51 CDT)
- AMBER: problems about compiling a parallel version of AMBER 9 Chengwen Chen (Thu Jun 22 2006 - 02:25:11 CDT)
- AMBER: Restraint internal coordinates in Amber 8.0 Guillaume Bollot (Thu Jun 22 2006 - 04:00:03 CDT)
- AMBER: average struct.problem bala (Thu Jun 22 2006 - 04:11:15 CDT)
- AMBER: can i use unusual amino acid priya priya (Thu Jun 22 2006 - 04:15:55 CDT)
- AMBER: help creating RNA sethl_at_gatech.edu (Thu Jun 22 2006 - 14:14:06 CDT)
- AMBER: ANN: APBS/Amber interface released Robert Konecny (Fri Jun 23 2006 - 01:23:35 CDT)
- AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8 Ricardo J. F. Branco (Fri Jun 23 2006 - 02:36:44 CDT)
- AMBER: references simon whitehead (Fri Jun 23 2006 - 05:35:56 CDT)
- AMBER: constant pressure equillibration simon whitehead (Fri Jun 23 2006 - 04:17:35 CDT)
- AMBER: Implicit solvent question Anthony Cruz (Fri Jun 23 2006 - 08:49:22 CDT)
- AMBER: problems with cpinutil.pl Abhilash Mohan (Fri Jun 23 2006 - 12:00:36 CDT)
- AMBER: how to create 2'-5' RNA sethl_at_gatech.edu (Fri Jun 23 2006 - 16:13:57 CDT)
- AMBER: periodic boundary condition in the X and Y dimensions only hbluo (Mon Jun 26 2006 - 17:15:51 CDT)
- AMBER:Checkoverlap query sangeeta_at_bioinfo.ernet.in (Mon Jun 26 2006 - 07:12:56 CDT)
- AMBER: Amber minimization with multiple restraints Qingning Shu (Mon Jun 26 2006 - 12:23:33 CDT)
- AMBER: Curves and Average Structures Lauren O'Neil (Mon Jun 26 2006 - 12:26:46 CDT)
- AMBER: manual/prmtop/missing bonds section David Mobley (Mon Jun 26 2006 - 15:27:39 CDT)
- AMBER: creating RNA, nucgen / leap sethl_at_gatech.edu (Mon Jun 26 2006 - 15:59:46 CDT)
- Re: AMBER: Second derivative matrix David A. Case (Tue Jun 27 2006 - 03:36:57 CDT)
- AMBER: MM-PBSA and gaff atom types anna ferrari (Tue Jun 27 2006 - 04:28:03 CDT)
- AMBER: Leap: neutralising the charge Miguel Ferreira (Tue Jun 27 2006 - 04:49:36 CDT)
- AMBER: rgbmax--something wrong with my input file? Kenley Barrett (Tue Jun 27 2006 - 16:10:27 CDT)
- AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering Cenk Andac (Wed Jun 28 2006 - 05:46:49 CDT)
- AMBER: REM test failures on IA-64 architecture Glass, Kevin A (Wed Jun 28 2006 - 10:28:07 CDT)
- AMBER: remlog option changed in amber9? Alik Widge (Wed Jun 28 2006 - 14:36:47 CDT)
- AMBER: problem with pattern searching in mm_pbsa_calceneent.pm, Amber8, when salt>0 using delphi version 4 Lwin, ThuZar (Wed Jun 28 2006 - 19:58:14 CDT)
- AMBER: How to calculate binding free energy using MM-PBSA Xioling Chuang (Thu Jun 29 2006 - 04:38:58 CDT)
- AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Fabian Boes (Thu Jun 29 2006 - 10:58:26 CDT)
- AMBER: Having trouble getting Iron parameters for QM/MM zachary hartman (Thu Jun 29 2006 - 14:23:06 CDT)
- AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl yxiong99 (Thu Jun 29 2006 - 15:49:50 CDT)
- AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Christophe Guilbert (Thu Jun 29 2006 - 16:48:31 CDT)
- Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Bill Ross (Thu Jun 29 2006 - 18:46:17 CDT)
- AMBER: general question about hydrogen bond energy vs electrostatic energy Eric Hu (Thu Jun 29 2006 - 19:58:24 CDT)
- AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. Christophe Guilbert (Thu Jun 29 2006 - 20:28:31 CDT)
- AMBER: GB simulation problem Anthony Cruz (Fri Jun 30 2006 - 11:49:53 CDT)
- AMBER: NAMOT sethl_at_gatech.edu (Fri Jun 30 2006 - 14:17:46 CDT)
- AMBER: Compiling / Installing Amber 8 on SUSE 10.1 Seth Lilavivat (Tue Jun 13 2006 - 22:23:25 CDT)
- AMBER: Creating an Intercalation site Seth Lilavivat (Sat Jun 17 2006 - 14:25:59 CDT)
Last message date: Sat Dec 30 2006 - 07:20:23 CST
Archived on: Wed Feb 21 2007 - 22:44:16 CST
358 messages sorted by: [ author ] [ date ] [ subject ]
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