Amber Archive Jun 2006: by subject

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

Amber Archive Jun 2006 by subject