Amber Archive Jun 2006 by thread
- AMBER: offset? Tonda March (Wed May 31 2006 - 23:12:19 PDT)
- AMBER: Bond Force Conctants in Amber Force Fields Егоров Д.А. (Wed May 31 2006 - 22:22:01 PDT)
- Re: AMBER: Different results for TI calculation David A. Case (Thu Jun 01 2006 - 07:33:32 PDT)
- Re: AMBER: AMBER mdcrd file bigger than 2GB snoze pa (Thu Jun 01 2006 - 08:41:02 PDT)
- Re: AMBER: Installation of Amber8 on Fedora Core 5. . Don.Bashford.stjude.org (Thu Jun 01 2006 - 09:23:11 PDT)
- AMBER: Another Installation Problem Seth Lilavivat (Thu Jun 01 2006 - 16:01:13 PDT)
- AMBER: compile error with pgf90 Evan Kelly (Thu Jun 01 2006 - 22:33:21 PDT)
- AMBER: some questions and problems about antechamber and divcon Zhihong Yu (Fri Jun 02 2006 - 00:11:22 PDT)
- AMBER: How to analyze the trajectory generated by LES simulation pang zhao (Fri Jun 02 2006 - 00:08:03 PDT)
- AMBER: attachments for my last mail Zhihong Yu (Fri Jun 02 2006 - 00:30:30 PDT)
- AMBER: Programes to calculate ligand RMSD nag raj (Fri Jun 02 2006 - 03:59:04 PDT)
- AMBER: individual torsion/bond energies from a minimization Thomas Pochapsky (Fri Jun 02 2006 - 06:25:33 PDT)
- AMBER: distance restraints Myunggi Yi (Fri Jun 02 2006 - 08:06:38 PDT)
- AMBER: bugfix for frcmod.ff03 in Amber 9 David A. Case (Fri Jun 02 2006 - 09:45:29 PDT)
- AMBER: NMR restraint Myunggi Yi (Fri Jun 02 2006 - 11:11:51 PDT)
- Re: AMBER: Thermodynamic integration using the amber 9 Ilyas Yildirim (Fri Jun 02 2006 - 13:12:18 PDT)
- Re: AMBER: Namelists in input files David A. Case (Fri Jun 02 2006 - 13:48:42 PDT)
- AMBER: trouble adding mdcrd files together Adam Pelzer (Fri Jun 02 2006 - 15:22:46 PDT)
- AMBER: manual docking mathew k varghese (Fri Jun 02 2006 - 20:39:13 PDT)
- AMBER: manual docking mathew k varghese (Fri Jun 02 2006 - 20:50:03 PDT)
- AMBER: How to use the prmtop and inpcrd files of ligand in a complex system? Zhihong Yu (Sat Jun 03 2006 - 00:00:23 PDT)
- Re: AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system? Zhihong Yu (Mon Jun 05 2006 - 01:57:44 PDT)
- AMBER: MM-PBSA and first solvation shell Andrea Bortolato (Mon Jun 05 2006 - 02:42:39 PDT)
- AMBER: process_mdout Navnit Kumar Mishra (Mon Jun 05 2006 - 05:00:40 PDT)
- AMBER: Amber: Segfault while running sander sethl.gatech.edu (Mon Jun 05 2006 - 11:19:33 PDT)
- AMBER: does the Amber8 or Amber9 contains Br,I and Sulfur parameter for MM-PBSA or MM-GBSA. linfu (Mon Jun 05 2006 - 19:24:17 PDT)
- AMBER: How to submit a job in cluster pkb bioinfo (Tue Jun 06 2006 - 01:46:21 PDT)
- AMBER: calculating box dimensions during MD Vlad Cojocaru (Tue Jun 06 2006 - 07:13:14 PDT)
- AMBER: antechamber and FMN David Mobley (Tue Jun 06 2006 - 10:47:03 PDT)
- AMBER: xleap problem Hashem Taha (Tue Jun 06 2006 - 11:29:31 PDT)
- AMBER: compiler error for Amber9 Weihua Li (Wed Jun 07 2006 - 07:34:49 PDT)
- AMBER: antechamber Steve Seibold (Wed Jun 07 2006 - 09:16:47 PDT)
- AMBER: RE: antechamber and FMN Junmei Wang (Wed Jun 07 2006 - 13:39:48 PDT)
- AMBER: pmemd_parallel_ins_prob pkmukher (Wed Jun 07 2006 - 14:00:20 PDT)
- AMBER: problem with amber 9 and igb=5 M. Scott Shell (Wed Jun 07 2006 - 18:06:02 PDT)
- AMBER: How to build N-terminal of alanine : NH2 jitrayut jitonnom (Thu Jun 08 2006 - 00:59:34 PDT)
- AMBER: save coordinates during SANDER minimisation Hannes Barsch (Thu Jun 08 2006 - 02:34:51 PDT)
- AMBER: Ask for help in pbsa error in AMBER9 Cheng Luo, Ph.D. (Thu Jun 08 2006 - 09:08:10 PDT)
- AMBER: software to visualize normal modes Douali, Latifa (Thu Jun 08 2006 - 10:03:26 PDT)
- AMBER: AMD 64 Installation / configuration clarification sethl.gatech.edu (Thu Jun 08 2006 - 12:09:50 PDT)
- AMBER: COM khn _ (Thu Jun 08 2006 - 17:13:27 PDT)
- AMBER: charmm force field in amber9 soo (Thu Jun 08 2006 - 21:23:26 PDT)
- AMBER: Problem with Leap jitrayut jitonnom (Thu Jun 08 2006 - 21:40:52 PDT)
- AMBER: use ptraj and two differenct prmtop file to analyze LES trajectory pang zhao (Fri Jun 09 2006 - 01:56:57 PDT)
- AMBER: MMPBSA problem jitrayut jitonnom (Fri Jun 09 2006 - 02:48:50 PDT)
- AMBER: ptraj Marcela Madrid (Fri Jun 09 2006 - 14:19:54 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: 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 - 19:57:42 PDT)
- AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? linfu (Fri Jun 09 2006 - 20:25:24 PDT)
- AMBER: MD stopped Miguel Ferreira (Sat Jun 10 2006 - 02:33:05 PDT)
- AMBER: Umbrella sampling Atsutoshi Okabe (Sat Jun 10 2006 - 03:42:34 PDT)
- AMBER: parmchk error Evan Kelly (Sat Jun 10 2006 - 20:30:11 PDT)
- Re: Re: AMBER:it seems that The SAS in MMPBSA is SES , not SAS. ???? linfu (Sat Jun 10 2006 - 20:27:20 PDT)
- AMBER: mm_pbsa calculation for calcium Navnit Kumar Mishra (Sun Jun 11 2006 - 22:59:06 PDT)
- AMBER: switching function for electrostatic interactions Fabien Cailliez (Mon Jun 12 2006 - 04:38:22 PDT)
- AMBER: How to calculate the mmpbsa for explicit MD ? jitrayut jitonnom (Mon Jun 12 2006 - 09:41:52 PDT)
- AMBER: How to strip waters in trajectorie ? jitrayut jitonnom (Mon Jun 12 2006 - 12:50:02 PDT)
- AMBER: Nmode memory allocation problem JunJun Liu (Mon Jun 12 2006 - 16:45:14 PDT)
- AMBER: SGI compiler problems Peter Gannett (Tue Jun 13 2006 - 05:46:18 PDT)
- AMBER: MMPBSA error jitrayut jitonnom (Tue Jun 13 2006 - 07:52:08 PDT)
- AMBER: Difficulty loading a pdb file Kara Di Giorgio (Tue Jun 13 2006 - 11:20:41 PDT)
- AMBER: LEaP Warning ... when do NH2-neutral fragment jitrayut jitonnom (Tue Jun 13 2006 - 11:40:47 PDT)
- AMBER: compiler requirement for SGI Fuel To install AMBER9 S.Sundar Raman (Tue Jun 13 2006 - 23:45:40 PDT)
- AMBER: How to simplify this big system rationally to perform MD studies Zhihong Yu (Wed Jun 14 2006 - 03:43:59 PDT)
- Fwd: Fwd: AMBER: MMPBSA error jitrayut jitonnom (Wed Jun 14 2006 - 04:27:51 PDT)
- AMBER: problems on mm_pbsa Giovanni (Wed Jun 14 2006 - 05:05:03 PDT)
- AMBER: saveamberparams error in Amber9 Weihua Li (Wed Jun 14 2006 - 06:28:43 PDT)
- AMBER: ptraj: rms per residue simon whitehead (Wed Jun 14 2006 - 07:14:28 PDT)
- AMBER: Fully QM periodic runs Steven Winfield (Wed Jun 14 2006 - 09:03:43 PDT)
- Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Kara Di Giorgio (Wed Jun 14 2006 - 10:20:40 PDT)
- AMBER: best way to customize linkages sethl.gatech.edu (Wed Jun 14 2006 - 13:25:07 PDT)
- AMBER: Re: Problem in compiling sander with MMTSB Scott Brozell (Wed Jun 14 2006 - 20:29:57 PDT)
- AMBER: RMS FLUCTUATIONS Jiang Jianwen (Thu Jun 15 2006 - 04:37:24 PDT)
- AMBER: GBSA of nonstandard cations Martin LEPSIK (Thu Jun 15 2006 - 15:46:16 PDT)
- AMBER: Re: Problem in compiling sander with MMTSB Scott Brozell (Thu Jun 15 2006 - 16:28:27 PDT)
- AMBER: repeat use of a trimer lib file Eric Hu (Thu Jun 15 2006 - 16:35:39 PDT)
- AMBER: MPICH and Sander Andrew Box (Thu Jun 15 2006 - 19:07:11 PDT)
- AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Fri Jun 16 2006 - 06:52:33 PDT)
- Fwd: Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Fri Jun 16 2006 - 10:28:08 PDT)
- AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand Christophe Guilbert (Fri Jun 16 2006 - 21:32:12 PDT)
- AMBER: Problems with restart file from pmemd sim. anna.schrey.gmx.de (Sat Jun 17 2006 - 05:30:56 PDT)
- AMBER: charge in LEaP step jitrayut jitonnom (Sat Jun 17 2006 - 11:14:24 PDT)
- AMBER: Non bond list overflow in amber8.0 program. nag raj (Sun Jun 18 2006 - 21:54:04 PDT)
- AMBER: Post-MD minimization sangeeta.bioinfo.ernet.in (Mon Jun 19 2006 - 04:33:58 PDT)
- AMBER: Amber7-CHARMM22-TRIPOS force fields opitz.che.udel.edu (Mon Jun 19 2006 - 08:37:24 PDT)
- AMBER: help with custom RNA molecule sethl.gatech.edu (Mon Jun 19 2006 - 11:55:59 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: ions+proteins Hannes Loeffler (Mon Jun 19 2006 - 18:45:57 PDT)
- 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 - 20:08:56 PDT)
- AMBER: second derivative matrix Marie Brut (Tue Jun 20 2006 - 05:28:02 PDT)
- AMBER: why has "ELE " a large fluctuation in MMP BSA? 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: ptraj vector Myunggi Yi (Tue Jun 20 2006 - 09:13:54 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 - 03:46:40 PDT)
- AMBER: MMTSB: phi-pdi-based clustering sangeeta.bioinfo.ernet.in (Wed Jun 21 2006 - 05:37:39 PDT)
- AMBER: terms in mm-pbsa Lwin, ThuZar (Wed Jun 21 2006 - 08:48:37 PDT)
- AMBER: openmpi snoze pa (Wed Jun 21 2006 - 10:28:28 PDT)
- AMBER: problems with cpinutil.pl Abhilash Mohan (Wed Jun 21 2006 - 14:06:05 PDT)
- AMBER: What's the meaning of NTYPES? JunJun Liu (Wed Jun 21 2006 - 13:27:51 PDT)
- AMBER: problems about compiling a parallel version of AMBER 9 Chengwen Chen (Thu Jun 22 2006 - 00:25:11 PDT)
- AMBER: Restraint internal coordinates in Amber 8.0 Guillaume Bollot (Thu Jun 22 2006 - 02:00:03 PDT)
- AMBER: average struct.problem bala (Thu Jun 22 2006 - 02:11:15 PDT)
- AMBER: can i use unusual amino acid priya priya (Thu Jun 22 2006 - 02:15:55 PDT)
- AMBER: help creating RNA sethl.gatech.edu (Thu Jun 22 2006 - 12:14:06 PDT)
- AMBER: ANN: APBS/Amber interface released Robert Konecny (Thu Jun 22 2006 - 23:23:35 PDT)
- AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8 Ricardo J. F. Branco (Fri Jun 23 2006 - 00:36:44 PDT)
- AMBER: references simon whitehead (Fri Jun 23 2006 - 03:35:56 PDT)
- AMBER: constant pressure equillibration simon whitehead (Fri Jun 23 2006 - 02:17:35 PDT)
- AMBER: Implicit solvent question Anthony Cruz (Fri Jun 23 2006 - 06:49:22 PDT)
- AMBER: problems with cpinutil.pl Abhilash Mohan (Fri Jun 23 2006 - 10:00:36 PDT)
- AMBER: how to create 2'-5' RNA sethl.gatech.edu (Fri Jun 23 2006 - 14:13:57 PDT)
- AMBER: Second derivative matrix mbrut.laas.fr (Sat Jun 24 2006 - 04:21:27 PDT)
- AMBER: about GBSA sishi.tang.utoronto.ca (Sun Jun 25 2006 - 11:45:11 PDT)
- AMBER: periodic boundary condition in the X and Y dimensions only hbluo (Mon Jun 26 2006 - 14:58:00 PDT)
- AMBER: periodic boundary condition in the X and Y dimensions only hbluo (Mon Jun 26 2006 - 15:15:51 PDT)
- AMBER:Checkoverlap query sangeeta.bioinfo.ernet.in (Mon Jun 26 2006 - 05:12:56 PDT)
- AMBER: Amber minimization with multiple restraints Qingning Shu (Mon Jun 26 2006 - 10:23:33 PDT)
- AMBER: Curves and Average Structures Lauren O'Neil (Mon Jun 26 2006 - 10:26:46 PDT)
- AMBER: manual/prmtop/missing bonds section David Mobley (Mon Jun 26 2006 - 13:27:39 PDT)
- AMBER: creating RNA, nucgen / leap sethl.gatech.edu (Mon Jun 26 2006 - 13:59:46 PDT)
- AMBER: MM-PBSA and gaff atom types anna ferrari (Tue Jun 27 2006 - 02:28:03 PDT)
- AMBER: Leap: neutralising the charge Miguel Ferreira (Tue Jun 27 2006 - 02:49:36 PDT)
- AMBER: rgbmax--something wrong with my input file? Kenley Barrett (Tue Jun 27 2006 - 14:10:27 PDT)
- AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering Cenk Andac (Wed Jun 28 2006 - 03:46:49 PDT)
- AMBER: REM test failures on IA-64 architecture Glass, Kevin A (Wed Jun 28 2006 - 08:28:07 PDT)
- AMBER: remlog option changed in amber9? Alik Widge (Wed Jun 28 2006 - 12:36:47 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: How to calculate binding free energy using MM-PBSA Xioling Chuang (Thu Jun 29 2006 - 02:38:58 PDT)
- AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Fabian Boes (Thu Jun 29 2006 - 08:58:26 PDT)
- AMBER: Having trouble getting Iron parameters for QM/MM zachary hartman (Thu Jun 29 2006 - 12:23:06 PDT)
- AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl yxiong99 (Thu Jun 29 2006 - 13:49:50 PDT)
- AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Christophe Guilbert (Thu Jun 29 2006 - 14:48:31 PDT)
- Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Bill Ross (Thu Jun 29 2006 - 16:46:17 PDT)
- AMBER: general question about hydrogen bond energy vs electrostatic energy Eric Hu (Thu Jun 29 2006 - 17:58:24 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: GB simulation problem Anthony Cruz (Fri Jun 30 2006 - 09:49:53 PDT)
- AMBER: NAMOT sethl.gatech.edu (Fri Jun 30 2006 - 12:17:46 PDT)
- AMBER: Compiling / Installing Amber 8 on SUSE 10.1 Seth Lilavivat (Tue Jun 13 2006 - 20:23:25 PDT)
- AMBER: Creating an Intercalation site Seth Lilavivat (Sat Jun 17 2006 - 12:25:59 PDT)
- Last message date: Wed Jul 19 2006 - 06:07:08 PDT
- Archived on: Mon Dec 23 2024 - 05:53:26 PST
