AMBER Archive (2006) - Dec 2006 By Author

Starting: Fri Dec 01 2006 - 04:26:51 CST
Ending: Sat Dec 30 2006 - 07:12:53 CST

• a a
  • Re: AMBER: MD with restraint (nmropt=1) (Wed Dec 06 2006 - 22:48:32 CST)
  • Re: AMBER: MD with restraint (nmropt=1) (Wed Dec 06 2006 - 00:11:59 CST)
  • AMBER: MD with restraint (nmropt=1) (Tue Dec 05 2006 - 02:11:38 CST)
  • Re: AMBER: How to apply a force to some atom in a residues? (Fri Dec 01 2006 - 04:26:51 CST)
  • AMBER: How to keep an hydrogen bond during an implicit MD calculation? (Fri Dec 01 2006 - 04:35:31 CST)
• A Box
  • AMBER: Amber 9 Leap install error (Sun Dec 17 2006 - 22:06:52 CST)
• Akshay Patny
  • RE: AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 11:46:45 CST)
  • AMBER: RESP procedure for DMPC monomer (Wed Dec 20 2006 - 10:04:00 CST)
  • AMBER: Renumber residues in LEAP (Tue Dec 19 2006 - 15:55:57 CST)
• Andy Purkiss-Trew
  • RE: AMBER: ibelly not work (Thu Dec 07 2006 - 06:33:24 CST)
• Angelo
  • Re: AMBER: MM-PBSA (Mon Dec 18 2006 - 10:30:00 CST)
• anna.schrey_at_gmx.de
  • AMBER: xleap problems (Mon Dec 04 2006 - 05:45:07 CST)
• Atsutoshi Okabe
  • AMBER: Volume of ucell too big (Sat Dec 16 2006 - 02:41:43 CST)
  • AMBER: Error message in methane solvent system (Thu Dec 07 2006 - 21:19:04 CST)
• bertrand russell
  • AMBER: .crd file (Tue Dec 26 2006 - 03:16:53 CST)
  • Re: AMBER: Installation help - SGI Altix 350 (Tue Dec 26 2006 - 02:25:10 CST)
  • Re: AMBER: Installation help - SGI Altix 350 (Thu Dec 21 2006 - 23:51:48 CST)
  • Re: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 23:09:48 CST)
  • Re: AMBER: Amber9 - openmpi? (Wed Dec 20 2006 - 22:16:22 CST)
  • Re: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 22:13:03 CST)
  • AMBER: Amber9 - openmpi? (Wed Dec 20 2006 - 05:22:37 CST)
  • AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 04:47:03 CST)
  • Re: AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 11:35:16 CST)
  • AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 04:03:53 CST)
  • AMBER: LEaP problem (Mon Dec 11 2006 - 23:10:48 CST)
  • Re: AMBER: LEaP not recognising Phosphate group in TYR (Thu Dec 07 2006 - 04:39:46 CST)
  • AMBER: LEaP not recognising Phosphate group in TYR (Sat Dec 02 2006 - 10:41:23 CST)
• Bill Ross
  • Re: AMBER: tree name generated by tleap is different from the input PREP parameter file (Fri Dec 29 2006 - 21:00:26 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 15:12:50 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 13:51:07 CST)
  • Re: AMBER: Nucgen Problem (Fri Dec 22 2006 - 12:51:25 CST)
  • Re: AMBER: Is there a way to simulate a box of pure water with amber (Fri Dec 15 2006 - 13:06:49 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Tue Dec 12 2006 - 13:47:48 CST)
  • Re: AMBER: LEaP problem (Tue Dec 12 2006 - 00:24:33 CST)
• Burkhard Heil
  • AMBER: Installing Amber 9 on Mac Pro (Thu Dec 07 2006 - 04:54:00 CST)
• Carlos Simmerling
  • Re: AMBER: sander ntc=2 ntf=1 (Tue Dec 19 2006 - 05:39:38 CST)
  • Re: AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 12:54:37 CST)
  • Re: AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 07:22:04 CST)
  • Re: AMBER: question on protein folding simulation (Mon Dec 04 2006 - 06:32:16 CST)
  • Re: AMBER: Problem with specifying NOSHAKEMASK (Sun Dec 03 2006 - 07:48:56 CST)
• Cenk Andac
  • AMBER: parallel computation time vs serial computation time (Thu Dec 14 2006 - 05:17:28 CST)
  • Re: AMBER: xleap problems (Mon Dec 04 2006 - 09:46:34 CST)
  • Re: AMBER: problem at the start of heating up (using extra-point) (Sat Dec 02 2006 - 11:32:50 CST)
  • AMBER: LogP (Sat Dec 02 2006 - 04:44:06 CST)
• Chengwen Chen
  • AMBER: AMBER complile problem (Fri Dec 29 2006 - 01:41:21 CST)
  • Re: AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes (Wed Dec 13 2006 - 01:01:03 CST)
• Chris Moth
  • Re: AMBER: Frozen at Minimization (Tue Dec 19 2006 - 09:01:16 CST)
  • Re: AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 12:35:13 CST)
  • Re: AMBER: Unit 5 Error on OPEN: md.in (Sat Dec 16 2006 - 12:27:17 CST)
  • Re: AMBER: Unit 5 Error on OPEN: md.in (Sat Dec 16 2006 - 12:25:03 CST)
  • AMBER: Free energy perturbation in SANDER (Thu Dec 14 2006 - 08:21:11 CST)
• Christophe Guilbert
  • Re: AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 13:51:18 CST)
• David A. Case
  • Re: AMBER: Simulated Annealing problem... (Fri Dec 29 2006 - 10:56:06 CST)
  • Re: AMBER: bad connectivity - more detail (Fri Dec 29 2006 - 02:15:16 CST)
  • Re: AMBER: problems with Calcium ions treatment in GB run (Fri Dec 29 2006 - 01:56:25 CST)
  • Re: AMBER: AMBER complile problem (Fri Dec 29 2006 - 01:51:49 CST)
  • Re: AMBER: chirality.c line 121 (Wed Dec 27 2006 - 16:46:21 CST)
  • Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 12:31:58 CST)
  • Re: AMBER: recompiling bondtype.C (Wed Dec 27 2006 - 12:30:10 CST)
  • Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 10:52:41 CST)
  • Re: AMBER: Error compiling amber on parallel (MPICH) (Wed Dec 27 2006 - 10:41:21 CST)
  • Re: AMBER: Installation help - SGI Altix 350 (Tue Dec 26 2006 - 15:45:54 CST)
  • Re: AMBER: Sander--NMR refinement (Tue Dec 26 2006 - 12:44:46 CST)
  • Re: AMBER: EXTRA_PTS: frtype 2 Should not be here (Mon Dec 25 2006 - 16:32:11 CST)
  • Re: AMBER: MM_PBSA (Mon Dec 25 2006 - 16:15:26 CST)
  • Re: AMBER: Renumber residues in LEAP (Mon Dec 25 2006 - 16:11:34 CST)
  • Re: AMBER: Compiling Amber8 with Sun HPC ClusterTools 5 Software (Sat Dec 23 2006 - 20:58:29 CST)
  • Re: AMBER: Amber 9 Leap install error (Sun Dec 17 2006 - 23:54:56 CST)
  • Re: AMBER: Error in sysdepend.c? (Fri Dec 15 2006 - 17:24:00 CST)
  • Re: AMBER: sander: cannot execute binary file (Fri Dec 15 2006 - 11:48:49 CST)
  • Re: AMBER: setBox with buffer in leap (Tue Dec 12 2006 - 10:30:25 CST)
  • Re: AMBER: Atoms overlapping (Mon Dec 11 2006 - 14:08:58 CST)
  • Re: AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel? (Sun Dec 10 2006 - 18:34:15 CST)
  • Re: AMBER: Compiling Amber 9 on SGI with gcc (Sat Dec 09 2006 - 10:55:20 CST)
  • Re: AMBER: dihedral angle problem (Fri Dec 08 2006 - 20:10:36 CST)
  • Re: AMBER: RDC refinement (Fri Dec 08 2006 - 17:52:11 CST)
  • Re: AMBER: dihedral angle problem (Fri Dec 08 2006 - 17:47:39 CST)
  • Re: AMBER: description of prep file (Fri Dec 08 2006 - 16:52:30 CST)
  • Re: AMBER: Error message in methane solvent system (Fri Dec 08 2006 - 10:41:49 CST)
  • Re: AMBER: MD with positional and NMR restraints (Thu Dec 07 2006 - 17:54:33 CST)
  • Re: AMBER: MD with positional and NMR restraints (Thu Dec 07 2006 - 15:51:53 CST)
  • Re: AMBER: LEaP not recognising Phosphate group in TYR (Thu Dec 07 2006 - 11:06:17 CST)
  • Re: AMBER: how to include EXTRA POINTS in AMBER8 (Thu Dec 07 2006 - 00:14:44 CST)
  • Re: AMBER: parameter definitions (Wed Dec 06 2006 - 13:00:34 CST)
  • Re: AMBER: perturbed and unperturbed charges (Wed Dec 06 2006 - 12:22:37 CST)
  • Re: AMBER: MD with restraint (nmropt=1) (Wed Dec 06 2006 - 09:59:43 CST)
  • Re: AMBER: MD with restraint (nmropt=1) (Tue Dec 05 2006 - 15:24:37 CST)
  • Re: AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions (Mon Dec 04 2006 - 11:45:11 CST)
  • Re: AMBER: Problem with specifying NOSHAKEMASK (Mon Dec 04 2006 - 10:33:02 CST)
  • Re: AMBER: how to include EXTRA POINTS in AMBER8 (Mon Dec 04 2006 - 10:23:15 CST)
  • Re: AMBER: xleap problems (Mon Dec 04 2006 - 10:26:20 CST)
  • Re: AMBER: Problem with specifying NOSHAKEMASK (Sun Dec 03 2006 - 16:06:10 CST)
  • Re: AMBER: problem at the start of heating up (using extra-point) (Sun Dec 03 2006 - 16:04:25 CST)
  • Re: AMBER: LEaP not recognising Phosphate group in TYR (Sat Dec 02 2006 - 11:52:44 CST)
  • Re: AMBER: Making sure that Amber jobs use Infiniband? (Fri Dec 01 2006 - 18:24:44 CST)
• Ed Pate
  • AMBER: problems trying to modify Amber8 (Thu Dec 28 2006 - 16:41:33 CST)
  • AMBER: amber 9 installation problem (Wed Dec 13 2006 - 18:34:19 CST)
  • AMBER: parameter definitions (Wed Dec 06 2006 - 12:27:15 CST)
• Esther Brugger
  • AMBER: Sander--NMR refinement (Thu Dec 21 2006 - 22:39:48 CST)
  • AMBER: RDF problem (Tue Dec 12 2006 - 13:45:14 CST)
  • Re: AMBER: dihedral angle problem (Fri Dec 08 2006 - 19:00:48 CST)
  • AMBER: dihedral angle problem (Fri Dec 08 2006 - 16:53:32 CST)
  • AMBER: dihedral calculation problem (Fri Dec 01 2006 - 15:39:23 CST)
  • Re: AMBER: H-bond analysis (Ptraj) (Fri Dec 01 2006 - 13:01:25 CST)
  • AMBER: H-bond analysis (Ptraj) input file (Fri Dec 01 2006 - 10:22:44 CST)
• Evan Kelly
  • AMBER: QM/MD energy conservation (Mon Dec 11 2006 - 21:17:59 CST)
• Fenghui Fan
  • Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 00:25:41 CST)
  • Re: AMBER: bad connectivity - more detail (Tue Dec 26 2006 - 22:19:41 CST)
  • Re: AMBER: bad connectivity (Tue Dec 26 2006 - 11:33:57 CST)
  • Re: AMBER: .crd file (Tue Dec 26 2006 - 10:17:33 CST)
  • Re: AMBER: LEaP problem (Tue Dec 12 2006 - 00:32:06 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Thu Dec 07 2006 - 19:56:02 CST)
  • Re: AMBER: What's going wrong when I use antechamber dealing with lipid molecular? (Wed Dec 06 2006 - 20:51:41 CST)
  • Re: AMBER: How could I simulate lipid membrane with AMBER9.0? (Wed Dec 06 2006 - 20:49:09 CST)
  • Re: AMBER: question on protein folding simulation (Mon Dec 04 2006 - 18:47:32 CST)
  • Re: AMBER: question on protein folding simulation (Fri Dec 01 2006 - 13:56:06 CST)
• FyD
  • AMBER: Problem with LEaP (Fri Dec 22 2006 - 13:42:13 CST)
  • Re: AMBER: Amber Input file from "qout", "resp.dat" (Thu Dec 21 2006 - 04:23:09 CST)
  • Re: AMBER: RED - help with installation / config (Thu Dec 21 2006 - 03:24:50 CST)
  • Re: AMBER: RESP charge fitting for HFIP (Wed Dec 20 2006 - 01:21:42 CST)
  • Re: AMBER: RESP charge fitting for HFIP (Tue Dec 19 2006 - 01:44:05 CST)
  • Re: AMBER: AMBER - leap - problems with impose command (Sat Dec 16 2006 - 00:22:36 CST)
  • Re: AMBER: ERROR: The PDB file is not in the working directory (Fri Dec 15 2006 - 02:21:21 CST)
  • Re: AMBER: ERROR: The PDB file is not in the working directory (Tue Dec 12 2006 - 06:57:56 CST)
  • Re: AMBER: nonplanarity of NH2 groups (Thu Dec 07 2006 - 11:17:54 CST)
• Gobind Singh Bisht
  • Re: AMBER: Problem with specifying NOSHAKEMASK (Mon Dec 04 2006 - 22:26:16 CST)
  • Re: AMBER: Problem with specifying NOSHAKEMASK (Sun Dec 03 2006 - 21:11:57 CST)
  • Re: AMBER: Problem with specifying NOSHAKEMASK (Sun Dec 03 2006 - 09:26:27 CST)
  • AMBER: Problem with specifying NOSHAKEMASK (Sun Dec 03 2006 - 04:42:01 CST)
• Gustavo Seabra
  • Re: AMBER: Installation help - SGI Altix 350 (Fri Dec 22 2006 - 19:42:03 CST)
  • Re: AMBER: Amber9 - openmpi? (Wed Dec 20 2006 - 09:34:53 CST)
  • Re: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 09:31:01 CST)
  • Re: AMBER: QM/MD energy conservation (Tue Dec 12 2006 - 08:02:39 CST)
  • Re: AMBER: question on protein folding simulation (Mon Dec 04 2006 - 12:31:54 CST)
• Ilyas Yildirim
  • Re: AMBER: AMBER - leap - problems with impose command (Sun Dec 17 2006 - 02:45:13 CST)
  • Re: AMBER: AMBER - leap - problems with impose command (Sat Dec 16 2006 - 05:17:22 CST)
• j j
  • Re: AMBER: coordinate out of bounds (Thu Dec 14 2006 - 04:21:50 CST)
  • Re: AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions (Mon Dec 04 2006 - 16:28:14 CST)
  • AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions (Mon Dec 04 2006 - 11:10:26 CST)
  • Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? (Mon Dec 04 2006 - 06:56:54 CST)
  • Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? (Fri Dec 01 2006 - 14:28:24 CST)
  • Re: AMBER: How to keep an hydrogen bond during an implicit MD calculation? (Fri Dec 01 2006 - 04:59:59 CST)
  • AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? (Fri Dec 01 2006 - 04:51:06 CST)
• J. Zhang
  • AMBER: The VDW correctioin (Sun Dec 03 2006 - 20:29:28 CST)
  • AMBER: About the creation of 1-4 pairs in AMBER program (Sun Dec 03 2006 - 20:17:02 CST)
• Jardas sucuriba
  • AMBER: PCA analysis (Wed Dec 27 2006 - 23:04:41 CST)
• Jarrod Smith
  • Re: AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 17:32:36 CST)
  • Re: AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 16:13:29 CST)
  • Re: AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 15:54:18 CST)
  • AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 12:42:06 CST)
• Jiri Sponer
  • Re: AMBER: nonplanarity of NH2 groups (Thu Dec 07 2006 - 11:37:52 CST)
• Jordi Camps
  • AMBER: Parallelization method (Tue Dec 19 2006 - 12:19:40 CST)
• JunJun Liu
  • AMBER: ibelly not work (Wed Dec 06 2006 - 17:22:34 CST)
• Junmei Wang
  • RE: AMBER: Problem about dummy atoms when running antechamber (Thu Dec 07 2006 - 11:14:58 CST)
• Kailee
  • AMBER: EXTRA_PTS: frtype 2 Should not be here (Thu Dec 21 2006 - 12:26:31 CST)
  • Re: AMBER: sander: cannot execute binary file (Tue Dec 19 2006 - 10:13:48 CST)
  • Re: AMBER: sander: cannot execute binary file (Mon Dec 18 2006 - 11:06:36 CST)
  • Re: AMBER: sander: cannot execute binary file (Mon Dec 18 2006 - 10:41:11 CST)
  • Re: AMBER: sander: cannot execute binary file (Fri Dec 15 2006 - 11:25:21 CST)
  • AMBER: sander: cannot execute binary file (Thu Dec 14 2006 - 09:53:50 CST)
• kakali sen
  • AMBER: addition of subroutine in pmemd module (Mon Dec 11 2006 - 12:52:37 CST)
• Karen Callahan
  • Re: AMBER: Simulating proteins with calcium ion (Tue Dec 12 2006 - 13:19:49 CST)
• Kevin Kelliher
  • AMBER: G5 OSX serial compile error (Tue Dec 26 2006 - 15:18:56 CST)
• Lachele Foley (Lists)
  • Re: AMBER: phantom sander8 in dmesg (Mon Dec 04 2006 - 11:21:12 CST)
• laura zanet
  • AMBER: nonplanarity of NH2 groups (Wed Dec 06 2006 - 09:48:33 CST)
• Lee, Young-Tae
  • AMBER: RDC refinement (Fri Dec 08 2006 - 14:50:42 CST)
• Li Su
  • AMBER: Is there a way to simulate a box of pure water with amber (Fri Dec 15 2006 - 12:28:12 CST)
• lily ferreira
  • AMBER: MM_PBSA (Wed Dec 20 2006 - 07:46:00 CST)
  • AMBER: MM_PBSA (Wed Dec 20 2006 - 07:42:20 CST)
  • AMBER: (no subject) (Mon Dec 18 2006 - 02:14:44 CST)
• linfu
  • Re: AMBER: RESP procedure for DMPC monomer (Wed Dec 20 2006 - 18:54:43 CST)
  • AMBER: charge problem in MM-PBSA (Tue Dec 19 2006 - 19:53:52 CST)
• M. L. Dodson
  • Re: AMBER: General Question about Abmer (Mon Dec 11 2006 - 08:34:45 CST)
• mahdi fathi
  • AMBER: bugfix (Sun Dec 03 2006 - 09:17:42 CST)
• Mathy Froeyen
  • Re: AMBER: G5 OSX serial compile error (Thu Dec 28 2006 - 05:12:13 CST)
  • Re: AMBER: Installing Amber 9 on Mac Pro (Thu Dec 07 2006 - 06:54:48 CST)
• Matthew Tessier
  • AMBER: Solvating a bilayer (Fri Dec 15 2006 - 13:32:25 CST)
• Mengjuei Hsieh
  • Re: AMBER: Installing Amber 9 on Mac Pro (Mon Dec 11 2006 - 19:52:07 CST)
• Michael Crowley
  • Re: AMBER: AMBER parallel run bombs (Mon Dec 04 2006 - 19:41:32 CST)
• Michael John Hanby
  • AMBER: PMEMD and OpenMPI, anyone have config options? (Wed Dec 27 2006 - 14:04:50 CST)
  • RE: AMBER: Can't compile PMEMD (Thu Dec 14 2006 - 17:13:47 CST)
  • RE: AMBER: sander: cannot execute binary file (Thu Dec 14 2006 - 15:52:23 CST)
  • AMBER: Can't compile PMEMD (Thu Dec 14 2006 - 15:47:15 CST)
  • RE: AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel? (Sun Dec 10 2006 - 21:31:57 CST)
  • AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel? (Sun Dec 10 2006 - 14:09:34 CST)
  • AMBER: Amber9 failure to compile parallel on Rocks 4.2.1 system (Wed Dec 06 2006 - 15:26:11 CST)
  • AMBER: Making sure that Amber jobs use Infiniband? (Fri Dec 01 2006 - 16:13:05 CST)
• Miguel Ferreira
  • AMBER: coordinate out of bounds (Wed Dec 13 2006 - 19:09:57 CST)
• Mike Summers
  • Re: AMBER: MD with positional and NMR restraints (Thu Dec 07 2006 - 17:34:07 CST)
  • AMBER: MD with positional and NMR restraints (Thu Dec 07 2006 - 14:46:26 CST)
• Mingfeng Yang
  • Re: AMBER: RESP charge fitting for HFIP (Wed Dec 20 2006 - 12:31:53 CST)
  • Re: AMBER: RESP charge fitting for HFIP (Tue Dec 19 2006 - 01:17:24 CST)
  • AMBER: RESP charge fitting for HFIP (Mon Dec 18 2006 - 20:44:19 CST)
• Muhammad Naim Mohmad Rouyan
  • AMBER: Error compiling amber on parallel (MPICH) (Wed Dec 27 2006 - 00:35:47 CST)
  • AMBER: Compiling Amber8 with Sun HPC ClusterTools 5 Software (Fri Dec 22 2006 - 01:40:32 CST)
• Myunggi Yi
  • Re: AMBER: A BUG report, "ptraj corrplane" (Sun Dec 10 2006 - 19:32:22 CST)
  • AMBER: A BUG report, "ptraj corrplane" (Tue Dec 05 2006 - 11:42:08 CST)
  • AMBER: ptraj vector corrplane bug (Mon Dec 04 2006 - 14:49:46 CST)
• Navnit Kumar Mishra
  • Re: AMBER: Nucgen Problem (Fri Dec 22 2006 - 03:55:26 CST)
• Nicolas Lux Fawzi
  • AMBER: sander ntc=2 ntf=1 (Mon Dec 18 2006 - 21:10:42 CST)
  • Re: AMBER: Volume of ucell too big (Sat Dec 16 2006 - 12:37:31 CST)
  • Re: AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 12:32:35 CST)
• Nikola Trbovic
  • Re: AMBER: amber9 parralel compiling (Fri Dec 01 2006 - 10:46:33 CST)
• Nitin Bhardwaj
  • AMBER: Coodinates not being unique (Mon Dec 11 2006 - 18:50:41 CST)
  • Re: AMBER: Atoms overlapping (Mon Dec 11 2006 - 14:48:53 CST)
  • AMBER: Atoms overlapping (Mon Dec 11 2006 - 13:43:44 CST)
• Noriaki Okimoto
  • Re: AMBER: question on protein folding simulation (Thu Dec 07 2006 - 06:25:51 CST)
  • Re: AMBER: question on protein folding simulation (Sun Dec 03 2006 - 20:43:11 CST)
  • Re: AMBER: question on protein folding simulation (Sun Dec 03 2006 - 20:51:17 CST)
  • AMBER: question on protein folding simulation (Fri Dec 01 2006 - 06:01:27 CST)
• Piotr Cieplak
  • AMBER: problems with Calcium ions treatment in GB run (Thu Dec 28 2006 - 17:44:23 CST)
  • Re: AMBER: AMBER - leap - problems with impose command (Sun Dec 17 2006 - 01:20:28 CST)
  • Re: AMBER: AMBER - leap - problems with impose command (Sat Dec 16 2006 - 01:04:05 CST)
  • AMBER: AMBER - leap - problems with impose command (Fri Dec 15 2006 - 12:18:06 CST)
  • AMBER: description of prep file (Fri Dec 08 2006 - 16:28:29 CST)
  • AMBER: Zn2+ and Ca2+ ions explicitly treated in MMPB/GB/SA (Mon Dec 04 2006 - 18:20:02 CST)
• puneet kacker
  • AMBER: Nucgen Problem (Fri Dec 22 2006 - 02:06:41 CST)
• Qing Zhang
  • Re: AMBER: Simulating proteins with calcium ion (Sat Dec 23 2006 - 01:26:11 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 14:22:53 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 14:17:05 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 13:32:43 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Fri Dec 08 2006 - 18:31:02 CST)
  • AMBER: Simulating proteins with calcium ion (Thu Dec 07 2006 - 18:15:42 CST)
• Qizhi Cui
  • AMBER: ISTRNG or SALT in MM_PBSA (Wed Dec 13 2006 - 21:23:48 CST)
• Rachel
  • Re: AMBER: Unit 5 Error on OPEN: md.in (Sat Dec 16 2006 - 12:01:12 CST)
  • AMBER: Unit 5 Error on OPEN: md.in (Wed Dec 13 2006 - 13:55:58 CST)
  • AMBER: perturbed and unperturbed charges (Wed Dec 06 2006 - 11:24:24 CST)
  • Re: AMBER: how to include EXTRA POINTS in AMBER8 (Mon Dec 04 2006 - 12:35:08 CST)
  • Re: AMBER: how to include EXTRA POINTS in AMBER8 (Mon Dec 04 2006 - 11:03:11 CST)
  • AMBER: how to include EXTRA POINTS in AMBER8 (Mon Dec 04 2006 - 09:59:34 CST)
  • AMBER: problem at the start of heating up (using extra-point) (Sat Dec 02 2006 - 09:29:09 CST)
• Rahaman, Asif
  • AMBER: AMBER parallel run bombs (Mon Dec 04 2006 - 18:29:53 CST)
• Ravinder Abrol
  • Re: AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 18:58:36 CST)
  • Re: AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 11:38:23 CST)
  • AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 01:09:08 CST)
• Raviprasad Aduri
  • Re: AMBER: RESP charge fitting for HFIP (Mon Dec 18 2006 - 21:46:05 CST)
• Ray Luo
  • RE: AMBER: MM-PBSA problem (Tue Dec 05 2006 - 13:16:32 CST)
  • RE: AMBER: MM-PBSA problem (Sat Dec 02 2006 - 09:55:46 CST)
  • RE: AMBER: MM-PBSA problem (Fri Dec 01 2006 - 15:51:52 CST)
• Robert Duke
  • Re: AMBER: Amber9 - openmpi? (Wed Dec 20 2006 - 07:23:10 CST)
  • Re: AMBER: Parallelization method (Tue Dec 19 2006 - 12:29:09 CST)
  • Re: AMBER: Can't compile PMEMD (Thu Dec 14 2006 - 17:42:02 CST)
  • Re: AMBER: Can't compile PMEMD (Thu Dec 14 2006 - 16:12:12 CST)
  • Re: AMBER: parallel computation time vs serial computation time (Thu Dec 14 2006 - 08:16:22 CST)
  • Re: AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 16:41:52 CST)
  • Re: AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 14:22:23 CST)
  • Re: AMBER: PMEMD scaling (Thu Dec 07 2006 - 08:17:46 CST)
• Ross Walker
  • AMBER: RE: protein simulation using AMBER (Sat Dec 30 2006 - 00:51:09 CST)
  • RE: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 23:30:53 CST)
  • RE: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 22:36:10 CST)
  • RE: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 10:38:16 CST)
  • RE: AMBER: sander: cannot execute binary file (Mon Dec 18 2006 - 13:52:05 CST)
  • RE: AMBER: Is there a way to simulate a box of pure water with amber (Fri Dec 15 2006 - 12:52:53 CST)
  • RE: AMBER: sander: cannot execute binary file (Thu Dec 14 2006 - 17:15:46 CST)
  • AMBER: Test Message Please Ignore. (Thu Dec 14 2006 - 15:01:07 CST)
  • AMBER: Test Message Please Ignore (Thu Dec 14 2006 - 15:01:07 CST)
  • RE: AMBER: Atom Type problem (Fri Dec 08 2006 - 10:21:19 CST)
  • RE: AMBER: atome type error (Fri Dec 08 2006 - 09:51:29 CST)
  • RE: AMBER: ibelly not work (Wed Dec 06 2006 - 18:07:45 CST)
  • RE: AMBER: Amber9 failure to compile parallel on Rocks 4.2.1 system (Wed Dec 06 2006 - 16:48:51 CST)
• Russell Glavey
  • AMBER: tetrolic acid (Thu Dec 21 2006 - 06:29:35 CST)
• sai vikram
  • Re: AMBER: Simulated Annealing problem... (Sat Dec 30 2006 - 07:12:53 CST)
  • AMBER: Simulated Annealing problem... (Fri Dec 29 2006 - 04:33:50 CST)
• Sanya Kryklia
  • AMBER: General Question about Abmer (Mon Dec 11 2006 - 08:23:11 CST)
• saurabh agrawal
  • AMBER: Amber Input file from "qout", "resp.dat" (Thu Dec 21 2006 - 03:41:47 CST)
  • Re: AMBER: ERROR: The PDB file is not in the working directory (Thu Dec 14 2006 - 05:38:05 CST)
  • Re: AMBER: ERROR: The PDB file is not in the working directory (Thu Dec 14 2006 - 01:18:33 CST)
  • AMBER: ERROR: The PDB file is not in the working directory (Tue Dec 12 2006 - 05:39:39 CST)
• Scott Brozell
  • RE: AMBER: Error in sysdepend.c? (Tue Dec 19 2006 - 13:19:38 CST)
  • Re: AMBER: Parallelization method (Tue Dec 19 2006 - 12:58:07 CST)
  • Re: AMBER: setBox with buffer in leap (Mon Dec 11 2006 - 23:08:38 CST)
  • Re: AMBER: Compiling Amber 9 on SGI with gcc (Fri Dec 08 2006 - 21:29:15 CST)
  • Re: AMBER: sander error about fortran (Mon Dec 04 2006 - 15:26:52 CST)
  • Re: AMBER: sander error about fortran (Sat Dec 02 2006 - 01:10:03 CST)
  • Re: AMBER: amber9 parralel compiling (Fri Dec 01 2006 - 13:40:54 CST)
• Seongeun Yang
  • AMBER: Replica exchange rate in REMD (Thu Dec 21 2006 - 05:42:59 CST)
• Sergey Samsonov
  • Re: AMBER: Is there a way to simulate a box of pure water with amber (Mon Dec 18 2006 - 01:43:27 CST)
  • Re: AMBER: Free energy perturbation in SANDER (Thu Dec 14 2006 - 03:38:46 CST)
• Seth Lilavivat
  • AMBER: chirality.c line 121 (Wed Dec 27 2006 - 15:43:56 CST)
  • Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 13:42:42 CST)
  • Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 11:44:29 CST)
  • AMBER: recompiling bondtype.C (Wed Dec 27 2006 - 10:49:32 CST)
  • Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 10:26:14 CST)
  • AMBER: bad connectivity (Tue Dec 26 2006 - 11:24:17 CST)
  • AMBER: bad connectivity - more detail (Tue Dec 26 2006 - 12:02:27 CST)
  • AMBER: xleap, generating prep file (Thu Dec 21 2006 - 10:49:56 CST)
  • AMBER: RED - help with installation / config (Wed Dec 20 2006 - 09:18:49 CST)
• Shin Tokumoto
  • Re: AMBER: RESP charges of iron-porphyrin system (Thu Dec 14 2006 - 03:31:13 CST)
• Shin, John Y CONTRACTOR WRAIR-Wash DC
  • RE: AMBER: Error in sysdepend.c? (Tue Dec 19 2006 - 15:29:12 CST)
  • RE: AMBER: Error in sysdepend.c? (Mon Dec 18 2006 - 14:27:24 CST)
  • AMBER: Error in sysdepend.c? (Fri Dec 15 2006 - 13:44:50 CST)
  • AMBER: Compiling Amber 9 on SGI with gcc (Fri Dec 08 2006 - 12:46:32 CST)
• Shozeb Haider
  • AMBER: MM-PBSA (Mon Dec 18 2006 - 11:57:17 CST)
• Shuting Wei
  • AMBER: DRMS setting for Nmode calculation (Thu Dec 07 2006 - 14:46:54 CST)
  • Re: AMBER: sander error about fortran (Mon Dec 04 2006 - 11:02:52 CST)
  • AMBER: sander error about fortran (Fri Dec 01 2006 - 09:58:25 CST)
• Steve Seibold
  • AMBER: Frozen at Minimization (Tue Dec 19 2006 - 08:18:21 CST)
  • AMBER: Building Parameters (Mon Dec 11 2006 - 15:29:15 CST)
  • RE: AMBER: Atom Type problem (Fri Dec 08 2006 - 12:09:05 CST)
  • AMBER: Atom Type problem (Fri Dec 08 2006 - 10:04:29 CST)
  • AMBER: Atom Type problem (Fri Dec 08 2006 - 10:01:23 CST)
  • AMBER: atome type error (Fri Dec 08 2006 - 09:08:35 CST)
• Steven Winfield
  • AMBER: setBox with buffer in leap (Wed Dec 06 2006 - 18:43:58 CST)
  • AMBER: setBox with buffer in leap (Wed Dec 06 2006 - 13:05:22 CST)
• Thomas Cheatham
  • Re: AMBER: rdparm (Sat Dec 16 2006 - 21:43:55 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Thu Dec 07 2006 - 21:23:26 CST)
  • Re: AMBER: MD with restraint (nmropt=1) (Wed Dec 06 2006 - 23:14:56 CST)
  • Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? (Fri Dec 01 2006 - 16:01:35 CST)
  • Re: AMBER: H-bond analysis (Ptraj) (Fri Dec 01 2006 - 12:00:05 CST)
  • Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? (Fri Dec 01 2006 - 11:53:50 CST)
  • Re: AMBER: H-bond analysis (Ptraj) input file (Fri Dec 01 2006 - 11:56:57 CST)
• Thomas Steinbrecher
  • Re: AMBER: Atoms overlapping (Mon Dec 11 2006 - 16:11:47 CST)
• Tim Meyer
  • Re: AMBER: rdparm (Tue Dec 19 2006 - 09:22:45 CST)
• Tiziano Tuccinardi
  • AMBER: PMEMD scaling (Thu Dec 07 2006 - 02:46:49 CST)
• tongli
  • AMBER: about the std of computational alanine scanning (Fri Dec 01 2006 - 05:50:11 CST)
• vanessa wai
  • Re: AMBER: MM-PBSA problem (Tue Dec 05 2006 - 19:33:35 CST)
  • Re: AMBER: MM-PBSA problem (Sun Dec 03 2006 - 19:52:25 CST)
  • Re: AMBER: MM-PBSA problem (Sat Dec 02 2006 - 03:08:15 CST)
  • Re: AMBER: MM-PBSA problem (Sat Dec 02 2006 - 03:11:18 CST)
• Varsha Goyal
  • Re: AMBER: MM-PBSA problem (Fri Dec 01 2006 - 15:35:27 CST)
• venditti2_at_unisi.it
  • AMBER: rdparm (Fri Dec 15 2006 - 10:08:17 CST)
• vic_at_mail.nankai.edu.cn
  • AMBER: A problem with mm_pbsa (Mon Dec 25 2006 - 19:41:41 CST)
• wenfei Li
  • Re: AMBER: problem of the REMD with nmr constraints (Thu Dec 07 2006 - 18:55:04 CST)
• xiaoqin huang
  • AMBER: tree name generated by tleap is different from the input PREP parameter file (Thu Dec 28 2006 - 18:53:39 CST)
  • AMBER: tree name generated by tleap is different from the input PREP parameter file (Thu Dec 28 2006 - 10:48:14 CST)
• Ye Mei
  • Re: AMBER: bugfix (Sun Dec 03 2006 - 09:38:40 CST)
• Yong Duan
  • RE: AMBER: question on protein folding simulation (Tue Dec 05 2006 - 13:57:45 CST)
  • RE: AMBER: question on protein folding simulation (Fri Dec 01 2006 - 12:32:58 CST)
• Yumi Nukusina
  • AMBER: Free energy perturbation in SANDER (Thu Dec 14 2006 - 02:59:36 CST)
• ²ÜȽ
  • Re:AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 11:12:05 CST)
  • Re: AMBER: How could I simulate lipid membrane with AMBER9.0? (Thu Dec 07 2006 - 19:46:44 CST)
  • AMBER: What's going wrong when I use antechamber dealing with lipid molecular? (Wed Dec 06 2006 - 19:05:55 CST)
  • AMBER: How could I simulate lipid membrane with AMBER9.0? (Wed Dec 06 2006 - 19:02:55 CST)
• ÕÅÓÂ
  • Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 19:02:57 CST)
  • Re: AMBER: Simulating proteins with calcium ion (Tue Dec 12 2006 - 18:25:03 CST)

Last message date: Sat Dec 30 2006 - 07:20:23 CST
Archived on: Wed Feb 21 2007 - 22:44:17 CST