Amber Archive Dec 2006: by author

a a
- Re: AMBER: MD with restraint (nmropt=1) (Wed Dec 06 2006 - 20:48:32 PST)
- Re: AMBER: MD with restraint (nmropt=1) (Tue Dec 05 2006 - 22:11:59 PST)
- AMBER: MD with restraint (nmropt=1) (Tue Dec 05 2006 - 00:11:38 PST)
- AMBER: How to keep an hydrogen bond during an implicit MD calculation? (Fri Dec 01 2006 - 02:35:31 PST)
- Re: AMBER: How to apply a force to some atom in a residues? (Fri Dec 01 2006 - 02:26:51 PST)
A Box
- AMBER: Amber 9 Leap install error (Sun Dec 17 2006 - 20:06:52 PST)
Akshay Patny
- RE: AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 09:46:45 PST)
- AMBER: RESP procedure for DMPC monomer (Wed Dec 20 2006 - 08:04:00 PST)
- AMBER: Renumber residues in LEAP (Tue Dec 19 2006 - 13:55:57 PST)
Andy Purkiss-Trew
- RE: AMBER: ibelly not work (Thu Dec 07 2006 - 04:33:24 PST)
Angelo
- Re: AMBER: MM-PBSA (Mon Dec 18 2006 - 08:30:00 PST)
anna.schrey.gmx.de
- AMBER: xleap problems (Mon Dec 04 2006 - 03:45:07 PST)
Atsutoshi Okabe
- AMBER: Volume of ucell too big (Sat Dec 16 2006 - 00:41:43 PST)
- AMBER: Error message in methane solvent system (Thu Dec 07 2006 - 19:19:04 PST)
bertrand russell
- AMBER: .crd file (Tue Dec 26 2006 - 01:16:53 PST)
- Re: AMBER: Installation help - SGI Altix 350 (Tue Dec 26 2006 - 00:25:10 PST)
- Re: AMBER: Installation help - SGI Altix 350 (Thu Dec 21 2006 - 21:51:48 PST)
- Re: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 21:09:48 PST)
- Re: AMBER: Amber9 - openmpi? (Wed Dec 20 2006 - 20:16:22 PST)
- Re: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 20:13:03 PST)
- AMBER: Amber9 - openmpi? (Wed Dec 20 2006 - 03:22:37 PST)
- AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 02:47:03 PST)
- Re: AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 09:35:16 PST)
- AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 02:03:53 PST)
- AMBER: LEaP problem (Mon Dec 11 2006 - 21:10:48 PST)
- Re: AMBER: LEaP not recognising Phosphate group in TYR (Thu Dec 07 2006 - 02:39:46 PST)
- AMBER: LEaP not recognising Phosphate group in TYR (Sat Dec 02 2006 - 08:41:23 PST)
Bill Ross
- Re: AMBER: tree name generated by tleap is different from the input PREP parameter file (Fri Dec 29 2006 - 19:00:26 PST)
- Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 13:12:50 PST)
- Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 11:51:07 PST)
- Re: AMBER: Nucgen Problem (Fri Dec 22 2006 - 10:51:25 PST)
- Re: AMBER: Is there a way to simulate a box of pure water with amber (Fri Dec 15 2006 - 11:06:49 PST)
- Re: AMBER: Simulating proteins with calcium ion (Tue Dec 12 2006 - 11:47:48 PST)
- Re: AMBER: LEaP problem (Mon Dec 11 2006 - 22:24:33 PST)
Burkhard Heil
- AMBER: Installing Amber 9 on Mac Pro (Thu Dec 07 2006 - 02:54:00 PST)
Carlos Simmerling
- Re: AMBER: sander ntc=2 ntf=1 (Tue Dec 19 2006 - 03:39:38 PST)
- Re: AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 10:54:37 PST)
- Re: AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 05:22:04 PST)
- Re: AMBER: question on protein folding simulation (Mon Dec 04 2006 - 04:32:16 PST)
- Re: AMBER: Problem with specifying NOSHAKEMASK (Sun Dec 03 2006 - 05:48:56 PST)
Cenk Andac
- AMBER: parallel computation time vs serial computation time (Thu Dec 14 2006 - 03:17:28 PST)
- Re: AMBER: xleap problems (Mon Dec 04 2006 - 07:46:34 PST)
- Re: AMBER: problem at the start of heating up (using extra-point) (Sat Dec 02 2006 - 09:32:50 PST)
- AMBER: LogP (Sat Dec 02 2006 - 02:44:06 PST)
Chengwen Chen
- AMBER: AMBER complile problem (Thu Dec 28 2006 - 23:41:21 PST)
- Re: AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes (Tue Dec 12 2006 - 23:01:03 PST)
Chris Moth
- Re: AMBER: Frozen at Minimization (Tue Dec 19 2006 - 07:01:16 PST)
- Re: AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 10:35:13 PST)
- Re: AMBER: Unit 5 Error on OPEN: md.in (Sat Dec 16 2006 - 10:27:17 PST)
- Re: AMBER: Unit 5 Error on OPEN: md.in (Sat Dec 16 2006 - 10:25:03 PST)
- AMBER: Free energy perturbation in SANDER (Thu Dec 14 2006 - 06:21:11 PST)
Christophe Guilbert
- Re: AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 11:51:18 PST)
David A. Case
- Re: AMBER: Simulated Annealing problem... (Fri Dec 29 2006 - 08:56:06 PST)
- Re: AMBER: bad connectivity - more detail (Fri Dec 29 2006 - 00:15:16 PST)
- Re: AMBER: problems with Calcium ions treatment in GB run (Thu Dec 28 2006 - 23:56:25 PST)
- Re: AMBER: AMBER complile problem (Thu Dec 28 2006 - 23:51:49 PST)
- Re: AMBER: chirality.c line 121 (Wed Dec 27 2006 - 14:46:21 PST)
- Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 10:31:58 PST)
- Re: AMBER: recompiling bondtype.C (Wed Dec 27 2006 - 10:30:10 PST)
- Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 08:52:41 PST)
- Re: AMBER: Error compiling amber on parallel (MPICH) (Wed Dec 27 2006 - 08:41:21 PST)
- Re: AMBER: Installation help - SGI Altix 350 (Tue Dec 26 2006 - 13:45:54 PST)
- Re: AMBER: Sander--NMR refinement (Tue Dec 26 2006 - 10:44:46 PST)
- Re: AMBER: EXTRA_PTS: frtype 2 Should not be here (Mon Dec 25 2006 - 14:32:11 PST)
- Re: AMBER: MM_PBSA (Mon Dec 25 2006 - 14:15:26 PST)
- Re: AMBER: Renumber residues in LEAP (Mon Dec 25 2006 - 14:11:34 PST)
- Re: AMBER: Compiling Amber8 with Sun HPC ClusterTools 5 Software (Sat Dec 23 2006 - 18:58:29 PST)
- Re: AMBER: Amber 9 Leap install error (Sun Dec 17 2006 - 21:54:56 PST)
- Re: AMBER: Error in sysdepend.c? (Fri Dec 15 2006 - 15:24:00 PST)
- Re: AMBER: sander: cannot execute binary file (Fri Dec 15 2006 - 09:48:49 PST)
- Re: AMBER: setBox with buffer in leap (Tue Dec 12 2006 - 08:30:25 PST)
- Re: AMBER: Atoms overlapping (Mon Dec 11 2006 - 12:08:58 PST)
- Re: AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel? (Sun Dec 10 2006 - 16:34:15 PST)
- Re: AMBER: Compiling Amber 9 on SGI with gcc (Sat Dec 09 2006 - 08:55:20 PST)
- Re: AMBER: dihedral angle problem (Fri Dec 08 2006 - 18:10:36 PST)
- Re: AMBER: RDC refinement (Fri Dec 08 2006 - 15:52:11 PST)
- Re: AMBER: dihedral angle problem (Fri Dec 08 2006 - 15:47:39 PST)
- Re: AMBER: description of prep file (Fri Dec 08 2006 - 14:52:30 PST)
- Re: AMBER: Error message in methane solvent system (Fri Dec 08 2006 - 08:41:49 PST)
- Re: AMBER: MD with positional and NMR restraints (Thu Dec 07 2006 - 15:54:33 PST)
- Re: AMBER: MD with positional and NMR restraints (Thu Dec 07 2006 - 13:51:53 PST)
- Re: AMBER: LEaP not recognising Phosphate group in TYR (Thu Dec 07 2006 - 09:06:17 PST)
- Re: AMBER: how to include EXTRA POINTS in AMBER8 (Wed Dec 06 2006 - 22:14:44 PST)
- Re: AMBER: parameter definitions (Wed Dec 06 2006 - 11:00:34 PST)
- Re: AMBER: perturbed and unperturbed charges (Wed Dec 06 2006 - 10:22:37 PST)
- Re: AMBER: MD with restraint (nmropt=1) (Wed Dec 06 2006 - 07:59:43 PST)
- Re: AMBER: MD with restraint (nmropt=1) (Tue Dec 05 2006 - 13:24:37 PST)
- Re: AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions (Mon Dec 04 2006 - 09:45:11 PST)
- Re: AMBER: Problem with specifying NOSHAKEMASK (Mon Dec 04 2006 - 08:33:02 PST)
- Re: AMBER: xleap problems (Mon Dec 04 2006 - 08:26:20 PST)
- Re: AMBER: how to include EXTRA POINTS in AMBER8 (Mon Dec 04 2006 - 08:23:15 PST)
- Re: AMBER: problem at the start of heating up (using extra-point) (Sun Dec 03 2006 - 14:04:25 PST)
- Re: AMBER: Problem with specifying NOSHAKEMASK (Sun Dec 03 2006 - 14:06:10 PST)
- Re: AMBER: LEaP not recognising Phosphate group in TYR (Sat Dec 02 2006 - 09:52:44 PST)
- Re: AMBER: Making sure that Amber jobs use Infiniband? (Fri Dec 01 2006 - 16:24:44 PST)
Ed Pate
- AMBER: problems trying to modify Amber8 (Thu Dec 28 2006 - 14:41:33 PST)
- AMBER: amber 9 installation problem (Wed Dec 13 2006 - 16:34:19 PST)
- AMBER: parameter definitions (Wed Dec 06 2006 - 10:27:15 PST)
Esther Brugger
- AMBER: Sander--NMR refinement (Thu Dec 21 2006 - 20:39:48 PST)
- AMBER: RDF problem (Tue Dec 12 2006 - 11:45:14 PST)
- Re: AMBER: dihedral angle problem (Fri Dec 08 2006 - 17:00:48 PST)
- AMBER: dihedral angle problem (Fri Dec 08 2006 - 14:53:32 PST)
- AMBER: dihedral calculation problem (Fri Dec 01 2006 - 13:39:23 PST)
- Re: AMBER: H-bond analysis (Ptraj) (Fri Dec 01 2006 - 11:01:25 PST)
- AMBER: H-bond analysis (Ptraj) input file (Fri Dec 01 2006 - 08:22:44 PST)
Evan Kelly
- AMBER: QM/MD energy conservation (Mon Dec 11 2006 - 19:17:59 PST)
Fenghui Fan
- Re: AMBER: bad connectivity - more detail (Tue Dec 26 2006 - 22:25:41 PST)
- Re: AMBER: bad connectivity - more detail (Tue Dec 26 2006 - 20:19:41 PST)
- Re: AMBER: bad connectivity (Tue Dec 26 2006 - 09:33:57 PST)
- Re: AMBER: .crd file (Tue Dec 26 2006 - 08:17:33 PST)
- Re: AMBER: LEaP problem (Mon Dec 11 2006 - 22:32:06 PST)
- Re: AMBER: Simulating proteins with calcium ion (Thu Dec 07 2006 - 17:56:02 PST)
- Re: AMBER: What's going wrong when I use antechamber dealing with lipid molecular? (Wed Dec 06 2006 - 18:51:41 PST)
- Re: AMBER: How could I simulate lipid membrane with AMBER9.0? (Wed Dec 06 2006 - 18:49:09 PST)
- Re: AMBER: question on protein folding simulation (Mon Dec 04 2006 - 16:47:32 PST)
- Re: AMBER: question on protein folding simulation (Fri Dec 01 2006 - 11:56:06 PST)
FyD
- AMBER: Problem with LEaP (Fri Dec 22 2006 - 11:42:13 PST)
- Re: AMBER: Amber Input file from "qout", "resp.dat" (Thu Dec 21 2006 - 02:23:09 PST)
- Re: AMBER: RED - help with installation / config (Thu Dec 21 2006 - 01:24:50 PST)
- Re: AMBER: RESP charge fitting for HFIP (Tue Dec 19 2006 - 23:21:42 PST)
- Re: AMBER: RESP charge fitting for HFIP (Mon Dec 18 2006 - 23:44:05 PST)
- Re: AMBER: AMBER - leap - problems with impose command (Fri Dec 15 2006 - 22:22:36 PST)
- Re: AMBER: ERROR: The PDB file is not in the working directory (Fri Dec 15 2006 - 00:21:21 PST)
- Re: AMBER: ERROR: The PDB file is not in the working directory (Tue Dec 12 2006 - 04:57:56 PST)
- Re: AMBER: nonplanarity of NH2 groups (Thu Dec 07 2006 - 09:17:54 PST)
Gobind Singh Bisht
- Re: AMBER: Problem with specifying NOSHAKEMASK (Mon Dec 04 2006 - 20:26:16 PST)
- Re: AMBER: Problem with specifying NOSHAKEMASK (Sun Dec 03 2006 - 19:11:57 PST)
- Re: AMBER: Problem with specifying NOSHAKEMASK (Sun Dec 03 2006 - 07:26:27 PST)
- AMBER: Problem with specifying NOSHAKEMASK (Sun Dec 03 2006 - 02:42:01 PST)
Gustavo Seabra
- Re: AMBER: Installation help - SGI Altix 350 (Fri Dec 22 2006 - 17:42:03 PST)
- Re: AMBER: Amber9 - openmpi? (Wed Dec 20 2006 - 07:34:53 PST)
- Re: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 07:31:01 PST)
- Re: AMBER: QM/MD energy conservation (Tue Dec 12 2006 - 06:02:39 PST)
- Re: AMBER: question on protein folding simulation (Mon Dec 04 2006 - 10:31:54 PST)
Ilyas Yildirim
- Re: AMBER: AMBER - leap - problems with impose command (Sun Dec 17 2006 - 00:45:13 PST)
- Re: AMBER: AMBER - leap - problems with impose command (Sat Dec 16 2006 - 03:17:22 PST)
j j
- Re: AMBER: coordinate out of bounds (Thu Dec 14 2006 - 02:21:50 PST)
- Re: AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions (Mon Dec 04 2006 - 14:28:14 PST)
- AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions (Mon Dec 04 2006 - 09:10:26 PST)
- Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? (Mon Dec 04 2006 - 04:56:54 PST)
- Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? (Fri Dec 01 2006 - 12:28:24 PST)
- Re: AMBER: How to keep an hydrogen bond during an implicit MD calculation? (Fri Dec 01 2006 - 02:59:59 PST)
- AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? (Fri Dec 01 2006 - 02:51:06 PST)
J. Zhang
- AMBER: The VDW correctioin (Sun Dec 03 2006 - 18:29:28 PST)
- AMBER: About the creation of 1-4 pairs in AMBER program (Sun Dec 03 2006 - 18:17:02 PST)
Jardas sucuriba
- AMBER: PCA analysis (Wed Dec 27 2006 - 21:04:41 PST)
Jarrod Smith
- Re: AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 15:32:36 PST)
- Re: AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 14:13:29 PST)
- Re: AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 13:54:18 PST)
- AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 10:42:06 PST)
Jiri Sponer
- Re: AMBER: nonplanarity of NH2 groups (Thu Dec 07 2006 - 09:37:52 PST)
Jordi Camps
- AMBER: Parallelization method (Tue Dec 19 2006 - 10:19:40 PST)
JunJun Liu
- AMBER: ibelly not work (Wed Dec 06 2006 - 15:22:34 PST)
Junmei Wang
- RE: AMBER: Problem about dummy atoms when running antechamber (Thu Dec 07 2006 - 09:14:58 PST)
Kailee
- AMBER: EXTRA_PTS: frtype 2 Should not be here (Thu Dec 21 2006 - 10:26:31 PST)
- Re: AMBER: sander: cannot execute binary file (Tue Dec 19 2006 - 08:13:48 PST)
- Re: AMBER: sander: cannot execute binary file (Mon Dec 18 2006 - 09:06:36 PST)
- Re: AMBER: sander: cannot execute binary file (Mon Dec 18 2006 - 08:41:11 PST)
- Re: AMBER: sander: cannot execute binary file (Fri Dec 15 2006 - 09:25:21 PST)
- AMBER: sander: cannot execute binary file (Thu Dec 14 2006 - 07:53:50 PST)
kakali sen
- AMBER: addition of subroutine in pmemd module (Mon Dec 11 2006 - 10:52:37 PST)
Karen Callahan
- Re: AMBER: Simulating proteins with calcium ion (Tue Dec 12 2006 - 11:19:49 PST)
Kevin Kelliher
- AMBER: G5 OSX serial compile error (Tue Dec 26 2006 - 13:18:56 PST)
Lachele Foley (Lists)
- Re: AMBER: phantom sander8 in dmesg (Mon Dec 04 2006 - 09:21:12 PST)
laura zanet
- AMBER: nonplanarity of NH2 groups (Wed Dec 06 2006 - 07:48:33 PST)
Lee, Young-Tae
- AMBER: RDC refinement (Fri Dec 08 2006 - 12:50:42 PST)
Li Su
- AMBER: Is there a way to simulate a box of pure water with amber (Fri Dec 15 2006 - 10:28:12 PST)
lily ferreira
- AMBER: MM_PBSA (Wed Dec 20 2006 - 05:46:00 PST)
- AMBER: MM_PBSA (Wed Dec 20 2006 - 05:42:20 PST)
- AMBER: (no subject) (Mon Dec 18 2006 - 00:14:44 PST)
linfu
- Re: AMBER: RESP procedure for DMPC monomer (Wed Dec 20 2006 - 16:54:43 PST)
- AMBER: charge problem in MM-PBSA (Tue Dec 19 2006 - 17:53:52 PST)
M. L. Dodson
- Re: AMBER: General Question about Abmer (Mon Dec 11 2006 - 06:34:45 PST)
mahdi fathi
- AMBER: bugfix (Sun Dec 03 2006 - 07:17:42 PST)
Mathy Froeyen
- Re: AMBER: G5 OSX serial compile error (Thu Dec 28 2006 - 03:12:13 PST)
- Re: AMBER: Installing Amber 9 on Mac Pro (Thu Dec 07 2006 - 04:54:48 PST)
Matthew Tessier
- AMBER: Solvating a bilayer (Fri Dec 15 2006 - 11:32:25 PST)
Mengjuei Hsieh
- Re: AMBER: Installing Amber 9 on Mac Pro (Mon Dec 11 2006 - 17:52:07 PST)
Michael Crowley
- Re: AMBER: AMBER parallel run bombs (Mon Dec 04 2006 - 17:41:32 PST)
Michael John Hanby
- AMBER: PMEMD and OpenMPI, anyone have config options? (Wed Dec 27 2006 - 12:04:50 PST)
- RE: AMBER: Can't compile PMEMD (Thu Dec 14 2006 - 15:13:47 PST)
- RE: AMBER: sander: cannot execute binary file (Thu Dec 14 2006 - 13:52:23 PST)
- AMBER: Can't compile PMEMD (Thu Dec 14 2006 - 13:47:15 PST)
- RE: AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel? (Sun Dec 10 2006 - 19:31:57 PST)
- AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel? (Sun Dec 10 2006 - 12:09:34 PST)
- AMBER: Amber9 failure to compile parallel on Rocks 4.2.1 system (Wed Dec 06 2006 - 13:26:11 PST)
- AMBER: Making sure that Amber jobs use Infiniband? (Fri Dec 01 2006 - 14:13:05 PST)
Miguel Ferreira
- AMBER: coordinate out of bounds (Wed Dec 13 2006 - 17:09:57 PST)
Mike Summers
- Re: AMBER: MD with positional and NMR restraints (Thu Dec 07 2006 - 15:34:07 PST)
- AMBER: MD with positional and NMR restraints (Thu Dec 07 2006 - 12:46:26 PST)
Mingfeng Yang
- Re: AMBER: RESP charge fitting for HFIP (Wed Dec 20 2006 - 10:31:53 PST)
- Re: AMBER: RESP charge fitting for HFIP (Mon Dec 18 2006 - 23:17:24 PST)
- AMBER: RESP charge fitting for HFIP (Mon Dec 18 2006 - 18:44:19 PST)
Muhammad Naim Mohmad Rouyan
- AMBER: Error compiling amber on parallel (MPICH) (Tue Dec 26 2006 - 22:35:47 PST)
- AMBER: Compiling Amber8 with Sun HPC ClusterTools 5 Software (Thu Dec 21 2006 - 23:40:32 PST)
Myunggi Yi
- Re: AMBER: A BUG report, "ptraj corrplane" (Sun Dec 10 2006 - 17:32:22 PST)
- AMBER: A BUG report, "ptraj corrplane" (Tue Dec 05 2006 - 09:42:08 PST)
- AMBER: ptraj vector corrplane bug (Mon Dec 04 2006 - 12:49:46 PST)
Navnit Kumar Mishra
- Re: AMBER: Nucgen Problem (Fri Dec 22 2006 - 01:55:26 PST)
Nicolas Lux Fawzi
- AMBER: sander ntc=2 ntf=1 (Mon Dec 18 2006 - 19:10:42 PST)
- Re: AMBER: Volume of ucell too big (Sat Dec 16 2006 - 10:37:31 PST)
- Re: AMBER: How to make a movie with .crd files in VMD? (Sat Dec 16 2006 - 10:32:35 PST)
Nikola Trbovic
- Re: AMBER: amber9 parralel compiling (Fri Dec 01 2006 - 08:46:33 PST)
Nitin Bhardwaj
- AMBER: Coodinates not being unique (Mon Dec 11 2006 - 16:50:41 PST)
- Re: AMBER: Atoms overlapping (Mon Dec 11 2006 - 12:48:53 PST)
- AMBER: Atoms overlapping (Mon Dec 11 2006 - 11:43:44 PST)
Noriaki Okimoto
- Re: AMBER: question on protein folding simulation (Thu Dec 07 2006 - 04:25:51 PST)
- Re: AMBER: question on protein folding simulation (Sun Dec 03 2006 - 18:51:17 PST)
- Re: AMBER: question on protein folding simulation (Sun Dec 03 2006 - 18:43:11 PST)
- AMBER: question on protein folding simulation (Fri Dec 01 2006 - 04:01:27 PST)
Piotr Cieplak
- AMBER: problems with Calcium ions treatment in GB run (Thu Dec 28 2006 - 15:44:23 PST)
- Re: AMBER: AMBER - leap - problems with impose command (Sat Dec 16 2006 - 23:20:28 PST)
- Re: AMBER: AMBER - leap - problems with impose command (Fri Dec 15 2006 - 23:04:05 PST)
- AMBER: AMBER - leap - problems with impose command (Fri Dec 15 2006 - 10:18:06 PST)
- AMBER: description of prep file (Fri Dec 08 2006 - 14:28:29 PST)
- AMBER: Zn2+ and Ca2+ ions explicitly treated in MMPB/GB/SA (Mon Dec 04 2006 - 16:20:02 PST)
puneet kacker
- AMBER: Nucgen Problem (Fri Dec 22 2006 - 00:06:41 PST)
Qing Zhang
- Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 23:26:11 PST)
- Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 12:17:05 PST)
- Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 12:22:53 PST)
- Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 11:32:43 PST)
- Re: AMBER: Simulating proteins with calcium ion (Fri Dec 08 2006 - 16:31:02 PST)
- AMBER: Simulating proteins with calcium ion (Thu Dec 07 2006 - 16:15:42 PST)
Qizhi Cui
- AMBER: ISTRNG or SALT in MM_PBSA (Wed Dec 13 2006 - 19:23:48 PST)
Rachel
- Re: AMBER: Unit 5 Error on OPEN: md.in (Sat Dec 16 2006 - 10:01:12 PST)
- AMBER: Unit 5 Error on OPEN: md.in (Wed Dec 13 2006 - 11:55:58 PST)
- AMBER: perturbed and unperturbed charges (Wed Dec 06 2006 - 09:24:24 PST)
- Re: AMBER: how to include EXTRA POINTS in AMBER8 (Mon Dec 04 2006 - 10:35:08 PST)
- Re: AMBER: how to include EXTRA POINTS in AMBER8 (Mon Dec 04 2006 - 09:03:11 PST)
- AMBER: how to include EXTRA POINTS in AMBER8 (Mon Dec 04 2006 - 07:59:34 PST)
- AMBER: problem at the start of heating up (using extra-point) (Sat Dec 02 2006 - 07:29:09 PST)
Rahaman, Asif
- AMBER: AMBER parallel run bombs (Mon Dec 04 2006 - 16:29:53 PST)
Ravinder Abrol
- Re: AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 16:58:36 PST)
- Re: AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 09:38:23 PST)
- AMBER: mixing GAFF and CHARMM (Tue Dec 19 2006 - 23:09:08 PST)
Raviprasad Aduri
- Re: AMBER: RESP charge fitting for HFIP (Mon Dec 18 2006 - 19:46:05 PST)
Ray Luo
- RE: AMBER: MM-PBSA problem (Tue Dec 05 2006 - 11:16:32 PST)
- RE: AMBER: MM-PBSA problem (Sat Dec 02 2006 - 07:55:46 PST)
- RE: AMBER: MM-PBSA problem (Fri Dec 01 2006 - 13:51:52 PST)
Robert Duke
- Re: AMBER: Amber9 - openmpi? (Wed Dec 20 2006 - 05:23:10 PST)
- Re: AMBER: Parallelization method (Tue Dec 19 2006 - 10:29:09 PST)
- Re: AMBER: Can't compile PMEMD (Thu Dec 14 2006 - 15:42:02 PST)
- Re: AMBER: Can't compile PMEMD (Thu Dec 14 2006 - 14:12:12 PST)
- Re: AMBER: parallel computation time vs serial computation time (Thu Dec 14 2006 - 06:16:22 PST)
- Re: AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 14:41:52 PST)
- Re: AMBER: floating point assist faults on IA64 PMEMD 9 (Wed Dec 13 2006 - 12:22:23 PST)
- Re: AMBER: PMEMD scaling (Thu Dec 07 2006 - 06:17:46 PST)
Ross Walker
- AMBER: RE: protein simulation using AMBER (Fri Dec 29 2006 - 22:51:09 PST)
- RE: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 21:30:53 PST)
- RE: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 20:36:10 PST)
- RE: AMBER: Installation help - SGI Altix 350 (Wed Dec 20 2006 - 08:38:16 PST)
- RE: AMBER: sander: cannot execute binary file (Mon Dec 18 2006 - 11:52:05 PST)
- RE: AMBER: Is there a way to simulate a box of pure water with amber (Fri Dec 15 2006 - 10:52:53 PST)
- RE: AMBER: sander: cannot execute binary file (Thu Dec 14 2006 - 15:15:46 PST)
- AMBER: Test Message Please Ignore. (Thu Dec 14 2006 - 13:01:07 PST)
- AMBER: Test Message Please Ignore (Thu Dec 14 2006 - 13:01:07 PST)
- RE: AMBER: Atom Type problem (Fri Dec 08 2006 - 08:21:19 PST)
- RE: AMBER: atome type error (Fri Dec 08 2006 - 07:51:29 PST)
- RE: AMBER: ibelly not work (Wed Dec 06 2006 - 16:07:45 PST)
- RE: AMBER: Amber9 failure to compile parallel on Rocks 4.2.1 system (Wed Dec 06 2006 - 14:48:51 PST)
Russell Glavey
- AMBER: tetrolic acid (Thu Dec 21 2006 - 04:29:35 PST)
sai vikram
- Re: AMBER: Simulated Annealing problem... (Sat Dec 30 2006 - 05:12:53 PST)
- AMBER: Simulated Annealing problem... (Fri Dec 29 2006 - 02:33:50 PST)
Sanya Kryklia
- AMBER: General Question about Abmer (Mon Dec 11 2006 - 06:23:11 PST)
saurabh agrawal
- AMBER: Amber Input file from "qout", "resp.dat" (Thu Dec 21 2006 - 01:41:47 PST)
- Re: AMBER: ERROR: The PDB file is not in the working directory (Thu Dec 14 2006 - 03:38:05 PST)
- Re: AMBER: ERROR: The PDB file is not in the working directory (Wed Dec 13 2006 - 23:18:33 PST)
- AMBER: ERROR: The PDB file is not in the working directory (Tue Dec 12 2006 - 03:39:39 PST)
Scott Brozell
- RE: AMBER: Error in sysdepend.c? (Tue Dec 19 2006 - 11:19:38 PST)
- Re: AMBER: Parallelization method (Tue Dec 19 2006 - 10:58:07 PST)
- Re: AMBER: setBox with buffer in leap (Mon Dec 11 2006 - 21:08:38 PST)
- Re: AMBER: Compiling Amber 9 on SGI with gcc (Fri Dec 08 2006 - 19:29:15 PST)
- Re: AMBER: sander error about fortran (Mon Dec 04 2006 - 13:26:52 PST)
- Re: AMBER: sander error about fortran (Fri Dec 01 2006 - 23:10:03 PST)
- Re: AMBER: amber9 parralel compiling (Fri Dec 01 2006 - 11:40:54 PST)
Seongeun Yang
- AMBER: Replica exchange rate in REMD (Thu Dec 21 2006 - 03:42:59 PST)
Sergey Samsonov
- Re: AMBER: Is there a way to simulate a box of pure water with amber (Sun Dec 17 2006 - 23:43:27 PST)
- Re: AMBER: Free energy perturbation in SANDER (Thu Dec 14 2006 - 01:38:46 PST)
Seth Lilavivat
- AMBER: chirality.c line 121 (Wed Dec 27 2006 - 13:43:56 PST)
- Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 11:42:42 PST)
- Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 09:44:29 PST)
- AMBER: recompiling bondtype.C (Wed Dec 27 2006 - 08:49:32 PST)
- Re: AMBER: bad connectivity - more detail (Wed Dec 27 2006 - 08:26:14 PST)
- AMBER: bad connectivity - more detail (Tue Dec 26 2006 - 10:02:27 PST)
- AMBER: bad connectivity (Tue Dec 26 2006 - 09:24:17 PST)
- AMBER: xleap, generating prep file (Thu Dec 21 2006 - 08:49:56 PST)
- AMBER: RED - help with installation / config (Wed Dec 20 2006 - 07:18:49 PST)
Shin Tokumoto
- Re: AMBER: RESP charges of iron-porphyrin system (Thu Dec 14 2006 - 01:31:13 PST)
Shin, John Y CONTRACTOR WRAIR-Wash DC
- RE: AMBER: Error in sysdepend.c? (Tue Dec 19 2006 - 13:29:12 PST)
- RE: AMBER: Error in sysdepend.c? (Mon Dec 18 2006 - 12:27:24 PST)
- AMBER: Error in sysdepend.c? (Fri Dec 15 2006 - 11:44:50 PST)
- AMBER: Compiling Amber 9 on SGI with gcc (Fri Dec 08 2006 - 10:46:32 PST)
Shozeb Haider
- AMBER: MM-PBSA (Mon Dec 18 2006 - 09:57:17 PST)
Shuting Wei
- AMBER: DRMS setting for Nmode calculation (Thu Dec 07 2006 - 12:46:54 PST)
- Re: AMBER: sander error about fortran (Mon Dec 04 2006 - 09:02:52 PST)
- AMBER: sander error about fortran (Fri Dec 01 2006 - 07:58:25 PST)
Steve Seibold
- AMBER: Frozen at Minimization (Tue Dec 19 2006 - 06:18:21 PST)
- AMBER: Building Parameters (Mon Dec 11 2006 - 13:29:15 PST)
- RE: AMBER: Atom Type problem (Fri Dec 08 2006 - 10:09:05 PST)
- AMBER: Atom Type problem (Fri Dec 08 2006 - 08:04:29 PST)
- AMBER: Atom Type problem (Fri Dec 08 2006 - 08:01:23 PST)
- AMBER: atome type error (Fri Dec 08 2006 - 07:08:35 PST)
Steven Winfield
- AMBER: setBox with buffer in leap (Wed Dec 06 2006 - 16:43:58 PST)
- AMBER: setBox with buffer in leap (Wed Dec 06 2006 - 11:05:22 PST)
Thomas Cheatham
- Re: AMBER: rdparm (Sat Dec 16 2006 - 19:43:55 PST)
- Re: AMBER: Simulating proteins with calcium ion (Thu Dec 07 2006 - 19:23:26 PST)
- Re: AMBER: MD with restraint (nmropt=1) (Wed Dec 06 2006 - 21:14:56 PST)
- Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? (Fri Dec 01 2006 - 14:01:35 PST)
- Re: AMBER: H-bond analysis (Ptraj) (Fri Dec 01 2006 - 10:00:05 PST)
- Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? (Fri Dec 01 2006 - 09:53:50 PST)
- Re: AMBER: H-bond analysis (Ptraj) input file (Fri Dec 01 2006 - 09:56:57 PST)
Thomas Steinbrecher
- Re: AMBER: Atoms overlapping (Mon Dec 11 2006 - 14:11:47 PST)
Tim Meyer
- Re: AMBER: rdparm (Tue Dec 19 2006 - 07:22:45 PST)
Tiziano Tuccinardi
- AMBER: PMEMD scaling (Thu Dec 07 2006 - 00:46:49 PST)
tongli
- AMBER: about the std of computational alanine scanning (Fri Dec 01 2006 - 03:50:11 PST)
vanessa wai
- Re: AMBER: MM-PBSA problem (Tue Dec 05 2006 - 17:33:35 PST)
- Re: AMBER: MM-PBSA problem (Sun Dec 03 2006 - 17:52:25 PST)
- Re: AMBER: MM-PBSA problem (Sat Dec 02 2006 - 01:08:15 PST)
- Re: AMBER: MM-PBSA problem (Sat Dec 02 2006 - 01:11:18 PST)
- AMBER: MM-PBSA problem (Thu Nov 30 2006 - 17:27:06 PST)
Varsha Goyal
- Re: AMBER: MM-PBSA problem (Fri Dec 01 2006 - 13:35:27 PST)
venditti2.unisi.it
- AMBER: rdparm (Fri Dec 15 2006 - 08:08:17 PST)
vic.mail.nankai.edu.cn
- AMBER: A problem with mm_pbsa (Mon Dec 25 2006 - 17:41:41 PST)
wenfei Li
- Re: AMBER: problem of the REMD with nmr constraints (Thu Dec 07 2006 - 16:55:04 PST)
xiaoqin huang
- AMBER: tree name generated by tleap is different from the input PREP parameter file (Thu Dec 28 2006 - 16:53:39 PST)
- AMBER: tree name generated by tleap is different from the input PREP parameter file (Thu Dec 28 2006 - 08:48:14 PST)
Ye Mei
- Re: AMBER: bugfix (Sun Dec 03 2006 - 07:38:40 PST)
Yong Duan
- RE: AMBER: question on protein folding simulation (Tue Dec 05 2006 - 11:57:45 PST)
- RE: AMBER: question on protein folding simulation (Fri Dec 01 2006 - 10:32:58 PST)
Yumi Nukusina
- AMBER: Free energy perturbation in SANDER (Thu Dec 14 2006 - 00:59:36 PST)
张勇
- Re: AMBER: Simulating proteins with calcium ion (Fri Dec 22 2006 - 17:02:57 PST)
- Re: AMBER: Simulating proteins with calcium ion (Tue Dec 12 2006 - 16:25:03 PST)
曹冉
- Re:AMBER: mixing GAFF and CHARMM (Wed Dec 20 2006 - 09:12:05 PST)
- Re: AMBER: How could I simulate lipid membrane with AMBER9.0? (Thu Dec 07 2006 - 17:46:44 PST)
- AMBER: What's going wrong when I use antechamber dealing with lipid molecular? (Wed Dec 06 2006 - 17:05:55 PST)
- AMBER: How could I simulate lipid membrane with AMBER9.0? (Wed Dec 06 2006 - 17:02:55 PST)

Amber Archive Dec 2006 by author