AMBER Archive (2005) - Jun 2005 By Author

Starting: Wed Jun 01 2005 - 03:48:46 CDT
Ending: Thu Jun 30 2005 - 23:33:25 CDT

• acb15885_at_uprm.edu
  • AMBER: pb_pgb test fail (Mon Jun 27 2005 - 13:17:48 CDT)
• alice
  • Re: Re: AMBER: bad atom type: H (Wed Jun 15 2005 - 20:35:00 CDT)
  • AMBER: bad atom type: H (Wed Jun 15 2005 - 05:53:50 CDT)
  • AMBER: How to run amber more efficiently? (Tue Jun 07 2005 - 21:59:26 CDT)
• Ananda Rama Krishnan Selvaraj
  • Re: AMBER: Extended bonds-MD (Wed Jun 15 2005 - 07:55:41 CDT)
  • AMBER: Extended bonds-MD (Wed Jun 15 2005 - 02:02:25 CDT)
  • AMBER: Extended bonds-MD (Tue Jun 14 2005 - 11:29:29 CDT)
  • AMBER: Restrained-MD (Mon Jun 13 2005 - 18:04:14 CDT)
  • Re: RE: AMBER: problem in minimization (Thu Jun 02 2005 - 02:39:36 CDT)
  • AMBER: problem in minimization (Wed Jun 01 2005 - 03:48:46 CDT)
• Andreas Kerzmann
  • AMBER: Sander is changing directories (Wed Jun 08 2005 - 04:39:23 CDT)
  • AMBER: Sander is changing directories (Wed Jun 08 2005 - 04:37:58 CDT)
• Andreas Svrcek-Seiler
  • Re: AMBER: GCC for AMBER on 64 bit machine (Thu Jun 23 2005 - 13:44:44 CDT)
  • RE: AMBER: Installation problem - wrong address (Fri Jun 17 2005 - 12:28:43 CDT)
  • RE: AMBER: Installation problem. . (Fri Jun 17 2005 - 12:12:10 CDT)
  • Re: AMBER: Installation problem. . (Thu Jun 16 2005 - 23:54:42 CDT)
  • Re: AMBER: Installation problem. . (Wed Jun 15 2005 - 07:31:46 CDT)
• Andy Purkiss
  • Re: AMBER: fail of minimization in sander (Tue Jun 07 2005 - 07:17:24 CDT)
• Angela Liu
  • AMBER: amber 8 leap topology file dihedral term problem (Tue Jun 28 2005 - 08:59:57 CDT)
• Angelo Pugliese
  • Re: AMBER: time and lifetime in hbond analysis (ptraj) (Tue Jun 14 2005 - 09:57:56 CDT)
  • Re: AMBER: creating pdb file.... (Tue Jun 14 2005 - 06:11:41 CDT)
• Anthony Cruz
  • Re: AMBER: Solvate question? (Tue Jun 07 2005 - 07:31:30 CDT)
  • AMBER: Solvents (Mon Jun 06 2005 - 11:00:07 CDT)
  • Re: AMBER: Solvate question? (Mon Jun 06 2005 - 10:59:06 CDT)
  • Re: AMBER: Compile question?? (Mon Jun 06 2005 - 08:24:40 CDT)
  • AMBER: Compile question?? (Mon Jun 06 2005 - 06:59:13 CDT)
  • AMBER: Solvate question? (Mon Jun 06 2005 - 05:30:44 CDT)
  • Re: AMBER: Protein ions? (Thu Jun 02 2005 - 11:45:34 CDT)
  • AMBER: Protein ions? (Thu Jun 02 2005 - 09:12:56 CDT)
• Bill Ross
  • Re: AMBER: question about Carnal (Wed Jun 22 2005 - 15:51:34 CDT)
  • RE: AMBER: vdw for terminal phosphate (Mon Jun 13 2005 - 15:22:47 CDT)
  • Re: AMBER: vdw for terminal phosphate (Fri Jun 10 2005 - 13:10:32 CDT)
  • Re: AMBER: nucgen problem (Tue Jun 07 2005 - 14:27:14 CDT)
  • Re: AMBER: AMBER frcmod+off input vs. prep input (Tue Jun 07 2005 - 12:58:06 CDT)
  • Re: AMBER: nucgen problem (Tue Jun 07 2005 - 11:47:42 CDT)
  • Re: AMBER: segmentation fault in sander (Tue Jun 07 2005 - 11:35:27 CDT)
  • Re: AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 19:03:38 CDT)
  • Re: AMBER: segmentation fault in sander (Mon Jun 06 2005 - 17:18:45 CDT)
  • Re: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 12:58:54 CDT)
  • Re: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 09:34:39 CDT)
  • Re: AMBER: fail of minimization in sander (Sun Jun 05 2005 - 22:50:48 CDT)
• Biswaroop Mukherjee
  • AMBER: Argon Box (Thu Jun 02 2005 - 03:44:46 CDT)
• Brent Krueger
  • AMBER: gaff.dat typo (Wed Jun 01 2005 - 20:35:58 CDT)
• caoch_at_cherry.bio.titech.ac.jp
  • AMBER: nonbond_list question . (Fri Jun 17 2005 - 20:38:27 CDT)
• Carlos Simmerling
  • Re: AMBER: fail of minimization in sander (Thu Jun 16 2005 - 06:06:42 CDT)
  • Re: AMBER: fail of minimization in sander (Wed Jun 15 2005 - 06:24:04 CDT)
  • Re: AMBER: Extended bonds-MD (Wed Jun 15 2005 - 06:22:29 CDT)
  • Re: AMBER: transfer data from Linux to windows (Thu Jun 09 2005 - 17:41:26 CDT)
  • Re: AMBER: GB/SA/LD parallel sander (Wed Jun 08 2005 - 15:09:59 CDT)
  • Re: AMBER: total energy leaps (Wed Jun 08 2005 - 06:22:06 CDT)
  • Re: AMBER: nucgen problem (Tue Jun 07 2005 - 14:34:17 CDT)
  • Re: AMBER: Solvate question? (Mon Jun 06 2005 - 11:13:37 CDT)
  • Re: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 11:12:38 CDT)
  • Re: AMBER: Solvate question? (Mon Jun 06 2005 - 06:26:53 CDT)
  • Re: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 06:24:25 CDT)
  • Re: AMBER: How does Amber8 implemnet ntf=4? (Thu Jun 02 2005 - 10:53:36 CDT)
  • Re: AMBER: question whem using leap (Thu Jun 02 2005 - 06:45:53 CDT)
• cbala_at_igib.res.in
  • Re: AMBER: nucgen problem (Tue Jun 07 2005 - 14:48:13 CDT)
  • AMBER: nucgen problem (Tue Jun 07 2005 - 08:41:27 CDT)
• chaiann ng
  • AMBER: advice needed for minimization and dynamic protocol (Thu Jun 02 2005 - 20:33:44 CDT)
• Chris Harrison
  • Re: AMBER: Installation problem (Mon Jun 13 2005 - 19:33:13 CDT)
  • Re: AMBER: Installation problem (Sun Jun 12 2005 - 18:04:22 CDT)
• Christoph Brockmann
  • AMBER: nmropt =1 AND ntr=1 in pmemd (Tue Jun 14 2005 - 04:33:39 CDT)
• Cordova, Luis E.
  • AMBER: question about spline in sander -- array size of eed_cub (Thu Jun 30 2005 - 23:33:25 CDT)
  • AMBER: precision switch from 64 to 32 bit (double from single precision) (Thu Jun 09 2005 - 00:39:59 CDT)
• cristian obiol
  • AMBER: total energy leaps (Wed Jun 08 2005 - 05:44:18 CDT)
  • RE:AMBER: density problem (Wed Jun 08 2005 - 03:56:23 CDT)
  • RE:AMBER: density problem (Thu Jun 02 2005 - 03:14:21 CDT)
• Daniel Wetzler
  • AMBER: Searching for NAD parameter files / Problems with parameter file creation (Thu Jun 23 2005 - 09:43:29 CDT)
• Dave S Walker
  • RE: AMBER: runtime error in sander? (Mon Jun 20 2005 - 13:02:16 CDT)
• David A. Case
  • Re: AMBER: Create new Unit (Thu Jun 30 2005 - 20:38:42 CDT)
  • Re: AMBER: antechamber error (Thu Jun 30 2005 - 16:38:11 CDT)
  • Re: AMBER: Re: TI tutorial (Wed Jun 29 2005 - 12:01:23 CDT)
  • Re: AMBER: Re: TI tutorial (Wed Jun 29 2005 - 09:30:31 CDT)
  • Re: AMBER: Re: TI tutorial (Tue Jun 28 2005 - 20:09:44 CDT)
  • Re: AMBER: Re: TI tutorial (Tue Jun 28 2005 - 10:49:53 CDT)
  • Re: AMBER: pb_pgb test fail (Mon Jun 27 2005 - 13:48:32 CDT)
  • Re: AMBER: a question about varying positions of dihedral restraints with step number (Fri Jun 24 2005 - 10:09:21 CDT)
  • Re: AMBER: large std error in entropy estimation (Thu Jun 23 2005 - 13:25:03 CDT)
  • Re: AMBER: fail of minimization in sander (Thu Jun 16 2005 - 09:44:21 CDT)
  • Re: AMBER: How to modify force constants and equalibrium values for standard residues (Thu Jun 16 2005 - 09:41:18 CDT)
  • Re: AMBER: Question about "quasih" (Wed Jun 15 2005 - 16:01:33 CDT)
  • Re: AMBER: Question about "quasih" (Wed Jun 15 2005 - 12:43:47 CDT)
  • Re: AMBER: atom type question (Wed Jun 15 2005 - 10:18:18 CDT)
  • Re: AMBER: bad atom type: H (Wed Jun 15 2005 - 10:09:17 CDT)
  • Re: AMBER: why the dipeptide always moving out the virtual box (Tue Jun 14 2005 - 17:50:03 CDT)
  • Re: AMBER: compiler (Tue Jun 14 2005 - 13:40:16 CDT)
  • Re: AMBER: Restrained-MD (Mon Jun 13 2005 - 18:10:00 CDT)
  • Re: AMBER: why the dipeptide always moving out the virtual box (Mon Jun 13 2005 - 17:55:19 CDT)
  • Re: AMBER: GBSA and thermodynamic ensemble (Mon Jun 13 2005 - 15:13:14 CDT)
  • Re: AMBER: atom type question (Mon Jun 13 2005 - 15:05:44 CDT)
  • Re: AMBER: Can constant pH be used for minimization? (Sat Jun 11 2005 - 07:42:51 CDT)
  • Re: AMBER: Make Distance restraints for non-standard residues (Fri Jun 10 2005 - 14:59:13 CDT)
  • Re: AMBER: TI tutorial in Amber 8 (Wed Jun 08 2005 - 23:27:42 CDT)
  • Re: AMBER: nmode with ibelly (Wed Jun 08 2005 - 23:30:01 CDT)
  • Re: AMBER: TI calculation using sander (Tue Jun 07 2005 - 20:32:34 CDT)
  • Re: AMBER: nucgen problem (Tue Jun 07 2005 - 15:17:12 CDT)
  • Re: AMBER: quadrupole in resp (Tue Jun 07 2005 - 12:30:12 CDT)
  • Re: AMBER: nmode with ibelly (Tue Jun 07 2005 - 09:41:41 CDT)
  • Re: AMBER: nucgen problem (Tue Jun 07 2005 - 09:38:15 CDT)
  • Re: AMBER: Protein dynamics. (Mon Jun 06 2005 - 17:37:10 CDT)
  • Re: AMBER: nmode with ibelly (Mon Jun 06 2005 - 15:09:08 CDT)
  • Re: AMBER: pressure output (Fri Jun 03 2005 - 10:05:59 CDT)
  • Re: AMBER: TI in Amber8 (Fri Jun 03 2005 - 10:04:45 CDT)
  • Re: AMBER: New problem of parallel sander (Fri Jun 03 2005 - 10:00:30 CDT)
  • Re: AMBER: How does Amber8 implemnet ntf=4? (Thu Jun 02 2005 - 10:52:10 CDT)
  • Re: AMBER: Protein ions? (Thu Jun 02 2005 - 10:25:07 CDT)
  • Re: AMBER: amber8 installation problems (Thu Jun 02 2005 - 10:07:19 CDT)
  • Re: AMBER: amber question about leap (Thu Jun 02 2005 - 10:05:12 CDT)
  • Re: AMBER: gaff.dat typo (Thu Jun 02 2005 - 10:01:58 CDT)
• David LeBard
  • Re: AMBER: dielectric constant (Tue Jun 28 2005 - 15:01:30 CDT)
  • Re: AMBER: compiler (Tue Jun 14 2005 - 12:45:27 CDT)
• Don.Bashford_at_stjude.org
  • Re: AMBER: Installation problem. . (Mon Jun 13 2005 - 12:56:46 CDT)
• Douali, Latifa
  • AMBER: Create new Unit (Thu Jun 30 2005 - 18:45:37 CDT)
  • AMBER: inpcrd file (Fri Jun 10 2005 - 18:04:24 CDT)
• du yongchun
  • AMBER: question whem using leap (Thu Jun 02 2005 - 02:25:16 CDT)
  • AMBER: amber question about leap (Thu Jun 02 2005 - 00:12:12 CDT)
• emilia wu
  • AMBER: average structure (Sun Jun 19 2005 - 19:15:53 CDT)
• Eric Hu
  • AMBER: normal mode mm/pbsa interupted (Thu Jun 09 2005 - 13:46:04 CDT)
  • Re: AMBER: mm/pbsa error (Wed Jun 01 2005 - 12:23:53 CDT)
• Fabian Boes
  • Re: AMBER: INTRA molecular hbonds (Mon Jun 27 2005 - 09:45:13 CDT)
  • Re: AMBER: Hbond analysis (Mon Jun 27 2005 - 08:12:34 CDT)
• Fabien CAILLIEZ
  • AMBER: 10-12 potential and create atom type (Thu Jun 30 2005 - 12:19:41 CDT)
• Fajar Rakhman Wibowo
  • Re: AMBER: transfer data from Linux to windows (Thu Jun 09 2005 - 18:11:33 CDT)
• Furse, Kristina Elisabet
  • Re: AMBER: nmropt =1 AND ntr=1 in pmemd (Fri Jun 17 2005 - 14:16:13 CDT)
• FyD
  • Re: AMBER: Create new Unit (Thu Jun 30 2005 - 19:25:02 CDT)
  • Re: AMBER: RED question (Wed Jun 29 2005 - 11:34:16 CDT)
  • Re: AMBER: RED question (Sun Jun 26 2005 - 22:37:59 CDT)
  • Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends (Wed Jun 22 2005 - 16:56:30 CDT)
  • Re: AMBER: Request for g98 (IOP...) (Tue Jun 14 2005 - 10:55:27 CDT)
  • Re: AMBER: Need help in charge fitting through RESP (Mon Jun 13 2005 - 11:15:42 CDT)
• Germán Sciaini
  • AMBER: dielectric constant (Wed Jun 29 2005 - 06:02:24 CDT)
  • Re: AMBER: SHAKE in md with partial solvation (Mon Jun 06 2005 - 05:34:09 CDT)
  • AMBER: pressure output (Thu Jun 02 2005 - 17:27:13 CDT)
• Gert Kiss
  • AMBER: Build of AMBER for YDL ? (Wed Jun 01 2005 - 18:15:57 CDT)
• Giulio Rastelli
  • AMBER: INTRA molecular hbonds (Mon Jun 27 2005 - 09:09:23 CDT)
  • AMBER: adenine test for LMOD in amber8 (Thu Jun 16 2005 - 04:57:16 CDT)
  • AMBER: time and lifetime in hbond analysis (ptraj) (Tue Jun 14 2005 - 09:23:50 CDT)
• gsciaini
  • Re: AMBER: How to modify force constants and equalibrium values for standard residues (Fri Jun 17 2005 - 08:41:44 CDT)
• gtg549i_at_mail.gatech.edu
  • Re: AMBER: Make Distance restraints for non-standard residues (Fri Jun 10 2005 - 15:45:00 CDT)
  • AMBER: Make Distance restraints for non-standard residues (Fri Jun 10 2005 - 10:47:41 CDT)
  • AMBER: transfer data from Linux to windows (Thu Jun 09 2005 - 17:24:05 CDT)
• Guanglei Cui
  • Re: AMBER: atom type for -CH=CH- (Fri Jun 10 2005 - 08:56:52 CDT)
  • Re: AMBER: radius parameter for Mg2+ in mm_pbsa calculation (Sat Jun 04 2005 - 10:17:11 CDT)
  • Re: AMBER: Error on restrained MD equilibration (AMBER 7) (Wed Jun 01 2005 - 09:18:37 CDT)
• Gustavo Pierdominici Sottile
  • AMBER: sp2 carbon atom parametrization (Tue Jun 14 2005 - 11:30:16 CDT)
  • AMBER: checkoverlap (Thu Jun 02 2005 - 12:45:19 CDT)
• haixiao jin
  • AMBER: how the phosphated threonine to be recognized in leap (Thu Jun 23 2005 - 04:03:26 CDT)
  • AMBER: no corrected reaction field energy in *.out files after running mm_pbsa (Sun Jun 12 2005 - 21:04:40 CDT)
• Herbert Georg
  • Re: AMBER: Question about GAFF atom types (Mon Jun 20 2005 - 11:47:38 CDT)
  • Re: AMBER: Question about GAFF atom types (Fri Jun 17 2005 - 17:31:52 CDT)
  • Re: AMBER: Question about GAFF atom types (Fri Jun 17 2005 - 14:49:53 CDT)
  • AMBER: Question about GAFF atom types (Thu Jun 16 2005 - 14:18:50 CDT)
• hj zou
  • AMBER: antechamber problems (Sun Jun 19 2005 - 08:50:08 CDT)
  • AMBER: antechamber problems (Fri Jun 17 2005 - 08:32:27 CDT)
• huhu
  • AMBER: TI tutorial in Amber 8 (Wed Jun 08 2005 - 04:52:24 CDT)
• Husni Fattayer
  • Re: AMBER: how to pull out frames (Mon Jun 13 2005 - 06:22:40 CDT)
• Hwankyu Lee
  • Re: AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 18:48:56 CDT)
  • Re: AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 18:26:16 CDT)
  • Re: AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 17:47:29 CDT)
  • AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 08:55:57 CDT)
  • AMBER: eigenvalues in vector of ptraj (Wed Jun 01 2005 - 07:53:51 CDT)
• Ilyas Yildirim
  • Re: AMBER: TI-FEP for ALA --> GLY (Tue Jun 28 2005 - 00:46:17 CDT)
  • Re: AMBER: TI-FEP for VAL --> ALA (Mon Jun 27 2005 - 18:43:16 CDT)
  • Re: AMBER: TI-FEP for VAL --> ALA (Sat Jun 25 2005 - 18:39:11 CDT)
  • Re: AMBER: TI-FEP for ALA --> GLY (Sat Jun 25 2005 - 01:48:36 CDT)
  • Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends (Wed Jun 22 2005 - 17:13:19 CDT)
  • AMBER: RESP charges of RNA nucleotides with 3' and 5' ends (Mon Jun 20 2005 - 20:51:11 CDT)
  • Re: AMBER: Question about GAFF atom types (Mon Jun 20 2005 - 14:51:59 CDT)
  • Re: AMBER: Analysing my simulation data.. (Sat Jun 18 2005 - 11:47:06 CDT)
  • Re: AMBER: Question about GAFF atom types (Fri Jun 17 2005 - 20:29:24 CDT)
  • Re: AMBER: Question about GAFF atom types (Fri Jun 17 2005 - 15:42:18 CDT)
• Istvan Kolossvary
  • Re: AMBER: adenine test for LMOD in amber8 (Thu Jun 16 2005 - 08:16:22 CDT)
  • AMBER: Announcing the LMOD website (Mon Jun 13 2005 - 13:18:52 CDT)
• ivan_at_mmb.pcb.ub.es
  • AMBER: Gibbs perturb DNA strands separate (Tue Jun 07 2005 - 06:16:41 CDT)
• JAVIER PEREZ
  • AMBER: center-of-mass distance restraints (Thu Jun 02 2005 - 06:14:15 CDT)
• Jiten
  • Re: AMBER: Re: TI tutorial (Wed Jun 29 2005 - 12:24:19 CDT)
  • Re: AMBER: Re: TI tutorial (Wed Jun 29 2005 - 11:22:04 CDT)
  • Re: AMBER: Re: TI tutorial (Tue Jun 28 2005 - 22:46:17 CDT)
  • Re: AMBER: Re: TI tutorial (Tue Jun 28 2005 - 11:36:59 CDT)
  • AMBER: Fw: TI tutorial --> ALA --> GLY TI calculation (Tue Jun 28 2005 - 10:02:42 CDT)
  • AMBER: Re: TI tutorial (Tue Jun 28 2005 - 09:17:39 CDT)
  • Re: AMBER: TI-FEP for ALA --> GLY (Mon Jun 27 2005 - 21:24:56 CDT)
  • Re: AMBER: TI-FEP for VAL --> ALA (Sun Jun 26 2005 - 21:11:03 CDT)
  • Re: AMBER: MM_PBSA ! (Sun Jun 26 2005 - 19:43:13 CDT)
  • Re: AMBER: TI-FEP for VAL --> ALA (Sat Jun 25 2005 - 11:13:44 CDT)
  • AMBER: TI-FEP for ALA --> GLY (Sat Jun 25 2005 - 00:07:03 CDT)
• John Mongan
  • Re: AMBER: Can constant pH be used for minimization? (Tue Jun 14 2005 - 19:03:38 CDT)
• Julien Michel
  • Re: AMBER: GBSA and thermodynamic ensemble (Mon Jun 13 2005 - 14:51:23 CDT)
• JunJun Liu
  • AMBER: How to read unformatted restart file in PTRAJ ? (Wed Jun 29 2005 - 01:20:57 CDT)
  • Re: AMBER: PBSA error: PB bomb in pd_aaradi (Wed Jun 22 2005 - 10:17:43 CDT)
• Junmei Wang
  • RE: AMBER: antechamber problems (Mon Jun 20 2005 - 11:35:12 CDT)
  • RE: RE: AMBER: Antechamber RESP failed for large organic molecule (Wed Jun 01 2005 - 11:54:42 CDT)
• junwang
  • Re: AMBER: Need help in charge fitting through RESP (Mon Jun 13 2005 - 12:51:41 CDT)
  • Re: RE: RE: AMBER: Antechamber RESP failed for large organic molecule (Wed Jun 01 2005 - 16:18:05 CDT)
• justin litchfield
  • AMBER: leap issues on a powerbook (Sun Jun 12 2005 - 18:21:02 CDT)
• K. Yarem
  • AMBER: AMBER frcmod+off input vs. prep input (Tue Jun 07 2005 - 11:57:19 CDT)
• Kara Di Giorgio
  • Re: AMBER: RED question (Mon Jun 27 2005 - 00:13:13 CDT)
  • AMBER: RED question (Sat Jun 25 2005 - 17:44:23 CDT)
• Kenley Barrett
  • AMBER: position of protonation info from constant pH run (Wed Jun 15 2005 - 20:27:44 CDT)
  • AMBER: Can constant pH be used for minimization? (Fri Jun 10 2005 - 16:34:41 CDT)
  • Re: AMBER: segmentation fault in sander (Tue Jun 07 2005 - 10:36:44 CDT)
  • AMBER: segmentation fault in sander (Mon Jun 06 2005 - 17:07:59 CDT)
• L Jin
  • Re: AMBER: Error on restrained MD equilibration (AMBER 7) (Wed Jun 01 2005 - 10:05:12 CDT)
  • RE: AMBER: Error on restrained MD equilibration (AMBER 7) (Wed Jun 01 2005 - 05:20:40 CDT)
  • Re: AMBER: Error on restrained MD equilibration (AMBER 7) (Wed Jun 01 2005 - 05:24:12 CDT)
• L.C. Heady
  • AMBER: Saturated DNA bases (Wed Jun 01 2005 - 03:55:54 CDT)
• Latifa Douali
  • AMBER: TI calculation using sander (Tue Jun 07 2005 - 19:10:54 CDT)
• Laurence Lavelle
  • AMBER: Protein dynamics. (Wed Jun 08 2005 - 00:52:00 CDT)
  • AMBER: Protein dynamics. (Mon Jun 06 2005 - 16:43:50 CDT)
• Li Su
  • AMBER: a question about varying positions of dihedral restraints with step number (Wed Jun 22 2005 - 14:42:02 CDT)
  • AMBER: How to turn off pme when using periodic box (Mon Jun 20 2005 - 13:31:09 CDT)
  • AMBER: How to set the virtual box size for a calculation run in vacuum (Mon Jun 20 2005 - 08:27:33 CDT)
  • Re: AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians (Thu Jun 16 2005 - 18:17:46 CDT)
  • AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians (Thu Jun 16 2005 - 16:19:36 CDT)
  • AMBER: How to modify force constants and equalibrium values for standard residues (Thu Jun 16 2005 - 08:30:41 CDT)
  • Re: AMBER: why the dipeptide always moving out the virtual box (Tue Jun 14 2005 - 16:11:41 CDT)
  • AMBER: why the dipeptide always moving out the virtual box (Mon Jun 13 2005 - 16:40:47 CDT)
  • AMBER: How does Amber8 implemnet ntf=4? (Thu Jun 02 2005 - 10:32:30 CDT)
• Lihua Wang
  • Re: AMBER: transfer data from Linux to windows (Thu Jun 09 2005 - 17:32:14 CDT)
• Lukasz Bielecki
  • AMBER: stripwater (Wed Jun 01 2005 - 09:16:05 CDT)
• Lwin, ThuZar
  • AMBER: setting up restraint with ntr option (Thu Jun 09 2005 - 16:49:04 CDT)
  • AMBER: GB/SA/LD parallel sander (Wed Jun 08 2005 - 14:36:41 CDT)
  • AMBER: GB/SA/LD parallel sander (Mon Jun 06 2005 - 11:48:27 CDT)
• Mark Williamson
  • Re: AMBER: Installation problem. . (Thu Jun 16 2005 - 10:15:58 CDT)
  • Re: AMBER: Installation problem. . (Thu Jun 16 2005 - 10:06:57 CDT)
  • Re: AMBER: Vibrational spectrum? [SOLUTION] (Fri Jun 10 2005 - 05:33:51 CDT)
• Martin Sippel
  • Re: AMBER: Free energy calculation for protein-protein complex usingMM_PBSA (Thu Jun 30 2005 - 05:32:11 CDT)
  • Re: AMBER: nmode with ibelly (Wed Jun 08 2005 - 12:48:04 CDT)
  • Re: AMBER: nmode with ibelly (Tue Jun 07 2005 - 05:11:44 CDT)
  • AMBER: nmode with ibelly (Mon Jun 06 2005 - 04:38:42 CDT)
  • AMBER: Nmode calculations (Fri Jun 03 2005 - 12:17:48 CDT)
  • AMBER: Nmode with residues excluded (Fri Jun 03 2005 - 11:56:42 CDT)
• mfyang
  • AMBER: GCC for AMBER on 64 bit machine (Thu Jun 23 2005 - 12:55:01 CDT)
• Michael Crowley
  • Re: AMBER: nonbond_list question . (Sat Jun 18 2005 - 14:51:01 CDT)
• milion_at_c-box.cz
  • AMBER: Vibrational spectrum? (Fri Jun 10 2005 - 03:31:27 CDT)
• Mohammed Mayeed
  • AMBER: Protein-surface interaction (Wed Jun 08 2005 - 13:37:30 CDT)
  • AMBER: (no subject) (Wed Jun 08 2005 - 12:26:15 CDT)
• mrbroad_at_ilstu.edu
  • AMBER: Free Energy Calculation torsion missing (Tue Jun 14 2005 - 13:21:54 CDT)
• Nadine Homeyer
  • AMBER: Parameters for phosphorylated amino acids (Thu Jun 23 2005 - 09:24:08 CDT)
  • AMBER: Parameters for phosphorylated amino acids (Thu Jun 23 2005 - 08:54:22 CDT)
  • Re: AMBER: Need help in charge fitting through RESP (Mon Jun 13 2005 - 11:20:49 CDT)
• Oliver Hucke
  • AMBER: puzzling gaff parameter (Tue Jun 14 2005 - 20:16:35 CDT)
  • Re: AMBER: Request for g98 (IOP...) (Tue Jun 14 2005 - 11:20:51 CDT)
• opitz_at_che.udel.edu
  • AMBER: question about Carnal (Wed Jun 22 2005 - 15:03:45 CDT)
  • Re: AMBER: atom type question (Mon Jun 13 2005 - 15:46:18 CDT)
  • AMBER: atom type question (Mon Jun 13 2005 - 14:41:30 CDT)
• Osmar Norberto de Souza
  • AMBER: GBSA and thermodynamic ensemble (Mon Jun 13 2005 - 13:29:18 CDT)
• Paramasivam Manikandan
  • AMBER: Request for g98 (IOP...) (Tue Jun 14 2005 - 10:04:30 CDT)
• Peter Gannett
  • AMBER: antechamber error (Thu Jun 30 2005 - 14:05:25 CDT)
  • AMBER: error - compiling antechamber (Wed Jun 29 2005 - 14:30:20 CDT)
  • AMBER: compiler error, SGI Octane (Tue Jun 28 2005 - 07:54:35 CDT)
• Peter Varnai
  • Re: AMBER: DNA base-flipping: TI vs PMF (Thu Jun 02 2005 - 12:21:56 CDT)
• Petr Kulhanek
  • Re: AMBER: nonbond_list question . (Sun Jun 19 2005 - 05:06:31 CDT)
  • Re: AMBER: Error on restrained MD equilibration (AMBER 7) (Wed Jun 01 2005 - 06:03:21 CDT)
• Pradipta Bandyopadhyay
  • AMBER: mm_pbsa script ! (Mon Jun 27 2005 - 01:43:53 CDT)
  • AMBER: MM_PBSA ! (Sun Jun 26 2005 - 07:43:18 CDT)
• Qizhi Cui
  • AMBER: atom type for -CH=CH- (Thu Jun 09 2005 - 20:46:13 CDT)
• Rhoad, Jonathan S.
  • RE: AMBER: Searching for NAD parameter files / Problems with parameter file creation (Thu Jun 23 2005 - 10:08:01 CDT)
  • RE: AMBER: vdw for terminal phosphate (Mon Jun 13 2005 - 11:21:49 CDT)
  • AMBER: vdw for terminal phosphate (Fri Jun 10 2005 - 11:16:47 CDT)
• Robert Duke
  • Re: AMBER: nonbond_list question . (Sun Jun 19 2005 - 09:25:37 CDT)
  • Re: AMBER: nonbond_list question . (Sat Jun 18 2005 - 22:03:07 CDT)
  • Re: AMBER: nmropt =1 AND ntr=1 in pmemd (Fri Jun 17 2005 - 16:58:44 CDT)
  • Re: AMBER: nmropt =1 AND ntr=1 in pmemd (Tue Jun 14 2005 - 07:18:20 CDT)
  • Re: AMBER: precision switch from 64 to 32 bit (double from single precision) (Thu Jun 09 2005 - 07:20:52 CDT)
  • Re: AMBER: Compile question?? (Mon Jun 06 2005 - 09:32:06 CDT)
  • Re: AMBER: Compile question?? (Mon Jun 06 2005 - 09:17:48 CDT)
  • Re: AMBER: Compile question?? (Mon Jun 06 2005 - 07:38:02 CDT)
• Roberto Gomperts
  • Re: AMBER: error - compiling antechamber (Wed Jun 29 2005 - 16:11:41 CDT)
  • Re: [pgannett@hsc.wvu.edu: AMBER: compiler error, SGI Octane] (Wed Jun 29 2005 - 10:01:00 CDT)
• Ross Walker
  • RE: AMBER: Is the MD simulation normal (Wed Jun 29 2005 - 11:09:13 CDT)
  • RE: AMBER: script for calculating hydrogen bond (Mon Jun 27 2005 - 22:04:43 CDT)
  • RE: AMBER: Searching for NAD parameter files / Problems with parameter file creation (Thu Jun 23 2005 - 11:26:56 CDT)
  • AMBER: RE: tutorial 8 (Wed Jun 22 2005 - 16:15:33 CDT)
  • RE: AMBER: How to turn off pme when using periodic box (Mon Jun 20 2005 - 15:31:04 CDT)
  • RE: AMBER: average structure (Sun Jun 19 2005 - 19:41:07 CDT)
  • AMBER: RE: AMBER :LINMIN problem (Fri Jun 17 2005 - 13:27:25 CDT)
  • RE: AMBER: Installation problem. . (Fri Jun 17 2005 - 12:39:15 CDT)
  • RE: AMBER: Installation problem. . (Fri Jun 17 2005 - 11:33:42 CDT)
  • RE: AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians (Thu Jun 16 2005 - 17:00:41 CDT)
  • RE: AMBER: How to modify force constants and equalibrium values for standard residues (Thu Jun 16 2005 - 16:05:33 CDT)
  • RE: AMBER: Installation problem. . (Wed Jun 15 2005 - 11:46:25 CDT)
  • RE: AMBER: solutions of amber installation problems (Tue Jun 14 2005 - 23:55:20 CDT)
  • RE: AMBER: creating pdb file.... (Tue Jun 14 2005 - 12:51:21 CDT)
  • RE: AMBER: compiler (Tue Jun 14 2005 - 12:43:58 CDT)
  • RE: AMBER: Extended bonds-MD (Tue Jun 14 2005 - 12:28:43 CDT)
  • RE: AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 22:49:05 CDT)
  • RE: AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 18:24:21 CDT)
  • RE: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 12:25:26 CDT)
  • RE: AMBER: Error: vlimit exceeded for step (Mon Jun 06 2005 - 12:19:04 CDT)
  • RE: AMBER: SHAKE in md with partial solvation (Mon Jun 06 2005 - 12:12:20 CDT)
  • RE: AMBER: New problem of parallel sander (Fri Jun 03 2005 - 11:53:55 CDT)
  • RE: AMBER: (Fri Jun 03 2005 - 11:51:48 CDT)
  • RE: AMBER: Build of AMBER for YDL ? (Wed Jun 01 2005 - 18:29:49 CDT)
  • RE: AMBER: problem in minimization (Wed Jun 01 2005 - 11:56:46 CDT)
  • RE: AMBER: density problem (Wed Jun 01 2005 - 11:21:33 CDT)
• S.Sundar Raman
  • AMBER: Request for calculating free energy using AMBER6 (Mon Jun 27 2005 - 06:59:00 CDT)
  • AMBER: Need help in charge fitting through RESP (Mon Jun 13 2005 - 08:55:29 CDT)
• Scott Pendley
  • Re: AMBER: MM-PBSA calculation (Wed Jun 01 2005 - 18:44:05 CDT)
• Shulin Zhuang
  • Re: AMBER: Is the MD simulation normal (Thu Jun 30 2005 - 09:52:03 CDT)
  • Re: AMBER: Is the MD simulation normal (Thu Jun 30 2005 - 10:00:11 CDT)
  • Re: AMBER: Is the MD simulation normal (Wed Jun 29 2005 - 10:03:20 CDT)
  • Re: AMBER: Is the MD simulation normal (Wed Jun 29 2005 - 05:11:53 CDT)
  • Re: AMBER: antechamber problems (Mon Jun 20 2005 - 20:07:56 CDT)
  • Re: AMBER: Need help in charge fitting through RESP (Mon Jun 13 2005 - 09:29:02 CDT)
• Simon Whitehead
  • AMBER: (Thu Jun 02 2005 - 07:44:03 CDT)
• Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
  • Re: AMBER: fail of minimization in sander (Wed Jun 15 2005 - 06:05:25 CDT)
  • Re: AMBER: Protein ions? (Thu Jun 02 2005 - 09:57:02 CDT)
• Stern, Julie
  • AMBER: SOURCE3 in gaff.dat (Fri Jun 10 2005 - 04:40:20 CDT)
  • AMBER: eelnb (Mon Jun 06 2005 - 15:16:31 CDT)
• Sukjoon Yoon
  • AMBER: Installation problem. . (Thu Jun 16 2005 - 09:49:19 CDT)
  • AMBER: Installation problem. . (Wed Jun 15 2005 - 01:08:51 CDT)
  • AMBER: Installation problem (Sun Jun 12 2005 - 23:07:26 CDT)
  • RE: AMBER: Installation problem (Sun Jun 12 2005 - 21:35:37 CDT)
  • AMBER: Installation problem (Sun Jun 12 2005 - 04:21:50 CDT)
• Suxin Zheng
  • AMBER: Have the parameters for dUMP been calculated by somebody? (Fri Jun 24 2005 - 20:30:12 CDT)
  • Re: AMBER: Parameters for phosphorylated amino acids (Thu Jun 23 2005 - 17:41:30 CDT)
  • AMBER: Compile Problems of Parallel Amber8 on Mac G5 (Wed Jun 08 2005 - 18:02:23 CDT)
• Thomas Patko
  • Re: AMBER: transfer data from Linux to windows (Thu Jun 09 2005 - 17:49:02 CDT)
• Thomas Steinbrecher
  • Re: AMBER: Free energy calculation for protein-protein complex using MM_PBSA (Thu Jun 30 2005 - 02:14:01 CDT)
  • Re: AMBER: radius parameter for Mg2+ in mm_pbsa calculation (Mon Jun 06 2005 - 02:23:16 CDT)
• Varsha Goyal
  • Re: AMBER: Analysing my simulation data.. (Sat Jun 18 2005 - 11:21:28 CDT)
  • AMBER: Question about tutorial-9 (Tue Jun 07 2005 - 11:27:57 CDT)
• Vijay Manickam Achari
  • AMBER: example script for hbond calculation (Thu Jun 30 2005 - 01:27:15 CDT)
  • AMBER: acceptor and donor in hbond calculation (Thu Jun 30 2005 - 00:01:58 CDT)
  • AMBER: calculating hydrogen bonds (Tue Jun 28 2005 - 21:50:36 CDT)
  • AMBER: calculating torsion angles (Tue Jun 28 2005 - 03:59:02 CDT)
  • AMBER: script for calculating hydrogen bond (Mon Jun 27 2005 - 21:57:30 CDT)
  • AMBER: using xmgrace.... (Thu Jun 23 2005 - 21:51:37 CDT)
  • AMBER: Analysing my simulation data.. (Sat Jun 18 2005 - 03:32:13 CDT)
  • AMBER: creating pdb file.... (Tue Jun 14 2005 - 05:49:09 CDT)
  • Re: AMBER: how to pull out frames (Mon Jun 13 2005 - 23:04:42 CDT)
  • AMBER: how to pull out frames (Mon Jun 13 2005 - 00:23:51 CDT)
• Viktor Hornak
  • Re: AMBER: setting up restraint with ntr option (Thu Jun 09 2005 - 18:53:05 CDT)
• Wai Keat Yam
  • AMBER: substitute missing residues? (Fri Jun 10 2005 - 03:20:29 CDT)
• wendy
  • Re: AMBER: fail of minimization in sander (Thu Jun 16 2005 - 21:43:11 CDT)
  • Re: AMBER: fail of minimization in sander (Thu Jun 16 2005 - 03:19:15 CDT)
  • Re: AMBER: fail of minimization in sander (Wed Jun 15 2005 - 02:54:59 CDT)
  • Re: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 11:13:10 CDT)
  • Re: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 10:57:08 CDT)
  • Re: AMBER: fail of minimization in sander (Mon Jun 06 2005 - 05:06:01 CDT)
  • Re: AMBER: fail of minimization in sander (Sun Jun 05 2005 - 23:59:15 CDT)
  • AMBER: fail of minimization in sander (Sun Jun 05 2005 - 22:01:25 CDT)
• xhu1_at_memphis.edu
  • AMBER: software for real polymer MD simulation (Wed Jun 22 2005 - 16:31:51 CDT)
• Xin Hu
  • AMBER: PBSA error: PB bomb in pd_aaradi (Wed Jun 22 2005 - 09:34:13 CDT)
• xinhuang_at_indiana.edu
  • AMBER: questions about RNA (Mon Jun 27 2005 - 22:19:58 CDT)
• xueping
  • AMBER: Hbond analysis (Sun Jun 26 2005 - 20:27:48 CDT)
• Ye Mei
  • AMBER: least square fit of snapshots in md trajectory to a reference frame (Thu Jun 30 2005 - 21:56:08 CDT)
  • AMBER: large std error in entropy estimation (Tue Jun 21 2005 - 21:51:43 CDT)
  • Re: RE: AMBER: SHAKE in md with partial solvation (Tue Jun 07 2005 - 08:46:49 CDT)
  • AMBER: Re: Re: AMBER: SHAKE in md with partial solvation (Mon Jun 06 2005 - 05:49:44 CDT)
  • Re: AMBER: SHAKE in md with partial solvation (Sun Jun 05 2005 - 06:19:45 CDT)
  • AMBER: SHAKE in md with partial solvation (Sun Jun 05 2005 - 02:30:00 CDT)
  • AMBER: radius parameter for Mg2+ in mm_pbsa calculation (Sat Jun 04 2005 - 09:37:04 CDT)
• Yen-Ting Lai
  • Re: AMBER: Question about "quasih" (Wed Jun 15 2005 - 14:25:57 CDT)
  • AMBER: Question about "quasih" (Wed Jun 15 2005 - 11:46:22 CDT)
• Yogesh Sabnis
  • AMBER: Cut pdb files (Thu Jun 16 2005 - 02:57:18 CDT)
• Yong Duan
  • Re: AMBER: Protein dynamics. (Wed Jun 08 2005 - 12:24:02 CDT)
• Zhang Bing
  • AMBER: parallel error (Mon Jun 27 2005 - 07:36:14 CDT)
  • AMBER: solutions of amber installation problems (Tue Jun 14 2005 - 21:42:13 CDT)
  • AMBER: Thanks (Tue Jun 14 2005 - 21:26:23 CDT)
  • AMBER: compiler (Tue Jun 14 2005 - 06:13:19 CDT)
  • AMBER: compiler (Tue Jun 14 2005 - 03:14:08 CDT)
  • AMBER: New problem of parallel sander (Thu Jun 02 2005 - 21:46:13 CDT)
  • AMBER: amber8 installation problems (Thu Jun 02 2005 - 01:55:48 CDT)
  • AMBER: amber8 installation problems (Thu Jun 02 2005 - 01:44:47 CDT)
• Zhiguo Liu
  • Re: Re: AMBER: Free energy calculation for protein-protein complex usingMM_PBSA (Thu Jun 30 2005 - 04:56:42 CDT)
  • AMBER: Free energy calculation for protein-protein complex using MM_PBSA (Wed Jun 29 2005 - 20:59:01 CDT)
• ½¨Æ½ ºú
  • AMBER: TI in Amber8 (Fri Jun 03 2005 - 04:49:02 CDT)

Last message date: Sat Dec 31 2005 - 12:51:27 CST
Archived on: Sat Dec 31 2005 - 12:51:45 CST