Amber Archive Aug 2007: by subject

AMBER:
- Melinda Layten (Fri Aug 31 2007 - 10:19:21 PDT)
- Beale, John (Thu Aug 30 2007 - 06:05:11 PDT)
- David A. Case (Mon Aug 20 2007 - 17:31:21 PDT)
- Beale, John (Mon Aug 20 2007 - 08:41:06 PDT)
- David A. Case (Tue Aug 14 2007 - 08:27:48 PDT)
- Thomas Pochapsky (Fri Aug 10 2007 - 13:34:32 PDT)
- Steve Seibold (Fri Aug 10 2007 - 13:17:47 PDT)
- msubhamoy.ibab.ac.in (Wed Aug 08 2007 - 06:01:00 PDT)
AMBER: $tleap is not normal
- Ross Walker (Mon Aug 20 2007 - 19:51:16 PDT)
- Qiang Zhong (Mon Aug 20 2007 - 18:34:00 PDT)
AMBER: (no subject)
- Ross Walker (Sat Aug 04 2007 - 08:30:36 PDT)
- Syed Tarique Moin (Sat Aug 04 2007 - 07:07:23 PDT)
- Carlos Simmerling (Sat Aug 04 2007 - 03:55:29 PDT)
- Syed Tarique Moin (Fri Aug 03 2007 - 23:11:51 PDT)
- Gustavo Seabra (Thu Aug 02 2007 - 13:19:05 PDT)
- Carlos Simmerling (Thu Aug 02 2007 - 05:48:36 PDT)
- Syed Tarique Moin (Thu Aug 02 2007 - 05:36:21 PDT)
- gurpreet singh (Thu Aug 02 2007 - 01:39:07 PDT)
- Syed Tarique Moin (Wed Aug 01 2007 - 23:50:59 PDT)
AMBER: a question about xleap
- WANG,YING (Tue Aug 21 2007 - 12:16:48 PDT)
AMBER: about parallelization in QM-MM
- Ross Walker (Fri Aug 17 2007 - 11:45:08 PDT)
- Ross Walker (Fri Aug 17 2007 - 09:58:54 PDT)
- Francesco Pietra (Thu Aug 16 2007 - 23:41:02 PDT)
AMBER: about shake
- linfu (Wed Aug 08 2007 - 18:10:05 PDT)
- Steven Winfield (Wed Aug 08 2007 - 08:59:45 PDT)
- linfu (Tue Aug 07 2007 - 18:36:59 PDT)
AMBER: Add hydrogen and charge calculation
- snoze pa (Mon Aug 27 2007 - 21:07:55 PDT)
- Chris Moth (Mon Aug 27 2007 - 13:33:25 PDT)
- snoze pa (Mon Aug 27 2007 - 12:06:44 PDT)
AMBER: AMBER at WESTGRID
- Gustavo Seabra (Thu Aug 30 2007 - 05:35:49 PDT)
- Eduardo Mendez-Villuendas (Thu Aug 30 2007 - 04:49:07 PDT)
AMBER: Antechamber formal charges with Gasteiger method
- Scott Brozell (Sat Aug 04 2007 - 12:42:43 PDT)
- David A. Case (Fri Aug 03 2007 - 13:17:11 PDT)
- Scott Brozell (Thu Aug 02 2007 - 18:44:28 PDT)
AMBER: antechamber question
- Junmei Wang (Fri Aug 31 2007 - 13:07:09 PDT)
- Beale, John (Fri Aug 31 2007 - 07:07:56 PDT)
AMBER: antechamber, how does it work
- Francesco Pietra (Thu Aug 16 2007 - 10:25:35 PDT)
- David A. Case (Thu Aug 16 2007 - 08:40:16 PDT)
- Francesco Pietra (Wed Aug 15 2007 - 22:53:34 PDT)
- Thomas Cheatham III (Wed Aug 15 2007 - 16:02:07 PDT)
- Francesco Pietra (Wed Aug 15 2007 - 14:53:55 PDT)
- David A. Case (Wed Aug 15 2007 - 10:07:22 PDT)
- Francesco Pietra (Wed Aug 15 2007 - 09:08:37 PDT)
- Seth Hayik (Wed Aug 15 2007 - 08:10:22 PDT)
- Francesco Pietra (Wed Aug 15 2007 - 08:05:31 PDT)
- Francesco Pietra (Wed Aug 15 2007 - 07:25:12 PDT)
- Gustavo Seabra (Wed Aug 15 2007 - 07:15:48 PDT)
- Junmei Wang (Wed Aug 15 2007 - 06:33:36 PDT)
- Francesco Pietra (Wed Aug 15 2007 - 01:43:45 PDT)
AMBER: Any experience on Dell two quad core system?
- Robert Duke (Tue Aug 14 2007 - 09:13:07 PDT)
- David Cerutti (Tue Aug 14 2007 - 08:05:34 PDT)
- Ilyas Yildirim (Mon Aug 13 2007 - 17:39:01 PDT)
- David Cerutti (Mon Aug 13 2007 - 13:59:58 PDT)
- Andreas Svrcek-Seiler (Mon Aug 13 2007 - 13:46:58 PDT)
- Ilyas Yildirim (Mon Aug 13 2007 - 12:25:22 PDT)
- M. L. Dodson (Mon Aug 13 2007 - 10:37:47 PDT)
- Andreas Svrcek-Seiler (Mon Aug 13 2007 - 10:21:39 PDT)
- M. L. Dodson (Mon Aug 13 2007 - 08:59:11 PDT)
- Andreas Svrcek-Seiler (Mon Aug 13 2007 - 08:12:15 PDT)
- Ilyas Yildirim (Fri Aug 03 2007 - 09:35:26 PDT)
- Ross Walker (Fri Aug 03 2007 - 09:28:57 PDT)
- Ilyas Yildirim (Thu Aug 02 2007 - 21:23:17 PDT)
- Andreas Svrcek-Seiler (Thu Aug 02 2007 - 21:18:42 PDT)
- Ye Mei (Thu Aug 02 2007 - 20:57:00 PDT)
- Ilyas Yildirim (Thu Aug 02 2007 - 17:33:40 PDT)
AMBER: articles
- Lili Peng (Fri Aug 24 2007 - 12:10:12 PDT)
- Beale, John (Fri Aug 24 2007 - 06:02:05 PDT)
AMBER: Average potential energies and conformer ratios
- Francesco Pietra (Wed Aug 01 2007 - 06:58:02 PDT)
AMBER: bad atom type:F
- David A. Case (Thu Aug 30 2007 - 08:35:00 PDT)
- Emilia Wu (Thu Aug 30 2007 - 05:36:14 PDT)
AMBER: Binary file curiosities
- David A. Case (Mon Aug 06 2007 - 08:03:07 PDT)
- David LeBard (Sat Aug 04 2007 - 14:34:23 PDT)
- Thomas Cheatham III (Fri Aug 03 2007 - 16:32:55 PDT)
- David A. Case (Fri Aug 03 2007 - 16:21:25 PDT)
- David LeBard (Fri Aug 03 2007 - 15:59:45 PDT)
AMBER: bug in nonbond_list.f (nee ew_setup.f)
- neville forlemu (Wed Aug 08 2007 - 11:35:51 PDT)
- David A. Case (Fri Aug 03 2007 - 08:14:27 PDT)
AMBER: Bug in ptraj mask processing?
- Steve Spronk (Wed Aug 15 2007 - 12:18:15 PDT)
AMBER: bugfix for impropers in parmchk
- Jiten (Wed Aug 01 2007 - 23:23:20 PDT)
- David A. Case (Wed Aug 01 2007 - 22:04:20 PDT)
- Jiten (Wed Aug 01 2007 - 21:02:24 PDT)
AMBER: Building parallel Amber 9.0
- Balvinder Singh (Wed Aug 15 2007 - 21:02:38 PDT)
- Balvinder Singh (Wed Aug 15 2007 - 20:53:44 PDT)
- Ross Walker (Wed Aug 15 2007 - 10:43:28 PDT)
- Rajendra P. OJHA (Wed Aug 15 2007 - 08:44:10 PDT)
- Rajendra P. OJHA (Wed Aug 15 2007 - 08:41:25 PDT)
- Ross Walker (Wed Aug 15 2007 - 07:26:36 PDT)
- Gustavo Seabra (Wed Aug 15 2007 - 06:46:59 PDT)
- Beale, John (Wed Aug 15 2007 - 05:21:56 PDT)
AMBER: Ca(2+) parameter
- David A. Case (Thu Aug 23 2007 - 08:04:01 PDT)
- Qiang Zhong (Thu Aug 23 2007 - 04:01:24 PDT)
AMBER: Calculating cumulative average
- Francesco Pietra (Thu Aug 02 2007 - 10:00:10 PDT)
AMBER: charges in PBSA calculation
- David A. Case (Sun Aug 19 2007 - 17:57:14 PDT)
- Neha Gandhi (Sun Aug 19 2007 - 16:01:47 PDT)
- Ray Luo (Sun Aug 19 2007 - 06:32:19 PDT)
- Neha Gandhi (Sat Aug 18 2007 - 19:20:16 PDT)
AMBER: Citation for Langevin thermostat?
- David A. Case (Sat Aug 11 2007 - 12:47:59 PDT)
- Marc Baaden (Sat Aug 11 2007 - 00:13:28 PDT)
AMBER: command tleap is not normal
- Ilyas Yildirim (Tue Aug 21 2007 - 01:50:35 PDT)
- Qiang Zhong (Tue Aug 21 2007 - 01:12:44 PDT)
AMBER: compile amber8 with mpich2
- Scott Brozell (Wed Aug 08 2007 - 19:46:22 PDT)
- Kailee (Tue Aug 07 2007 - 06:18:14 PDT)
AMBER: Confusion about Langevin dymamics
- David Mobley (Fri Aug 31 2007 - 09:05:13 PDT)
- David A. Case (Fri Aug 31 2007 - 07:53:47 PDT)
- Hayden Eastwood (Fri Aug 31 2007 - 06:46:28 PDT)
- Carlos Simmerling (Fri Aug 31 2007 - 06:52:02 PDT)
AMBER: Connecting two ethanes in LEaP
- David A. Case (Fri Aug 31 2007 - 09:18:18 PDT)
- Kliman, Michal (Thu Aug 30 2007 - 13:53:46 PDT)
AMBER: Converting AMBER-format force fields for tinker
- Aaron Virshup (Fri Aug 31 2007 - 12:04:12 PDT)
AMBER: CRESP charges in antechamber prepin
- Francesco Pietra (Mon Aug 20 2007 - 00:23:24 PDT)
AMBER: Criteria for classical md being OK to move to QM-MM
- Ross Walker (Wed Aug 29 2007 - 11:40:30 PDT)
- M. L. Dodson (Wed Aug 29 2007 - 11:24:43 PDT)
- Gustavo Seabra (Wed Aug 29 2007 - 11:13:05 PDT)
- Francesco Pietra (Wed Aug 29 2007 - 10:40:36 PDT)
- M. L. Dodson (Wed Aug 29 2007 - 10:11:29 PDT)
- Francesco Pietra (Wed Aug 29 2007 - 09:51:15 PDT)
AMBER: Cygwin error
- Gustavo Seabra (Thu Aug 09 2007 - 14:40:14 PDT)
- Bill Ross (Thu Aug 09 2007 - 13:42:48 PDT)
- Gustavo Seabra (Thu Aug 09 2007 - 13:30:19 PDT)
- Lili Peng (Thu Aug 09 2007 - 12:16:20 PDT)
- Gustavo Seabra (Thu Aug 09 2007 - 12:08:27 PDT)
- Lili Peng (Thu Aug 09 2007 - 12:06:03 PDT)
- Ross Walker (Thu Aug 09 2007 - 11:52:36 PDT)
- Lili Peng (Thu Aug 09 2007 - 11:13:27 PDT)
- Gustavo Seabra (Wed Aug 08 2007 - 16:36:29 PDT)
- Lili Peng (Wed Aug 08 2007 - 16:04:31 PDT)
- Bill Ross (Wed Aug 08 2007 - 15:29:24 PDT)
- Gustavo Seabra (Wed Aug 08 2007 - 15:21:01 PDT)
- Lili Peng (Wed Aug 08 2007 - 15:13:54 PDT)
- Mark Williamson (Wed Aug 08 2007 - 15:02:15 PDT)
- Lili Peng (Wed Aug 08 2007 - 14:56:00 PDT)
- Bill Ross (Wed Aug 08 2007 - 14:43:49 PDT)
- Lili Peng (Wed Aug 08 2007 - 14:33:22 PDT)
AMBER: DFTB email address
- tomas.kubar.marge.uochb.cas.cz (Sun Aug 19 2007 - 13:27:48 PDT)
- Francesco Pietra (Sat Aug 18 2007 - 00:14:53 PDT)
AMBER: Dihedrals in Sander
- Martin Stennett (Thu Aug 30 2007 - 01:36:17 PDT)
AMBER: Distance restraints between center of mass of two molecules
- Carlos Simmerling (Wed Aug 15 2007 - 14:17:33 PDT)
- Sudha Mani Karra (Wed Aug 15 2007 - 14:02:55 PDT)
- Carlos Simmerling (Wed Aug 15 2007 - 08:52:27 PDT)
- Sudha Mani Karra (Wed Aug 15 2007 - 08:40:37 PDT)
- Carlos Simmerling (Wed Aug 15 2007 - 07:54:40 PDT)
- Sudha Mani Karra (Wed Aug 15 2007 - 07:38:06 PDT)
AMBER: docking ability
- Scott Brozell (Sun Aug 19 2007 - 11:19:08 PDT)
- anna duraj (Wed Aug 15 2007 - 10:34:37 PDT)
AMBER: edit.out amber version 9
- WANG,YING (Thu Aug 02 2007 - 13:33:49 PDT)
- David A. Case (Thu Aug 02 2007 - 12:00:22 PDT)
- Greg Gannon (Thu Aug 02 2007 - 11:21:31 PDT)
AMBER: energy minimization parameter
- Lorenzo Gontrani (Wed Aug 29 2007 - 00:54:58 PDT)
- Qiang Zhong (Wed Aug 29 2007 - 00:54:12 PDT)
AMBER: Entropy in MM_PBSA
- David Mobley (Fri Aug 24 2007 - 09:31:28 PDT)
- Sergey Samsonov (Mon Aug 20 2007 - 08:01:37 PDT)
AMBER: Error in MMPBSA Calculation
- jitrayut jitonnom (Tue Aug 21 2007 - 00:11:52 PDT)
- msubhamoy.ibab.ac.in (Mon Aug 20 2007 - 22:53:17 PDT)
AMBER: EXTRA_PTS: frtype 2 Should not be here
- Dilip Dagade (Thu Aug 16 2007 - 09:52:56 PDT)
- David A. Case (Thu Aug 16 2007 - 09:33:52 PDT)
- Dilip Dagade (Wed Aug 15 2007 - 21:39:37 PDT)
- David A. Case (Wed Aug 15 2007 - 10:34:49 PDT)
- Dilip Dagade (Wed Aug 15 2007 - 09:50:57 PDT)
AMBER: Failure to SCF convergence
- Ross Walker (Sat Aug 11 2007 - 16:14:54 PDT)
- Francesco Pietra (Sat Aug 11 2007 - 09:56:53 PDT)
AMBER: Failure to SCF convergence & parallelization and memory
- Ross Walker (Mon Aug 13 2007 - 10:16:25 PDT)
- Francesco Pietra (Sun Aug 12 2007 - 00:37:33 PDT)
AMBER: force field for hydrogels
- Prem Prakash Pathak (Thu Aug 02 2007 - 23:03:48 PDT)
AMBER: force field for irregulate DNA ends
- Hu, Shaowen (JSC-SK)[USRA] (Sat Aug 04 2007 - 11:20:42 PDT)
AMBER: Force field for RNA with U-turn motif
- Cenk Andac (Wed Aug 22 2007 - 11:31:04 PDT)
- Jiri Sponer (Wed Aug 22 2007 - 09:33:46 PDT)
- Cenk Andac (Wed Aug 22 2007 - 09:08:29 PDT)
- Vlad Cojocaru (Wed Aug 22 2007 - 01:07:24 PDT)
- Cenk Andac (Tue Aug 21 2007 - 06:52:48 PDT)
AMBER: Force Field Parameters
- Raviprasad Aduri (Thu Aug 02 2007 - 12:49:37 PDT)
- Prashanth Athri (Thu Aug 02 2007 - 10:39:10 PDT)
- Beale, John (Thu Aug 02 2007 - 09:46:16 PDT)
AMBER: Fwd: QM region + cutoff larger that box
- Gustavo Seabra (Mon Aug 06 2007 - 08:38:19 PDT)
- M. L. Dodson (Mon Aug 06 2007 - 08:29:43 PDT)
- Francesco Pietra (Mon Aug 06 2007 - 08:07:09 PDT)
- M. L. Dodson (Mon Aug 06 2007 - 05:58:56 PDT)
- Francesco Pietra (Sun Aug 05 2007 - 23:28:13 PDT)
- Francesco Pietra (Sat Aug 04 2007 - 09:42:33 PDT)
- Gustavo Seabra (Sat Aug 04 2007 - 08:33:12 PDT)
- M. L. Dodson (Sat Aug 04 2007 - 07:51:22 PDT)
- Francesco Pietra (Sat Aug 04 2007 - 07:33:35 PDT)
- M. L. Dodson (Sat Aug 04 2007 - 07:32:17 PDT)
- Francesco Pietra (Sat Aug 04 2007 - 01:32:40 PDT)
AMBER: Fwd: SCC convergence failure in QM-MM DFTB
- Gustavo Seabra (Mon Aug 27 2007 - 13:50:40 PDT)
- Gustavo Seabra (Mon Aug 27 2007 - 12:12:23 PDT)
- Francesco Pietra (Sun Aug 26 2007 - 23:24:33 PDT)
- Francesco Pietra (Sun Aug 26 2007 - 09:28:14 PDT)
- M. L. Dodson (Sun Aug 26 2007 - 08:42:14 PDT)
- Francesco Pietra (Sun Aug 26 2007 - 07:34:57 PDT)
- Francesco Pietra (Sun Aug 26 2007 - 00:26:42 PDT)
AMBER: Fwd: Schedule for QM-MM with Amber9/Amber10
- Francesco Pietra (Thu Aug 30 2007 - 06:17:41 PDT)
AMBER: Fwd: unable to save prmtop/inpcrd for chcl3box
- Francesco Pietra (Fri Aug 03 2007 - 05:24:24 PDT)
AMBER: GAFF atom typing for flavin
- Hans Martin Senn (Sat Aug 04 2007 - 09:15:30 PDT)
AMBER: generating a .rst file from an .mdcrd file
- Gustavo Seabra (Mon Aug 27 2007 - 12:15:23 PDT)
- Thomas Pochapsky (Mon Aug 27 2007 - 11:41:56 PDT)
AMBER: heating up system
- Adrian Roitberg (Tue Aug 28 2007 - 11:45:26 PDT)
- Francesco Pietra (Tue Aug 28 2007 - 09:16:57 PDT)
AMBER: heical content in simulations
- priya priya (Tue Aug 07 2007 - 01:41:16 PDT)
- Chng Choon-Peng (Tue Aug 07 2007 - 01:19:26 PDT)
- priya priya (Tue Aug 07 2007 - 00:58:12 PDT)
AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA
- linfu (Wed Aug 08 2007 - 06:33:58 PDT)
- Ross Walker (Wed Aug 08 2007 - 07:49:11 PDT)
- msubhamoy.ibab.ac.in (Wed Aug 08 2007 - 06:08:04 PDT)
AMBER: how to calculate the ps/day of md simulation using using my cluster system in amber7
- Syed Tarique Moin (Wed Aug 01 2007 - 02:36:31 PDT)
AMBER: How to carry out drug-dna complex simulations
- Scott Brozell (Sun Aug 19 2007 - 11:06:22 PDT)
- David A. Case (Tue Aug 14 2007 - 08:18:47 PDT)
- Anju Sharma (Tue Aug 14 2007 - 01:50:04 PDT)
AMBER: how to combine two molecules
- Wenyong Tong (Mon Aug 13 2007 - 16:14:49 PDT)
- David A. Case (Mon Aug 13 2007 - 09:43:57 PDT)
- Wenyong Tong (Sat Aug 11 2007 - 18:48:48 PDT)
- Benjamin Juhl (Fri Aug 10 2007 - 02:11:07 PDT)
- Wenyong Tong (Wed Aug 08 2007 - 22:34:33 PDT)
AMBER: How to couple only one residue to the temperature bath?
- Carlos Simmerling (Fri Aug 10 2007 - 15:43:29 PDT)
- Michael Lerner (Fri Aug 10 2007 - 14:35:38 PDT)
- Carlos Simmerling (Fri Aug 10 2007 - 08:55:02 PDT)
- Michael Lerner (Fri Aug 10 2007 - 07:45:10 PDT)
AMBER: How to delete particular frame from mdcrd file (not with ptraj).
- Adrian Roitberg (Thu Aug 23 2007 - 06:32:28 PDT)
- Steve Spronk (Thu Aug 23 2007 - 06:25:50 PDT)
- saurabh agrawal (Wed Aug 22 2007 - 03:25:53 PDT)
- Steven Winfield (Wed Aug 22 2007 - 03:12:16 PDT)
- saurabh agrawal (Wed Aug 22 2007 - 02:48:52 PDT)
AMBER: How to delete particular frame from mdcrd file (not with ptraj).]
- Steven Winfield (Thu Aug 23 2007 - 06:31:49 PDT)
AMBER: how to include mpirun in this script
- Ross Walker (Tue Aug 21 2007 - 11:45:23 PDT)
- Syed Tarique Moin (Tue Aug 21 2007 - 03:50:12 PDT)
AMBER: How to perform MD simulation in NVT ensemble?
- Gustavo Seabra (Wed Aug 29 2007 - 07:53:11 PDT)
- WANG,YING (Wed Aug 29 2007 - 06:50:30 PDT)
- Gustavo Seabra (Fri Aug 24 2007 - 19:21:59 PDT)
- WANG,YING (Thu Aug 23 2007 - 13:53:05 PDT)
- Chris Moth (Thu Aug 23 2007 - 10:07:30 PDT)
- WANG,YING (Thu Aug 23 2007 - 09:13:51 PDT)
AMBER: How to use AMBER Parameter Database ?
- David A. Case (Thu Aug 23 2007 - 09:53:55 PDT)
- Qiang Zhong (Wed Aug 22 2007 - 01:53:04 PDT)
- Qiang Zhong (Tue Aug 21 2007 - 05:36:46 PDT)
AMBER: hybridization in Amber, pertaining to resonant structures, ions
- David A. Case (Sat Aug 11 2007 - 13:35:15 PDT)
- Karen Callahan (Mon Aug 06 2007 - 21:13:27 PDT)
AMBER: imin=5 and inptraj
- Chris Moth (Sat Aug 11 2007 - 14:37:11 PDT)
- Nikola Trbovic (Sat Aug 11 2007 - 14:31:40 PDT)
- Carlos Simmerling (Sat Aug 11 2007 - 14:23:29 PDT)
- Nikola Trbovic (Sat Aug 11 2007 - 13:11:08 PDT)
AMBER: Implicit solvent simulation is too slow.
- Ross Walker (Fri Aug 10 2007 - 08:56:32 PDT)
- SeungPyo Hong (Fri Aug 10 2007 - 07:04:28 PDT)
- Carlos Simmerling (Fri Aug 10 2007 - 06:07:50 PDT)
- SeungPyo Hong (Fri Aug 10 2007 - 05:42:11 PDT)
AMBER: Information about Amber 9
- David A. Case (Fri Aug 03 2007 - 07:53:22 PDT)
- Lycourgos Chiniadis (Thu Aug 02 2007 - 22:11:17 PDT)
AMBER: Integrating the alpha-helix bias correction into ff94
- Carlos Simmerling (Mon Aug 06 2007 - 12:42:17 PDT)
- Andrew Borgert (Mon Aug 06 2007 - 12:18:58 PDT)
AMBER: Machine environment to install AMBER 8
- Bertrand Russell (Tue Aug 14 2007 - 23:34:02 PDT)
- M. Maeda (Tue Aug 14 2007 - 22:17:03 PDT)
- Benjamin Juhl (Tue Aug 14 2007 - 03:49:13 PDT)
- Bertrand Russell (Tue Aug 14 2007 - 02:50:07 PDT)
- M. Maeda (Tue Aug 14 2007 - 02:45:53 PDT)
- Bertrand Russell (Tue Aug 14 2007 - 02:21:07 PDT)
- M. Maeda (Tue Aug 14 2007 - 02:19:37 PDT)
- Benjamin Juhl (Tue Aug 14 2007 - 02:10:16 PDT)
- M. Maeda (Tue Aug 14 2007 - 01:54:03 PDT)
- Benjamin Juhl (Tue Aug 14 2007 - 01:28:09 PDT)
- M. Maeda (Mon Aug 13 2007 - 23:03:07 PDT)
AMBER: Measuring Bond Angle over simulation
- Carlos Simmerling (Fri Aug 31 2007 - 12:34:13 PDT)
- Seth Lilavivat (Fri Aug 31 2007 - 12:25:20 PDT)
AMBER: metalloprotein dynamics
- Sally Pias (Mon Aug 27 2007 - 10:55:51 PDT)
AMBER: Missplaced TERs
- Steve Seibold (Thu Aug 16 2007 - 12:47:38 PDT)
- David A. Case (Thu Aug 16 2007 - 11:53:10 PDT)
- Steve Seibold (Thu Aug 16 2007 - 11:35:26 PDT)
AMBER: MM-PBSA calculations of entropy within the sphere
- Sergey Samsonov (Wed Aug 22 2007 - 06:49:25 PDT)
AMBER: MM_PBSA No radius found for Br!!
- Scott Brozell (Sun Aug 19 2007 - 10:40:20 PDT)
- Urszula Uciechowska (Tue Aug 14 2007 - 08:53:32 PDT)
- Urszula Uciechowska (Tue Aug 14 2007 - 06:49:06 PDT)
- Antonio Morreale (Mon Aug 13 2007 - 04:39:52 PDT)
- Urszula Uciechowska (Mon Aug 13 2007 - 02:52:34 PDT)
AMBER: mmpbsa calculation
- msubhamoy.ibab.ac.in (Mon Aug 20 2007 - 02:53:42 PDT)
AMBER: MMPBSA NOT Getting results
- Rafi Ahmad (Tue Aug 14 2007 - 01:34:35 PDT)
- msubhamoy.ibab.ac.in (Tue Aug 14 2007 - 01:26:57 PDT)
AMBER: modified leaprc for glycoproteins
- Irene Newhouse (Fri Aug 31 2007 - 18:14:32 PDT)
- David A. Case (Fri Aug 31 2007 - 14:42:03 PDT)
- Irene Newhouse (Fri Aug 31 2007 - 13:53:05 PDT)
AMBER: Molsurf error
- Pankaj R. Daga (Fri Aug 17 2007 - 10:46:54 PDT)
AMBER: MPI
- Mark Williamson (Fri Aug 17 2007 - 05:58:00 PDT)
- Beale, John (Fri Aug 17 2007 - 05:00:33 PDT)
AMBER: MPI Quiescence problem in REMD
- In Hee Park (Thu Aug 16 2007 - 15:56:37 PDT)
AMBER: NAN and vlimit exceeded errors in restrained MD.. using IBELLY
- Sandeep Kaushik (Thu Aug 16 2007 - 22:44:17 PDT)
AMBER: NETCDF
- Geoff Wood (Mon Aug 27 2007 - 00:18:48 PDT)
- Chris Moth (Fri Aug 24 2007 - 06:03:37 PDT)
- Chris Moth (Fri Aug 24 2007 - 05:58:34 PDT)
- Geoff Wood (Fri Aug 24 2007 - 03:43:11 PDT)
AMBER: neutral terminals
- Carlos Simmerling (Thu Aug 02 2007 - 05:04:15 PDT)
- Jena M (Wed Aug 01 2007 - 17:15:46 PDT)
AMBER: Neutralize charges for simulated annealing?
- Francesco Pietra (Sat Aug 11 2007 - 15:35:30 PDT)
AMBER: Normal Mode Analysis
- David A. Case (Wed Aug 15 2007 - 15:56:46 PDT)
- Kresimir Sikic (Mon Aug 13 2007 - 08:12:59 PDT)
AMBER: nucleic acid electrostatic energy
- David A. Case (Sat Aug 04 2007 - 08:28:36 PDT)
- Tiago Sobreira (Sat Aug 04 2007 - 06:45:46 PDT)
AMBER: NVE energy and temperature drift
- Nikola Trbovic (Sat Aug 11 2007 - 14:33:09 PDT)
- David A. Case (Sat Aug 11 2007 - 13:28:30 PDT)
- Vlad Cojocaru (Fri Aug 10 2007 - 02:10:51 PDT)
- Vlad Cojocaru (Fri Aug 10 2007 - 02:03:15 PDT)
- Robert Duke (Thu Aug 09 2007 - 19:15:19 PDT)
- Nikola Trbovic (Thu Aug 09 2007 - 17:11:07 PDT)
- Robert Duke (Thu Aug 09 2007 - 16:43:42 PDT)
- Nikola Trbovic (Thu Aug 09 2007 - 15:50:45 PDT)
- Thomas Cheatham III (Thu Aug 09 2007 - 15:27:50 PDT)
- Robert Duke (Thu Aug 09 2007 - 15:15:58 PDT)
- Nikola Trbovic (Thu Aug 09 2007 - 13:24:11 PDT)
AMBER: Octahedral box orientation
- David Cerutti (Tue Aug 21 2007 - 17:07:32 PDT)
- David Cerutti (Tue Aug 21 2007 - 06:08:38 PDT)
AMBER: ow to split MDCRD file using ptraj
- Gustavo Seabra (Fri Aug 24 2007 - 19:17:27 PDT)
- priya priya (Fri Aug 24 2007 - 00:34:27 PDT)
AMBER: Parallelizin antechamber?
- Junmei Wang (Wed Aug 15 2007 - 06:41:45 PDT)
- M. L. Dodson (Tue Aug 14 2007 - 07:29:16 PDT)
- Francesco Pietra (Tue Aug 14 2007 - 06:29:11 PDT)
AMBER: Parse charges for small molecules
- Neha Gandhi (Wed Aug 22 2007 - 21:50:38 PDT)
AMBER: Performance of polarizable model simulations
- Jones de Andrade (Wed Aug 22 2007 - 21:17:52 PDT)
AMBER: personal computer configuration for parallel computing
- emine cebe (Sun Aug 26 2007 - 04:36:28 PDT)
AMBER: planarity restraints for NA
- Seth Lilavivat (Thu Aug 02 2007 - 12:29:42 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Thu Aug 02 2007 - 11:49:15 PDT)
- Seth Lilavivat (Thu Aug 02 2007 - 10:01:39 PDT)
- Carlos Simmerling (Thu Aug 02 2007 - 07:17:32 PDT)
- Seth Lilavivat (Thu Aug 02 2007 - 07:07:23 PDT)
- Carlos Simmerling (Thu Aug 02 2007 - 06:17:56 PDT)
- Seth Lilavivat (Thu Aug 02 2007 - 06:12:18 PDT)
AMBER: PM6?
- Ross Walker (Fri Aug 24 2007 - 13:19:22 PDT)
- Thomas Patko (Fri Aug 24 2007 - 10:43:35 PDT)
- Ross Walker (Fri Aug 24 2007 - 09:36:26 PDT)
- Thomas Patko (CSULB) (Fri Aug 24 2007 - 06:46:16 PDT)
AMBER: Positive EPtot in QM-MM
- Francesco Pietra (Tue Aug 07 2007 - 07:34:35 PDT)
AMBER: Prepin error (?) in xleap
- Junmei Wang (Fri Aug 31 2007 - 13:22:07 PDT)
- Lili Peng (Thu Aug 30 2007 - 13:48:34 PDT)
- David A. Case (Mon Aug 27 2007 - 15:29:49 PDT)
- Junmei Wang (Mon Aug 27 2007 - 15:17:53 PDT)
- Lili Peng (Mon Aug 27 2007 - 14:38:30 PDT)
- David A. Case (Mon Aug 27 2007 - 08:58:20 PDT)
- Lili Peng (Fri Aug 24 2007 - 12:26:17 PDT)
- Lili Peng (Fri Aug 24 2007 - 12:19:07 PDT)
- David A. Case (Thu Aug 23 2007 - 17:28:29 PDT)
- Lili Peng (Thu Aug 23 2007 - 14:04:03 PDT)
AMBER: problem compiling Amber9 on 64-machine
- S.Sundar Raman (Wed Aug 01 2007 - 22:03:32 PDT)
- David A. Case (Wed Aug 01 2007 - 09:43:21 PDT)
- David A. Case (Wed Aug 01 2007 - 09:36:37 PDT)
- Ross Walker (Wed Aug 01 2007 - 09:10:17 PDT)
- fatima.chami.durham.ac.uk (Wed Aug 01 2007 - 08:55:26 PDT)
- fatima.chami.durham.ac.uk (Wed Aug 01 2007 - 08:52:13 PDT)
- S.Sundar Raman (Wed Aug 01 2007 - 08:46:10 PDT)
- David A. Case (Wed Aug 01 2007 - 07:50:30 PDT)
- fatima.chami.durham.ac.uk (Wed Aug 01 2007 - 04:03:48 PDT)
AMBER: Problem generating .prepin file in Antechamber
- David A. Case (Thu Aug 02 2007 - 13:53:03 PDT)
- Lili Peng (Thu Aug 02 2007 - 12:15:41 PDT)
- Lili Peng (Thu Aug 02 2007 - 12:07:11 PDT)
AMBER: Problem while carrying out minimisation of drug molecule using sander
- Carlos Simmerling (Tue Aug 07 2007 - 03:57:53 PDT)
- Anju Sharma (Mon Aug 06 2007 - 22:32:43 PDT)
- David A. Case (Mon Aug 06 2007 - 07:35:25 PDT)
- Anju Sharma (Sun Aug 05 2007 - 20:51:11 PDT)
AMBER: Problem while saving .top and .crd files.
- Ross Walker (Thu Aug 02 2007 - 07:54:21 PDT)
- Anju Sharma (Wed Aug 01 2007 - 22:25:19 PDT)
AMBER: Problem with antechamber
- Bill Ross (Thu Aug 02 2007 - 13:14:37 PDT)
- Ross Walker (Thu Aug 02 2007 - 08:22:52 PDT)
- David A. Case (Thu Aug 02 2007 - 08:07:30 PDT)
- Anju Sharma (Thu Aug 02 2007 - 02:03:36 PDT)
- gurpreet singh (Thu Aug 02 2007 - 01:24:18 PDT)
- Anju Sharma (Wed Aug 01 2007 - 23:34:39 PDT)
AMBER: Problem with Antechamber and point charges
- Carlos Simmerling (Fri Aug 03 2007 - 12:55:43 PDT)
- anna duraj (Fri Aug 03 2007 - 12:47:17 PDT)
- Carlos Simmerling (Wed Aug 01 2007 - 12:52:53 PDT)
- anna duraj (Wed Aug 01 2007 - 12:40:44 PDT)
AMBER: Problem with minimization
- Ross Walker (Tue Aug 07 2007 - 06:57:18 PDT)
- Syed Tarique Moin (Tue Aug 07 2007 - 06:11:32 PDT)
AMBER: program bug?
- M. Maeda (Wed Aug 08 2007 - 19:37:13 PDT)
AMBER: protocols for high pressure simulation
- David A. Case (Tue Aug 28 2007 - 08:41:58 PDT)
- brmeher.iitg.ernet.in (Tue Aug 28 2007 - 08:23:00 PDT)
AMBER: protonation of His residue!
- jitrayut jitonnom (Thu Aug 23 2007 - 20:52:51 PDT)
- Qiang Zhong (Thu Aug 23 2007 - 19:39:51 PDT)
AMBER: ptraj hydrogen bonding defaults
- Thomas Cheatham (Fri Aug 17 2007 - 19:33:55 PDT)
- Michael Lerner (Fri Aug 17 2007 - 15:26:09 PDT)
AMBER: QM/MM in reaction pathways?
- Qiang Zhong (Tue Aug 28 2007 - 17:52:21 PDT)
- Ross Walker (Tue Aug 28 2007 - 08:21:40 PDT)
- Gustavo Seabra (Tue Aug 28 2007 - 07:55:20 PDT)
- Qiang Zhong (Tue Aug 28 2007 - 00:51:30 PDT)
- Qiang Zhong (Fri Aug 24 2007 - 01:00:50 PDT)
AMBER: question about a 20 kDa protein
- David A. Case (Sat Aug 18 2007 - 09:07:09 PDT)
AMBER: RDF unit cell volume
- BJÖRN KARLSSON (Thu Aug 30 2007 - 01:14:20 PDT)
AMBER: refinement of NMR struture using AMBER
- Prem Prakash Pathak (Wed Aug 29 2007 - 03:57:11 PDT)
AMBER: Regarding free energy calculation and covalent bond
- David A. Case (Thu Aug 23 2007 - 09:52:17 PDT)
- nag raj (Mon Aug 20 2007 - 21:07:04 PDT)
AMBER: regarding implicit simulation
- Carlos Simmerling (Tue Aug 14 2007 - 04:22:24 PDT)
- gurpreet singh (Mon Aug 13 2007 - 23:21:35 PDT)
AMBER: restrained md and mm pbsa
- Christopher Gaughan (Thu Aug 02 2007 - 07:15:17 PDT)
AMBER: Running Gaussian to get .out files
- Steve Spronk (Fri Aug 24 2007 - 07:08:13 PDT)
- Steve Spronk (Thu Aug 23 2007 - 06:05:25 PDT)
- Lili Peng (Wed Aug 22 2007 - 13:27:25 PDT)
AMBER: Scaling for octahedral versus rectilinear boxes
- Robert Duke (Fri Aug 31 2007 - 07:23:11 PDT)
- David Cerutti (Fri Aug 31 2007 - 06:27:38 PDT)
- Robert Duke (Fri Aug 31 2007 - 05:40:48 PDT)
- David Cerutti (Thu Aug 30 2007 - 22:32:49 PDT)
AMBER: SCC convergence failure in QM-MM DFTB
- Gustavo Seabra (Mon Aug 27 2007 - 10:20:37 PDT)
- Adrian Roitberg (Sat Aug 25 2007 - 11:10:35 PDT)
- Francesco Pietra (Sat Aug 25 2007 - 10:54:12 PDT)
AMBER: Schedule for QM-MM with Amber9/Amber10
- Gustavo Seabra (Fri Aug 31 2007 - 10:41:18 PDT)
- Francesco Pietra (Wed Aug 29 2007 - 23:30:10 PDT)
AMBER: setbox command error
- Steven Winfield (Tue Aug 14 2007 - 02:00:39 PDT)
- priya priya (Tue Aug 14 2007 - 01:58:40 PDT)
- Steven Winfield (Tue Aug 14 2007 - 00:45:08 PDT)
- priya priya (Mon Aug 13 2007 - 23:42:45 PDT)
- David A. Case (Mon Aug 13 2007 - 13:38:30 PDT)
- priya priya (Mon Aug 13 2007 - 09:18:16 PDT)
AMBER: setting dimensions of truncated octahedron
- Lillian chong (Sun Aug 05 2007 - 06:25:01 PDT)
- Thomas Cheatham (Sat Aug 04 2007 - 15:38:15 PDT)
- Lillian chong (Sat Aug 04 2007 - 13:34:59 PDT)
AMBER: short 2'OH-OP contacts in RNA
- Jose Gallego (Fri Aug 10 2007 - 09:22:35 PDT)
AMBER: SMD simulation
- Qiang Zhong (Sat Aug 25 2007 - 02:49:09 PDT)
- Ross Walker (Fri Aug 24 2007 - 06:12:43 PDT)
- Adrian Roitberg (Fri Aug 24 2007 - 05:43:35 PDT)
- Qiang Zhong (Fri Aug 24 2007 - 03:33:41 PDT)
AMBER: solvateCap minin and mdin for qm-mm dftb
- Francesco Pietra (Fri Aug 24 2007 - 14:37:12 PDT)
- Ross Walker (Fri Aug 24 2007 - 14:05:24 PDT)
- M. L. Dodson (Fri Aug 24 2007 - 13:59:04 PDT)
- Francesco Pietra (Fri Aug 24 2007 - 13:42:50 PDT)
- Francesco Pietra (Fri Aug 24 2007 - 10:28:32 PDT)
- Ross Walker (Fri Aug 24 2007 - 09:57:55 PDT)
- M. L. Dodson (Fri Aug 24 2007 - 09:17:37 PDT)
- Francesco Pietra (Fri Aug 24 2007 - 09:01:31 PDT)
- M. L. Dodson (Fri Aug 24 2007 - 06:11:06 PDT)
- Ross Walker (Fri Aug 24 2007 - 06:10:54 PDT)
- Francesco Pietra (Fri Aug 24 2007 - 03:19:30 PDT)
AMBER: Specific heat graph is a straight line
- priya priya (Mon Aug 06 2007 - 06:33:52 PDT)
AMBER: Squished dimer during transition from NVT to NPT
- Katrina Lexa (Thu Aug 30 2007 - 14:02:20 PDT)
AMBER: Successful compile on Mac OSX + Intel compilers
- Viv Kendon (Fri Aug 03 2007 - 09:00:57 PDT)
- Viv Kendon (Fri Aug 03 2007 - 05:28:56 PDT)
AMBER: TEST_FAILURES
- Qiang Zhong (Mon Aug 20 2007 - 17:43:23 PDT)
- Martin Stennett (Mon Aug 20 2007 - 05:56:36 PDT)
- Qiang Zhong (Mon Aug 20 2007 - 05:59:28 PDT)
AMBER: Thermodynamic Integration for a CHARGED molecule
- David A. Case (Fri Aug 17 2007 - 08:46:38 PDT)
- David Mobley (Fri Aug 17 2007 - 06:56:33 PDT)
- ming hui (Fri Aug 17 2007 - 02:12:38 PDT)
AMBER: Thermodynamic Integration for conformational changes?
- Francesco Pietra (Tue Aug 21 2007 - 23:53:15 PDT)
- Gustavo Seabra (Tue Aug 21 2007 - 20:41:23 PDT)
- Gustavo Seabra (Tue Aug 21 2007 - 20:33:36 PDT)
- Francesco Pietra (Tue Aug 21 2007 - 09:57:47 PDT)
AMBER: torsional restraints in a solvated MD simulation.
- Tom Pochapsky (Tue Aug 14 2007 - 18:04:24 PDT)
- Tom Pochapsky (Tue Aug 14 2007 - 16:15:06 PDT)
- Tom Pochapsky (Tue Aug 14 2007 - 16:11:27 PDT)
- David A. Case (Tue Aug 14 2007 - 13:50:31 PDT)
- Carlos Simmerling (Tue Aug 14 2007 - 13:41:52 PDT)
- Tom Pochapsky (Tue Aug 14 2007 - 13:31:34 PDT)
AMBER: Tutorial about SMD?
- Qiang Zhong (Tue Aug 14 2007 - 03:19:09 PDT)
AMBER: Tutorial of document about QM/MM in reaction pathways?
- Qiang Zhong (Tue Aug 21 2007 - 07:06:53 PDT)
AMBER: Unable to open MDCRD file using vmd
- Ross Walker (Thu Aug 23 2007 - 13:40:27 PDT)
- priya priya (Thu Aug 23 2007 - 08:04:19 PDT)
AMBER: unable to save prmtop/inpcrd for chcl3box
- David A. Case (Fri Aug 03 2007 - 07:58:03 PDT)
- Francesco Pietra (Fri Aug 03 2007 - 03:09:03 PDT)
AMBER: unsubscribe
- Pan, Yongmei (Mon Aug 13 2007 - 10:35:12 PDT)
AMBER: Using charmm force field in amber
- Seongeun Yang (Sat Aug 11 2007 - 01:44:44 PDT)
AMBER: Using ntr=1 in xleap
- Carlos Simmerling (Fri Aug 31 2007 - 14:49:14 PDT)
- David A. Case (Fri Aug 31 2007 - 15:52:13 PDT)
- Lili Peng (Fri Aug 31 2007 - 14:27:44 PDT)
AMBER: Using TLEAP to set up MD in the crystal lattice space?
- Thomas Cheatham (Mon Aug 13 2007 - 19:45:19 PDT)
- David A. Case (Mon Aug 13 2007 - 18:26:24 PDT)
- David Cerutti (Mon Aug 13 2007 - 14:09:51 PDT)
AMBER: vector corrplane
- Servaas Michielssens (Thu Aug 02 2007 - 08:25:45 PDT)
AMBER: vlimit exceeded for the step
- Ross Walker (Fri Aug 10 2007 - 13:04:10 PDT)
- Sudha Mani Karra (Fri Aug 10 2007 - 12:31:08 PDT)
AMBER: What is the best computer for running AMBER simulations?
- Prem Prakash Pathak (Sat Aug 18 2007 - 02:36:00 PDT)
- Lili Peng (Thu Aug 16 2007 - 21:50:42 PDT)
- Yu Chen (Thu Aug 16 2007 - 20:44:49 PDT)
- David A. Case (Thu Aug 16 2007 - 16:42:54 PDT)
- Andreas Svrcek-Seiler (Thu Aug 16 2007 - 15:51:06 PDT)
- David LeBard (Thu Aug 16 2007 - 15:17:42 PDT)
- Lili Peng (Thu Aug 16 2007 - 14:37:03 PDT)
AMBER: xLeap "Could not find type" error
- David A. Case (Wed Aug 22 2007 - 08:45:02 PDT)
- WANG,YING (Wed Aug 22 2007 - 08:46:58 PDT)
- Wei Zhang (Wed Aug 22 2007 - 08:18:11 PDT)
- David A. Case (Wed Aug 22 2007 - 08:15:25 PDT)
- WANG,YING (Wed Aug 22 2007 - 07:04:37 PDT)
- Lili Peng (Tue Aug 21 2007 - 18:17:44 PDT)
- David A. Case (Tue Aug 21 2007 - 17:40:09 PDT)
- Lili Peng (Tue Aug 21 2007 - 12:28:46 PDT)
Problem loading pdf into tleap
- Ross Walker (Wed Aug 08 2007 - 10:29:19 PDT)
TUTORIAL B1 file polyAT_vac.prmtop
- Ross Walker (Wed Aug 08 2007 - 07:52:39 PDT)
tutorial file polyAT_vac.prmtop
- Ross Walker (Sun Aug 05 2007 - 20:09:46 PDT)

Amber Archive Aug 2007 by subject