Amber Archive Mar 2010: by subject

Jason Swails (Tue Mar 30 2010 - 10:58:22 PDT)
case (Tue Mar 30 2010 - 05:36:09 PDT)
MENZIES G. (569332) (Tue Mar 30 2010 - 03:45:34 PDT)
[AMBER] (no subject)
- Nicee (Mon Mar 29 2010 - 21:31:51 PDT)
[AMBER] 10Gb Interconnect profile
- Ross Walker (Wed Mar 10 2010 - 07:07:27 PST)
- Alessandro Nascimento (Tue Mar 09 2010 - 06:42:17 PST)
[AMBER] _getcor.f Fortran runtime error: End of file
- Jason Swails (Fri Mar 05 2010 - 16:19:26 PST)
- Bill Ross (Fri Mar 05 2010 - 09:30:18 PST)
- Syed Tarique Moin (Fri Mar 05 2010 - 02:44:42 PST)
- sikander azam (Fri Mar 05 2010 - 00:25:58 PST)
- sikander azam (Thu Mar 04 2010 - 02:26:49 PST)
[AMBER] about amber force field
- geyan (Mon Mar 22 2010 - 19:36:44 PDT)
- Carlos Simmerling (Mon Mar 22 2010 - 08:37:47 PDT)
- Carlos Simmerling (Mon Mar 22 2010 - 08:34:29 PDT)
- Alan (Mon Mar 22 2010 - 08:20:11 PDT)
- mattia (Mon Mar 22 2010 - 08:04:01 PDT)
- Alan (Mon Mar 22 2010 - 07:47:26 PDT)
- Alan (Mon Mar 22 2010 - 07:43:47 PDT)
- case (Mon Mar 22 2010 - 07:41:43 PDT)
- Carlos Simmerling (Mon Mar 22 2010 - 07:24:39 PDT)
- Alan (Mon Mar 22 2010 - 06:59:35 PDT)
- mattia (Mon Mar 22 2010 - 06:08:48 PDT)
- geyan (Mon Mar 22 2010 - 01:12:44 PDT)
[AMBER] ACS Division of Computers in Chemistry: award applications due March 30
- Carlos Simmerling (Wed Mar 17 2010 - 17:20:57 PDT)
- Ross Walker (Wed Mar 17 2010 - 17:09:46 PDT)
- Ross Walker (Wed Mar 17 2010 - 17:03:29 PDT)
- Carlos Simmerling (Wed Mar 17 2010 - 16:16:20 PDT)
[AMBER] addions or solvate-which one first
- Nicee (Sun Mar 14 2010 - 21:00:22 PDT)
- Bill Ross (Sat Mar 13 2010 - 12:25:58 PST)
- Bill Ross (Sat Mar 13 2010 - 12:18:46 PST)
- InSuk Joung (Sat Mar 13 2010 - 08:46:03 PST)
- Nicee (Sat Mar 13 2010 - 02:51:06 PST)
[AMBER] Adenine in water
- Jason Swails (Sat Mar 20 2010 - 23:41:35 PDT)
- ros (Fri Mar 19 2010 - 06:42:23 PDT)
[AMBER] AMBER
- case (Fri Mar 05 2010 - 04:50:47 PST)
- Asfa Ali (Thu Mar 04 2010 - 21:24:15 PST)
- Imtiaz Shafiq (Thu Mar 04 2010 - 02:09:56 PST)
- Asfa Ali (Thu Mar 04 2010 - 01:16:31 PST)
[AMBER] Amber 10 and bugfix.all
- Lars Packschies (Mon Mar 08 2010 - 08:04:11 PST)
- Philipp Marquetand (Mon Mar 08 2010 - 05:23:36 PST)
- Dr. Lars Packschies (Mon Mar 08 2010 - 04:52:50 PST)
[AMBER] AMBER ff99sb
- Carlos Simmerling (Tue Mar 30 2010 - 04:19:40 PDT)
- Mannan (Tue Mar 30 2010 - 03:26:44 PDT)
- Carlos Simmerling (Mon Mar 29 2010 - 04:32:27 PDT)
- gloglo_at_work (Mon Mar 29 2010 - 03:03:33 PDT)
- Mannan (Mon Mar 29 2010 - 02:04:59 PDT)
[AMBER] amber job hangs
- Robert Duke (Fri Mar 26 2010 - 17:53:43 PDT)
- Ed Pate (Fri Mar 26 2010 - 17:29:33 PDT)
[AMBER] AMBER plus GLYCAM
- Lekpa Duukori (Wed Mar 24 2010 - 16:28:35 PDT)
- Ross Walker (Wed Mar 24 2010 - 16:00:55 PDT)
- Lekpa Duukori (Wed Mar 24 2010 - 15:43:32 PDT)
[AMBER] AMBER prmtop and mdcrd files to CHARMM psf and dcd files
- Nancy (Wed Mar 17 2010 - 19:42:52 PDT)
[AMBER] Amber, CASP
- case (Wed Mar 03 2010 - 19:23:26 PST)
- Carlos Simmerling (Wed Mar 03 2010 - 18:52:31 PST)
- Shaandar Nyamtulga (Wed Mar 03 2010 - 18:48:55 PST)
[AMBER] Amber, CASP again
- Imtiaz Shafiq (Thu Mar 04 2010 - 04:36:29 PST)
- Carlos Simmerling (Thu Mar 04 2010 - 04:25:19 PST)
- Shaandar Nyamtulga (Thu Mar 04 2010 - 00:52:20 PST)
[AMBER] AMBER10 installation: make test error 1
- case (Wed Mar 31 2010 - 10:56:33 PDT)
- Anna Dejardin (Wed Mar 31 2010 - 08:09:00 PDT)
- Bill Ross (Fri Mar 05 2010 - 16:17:11 PST)
- Jason Swails (Fri Mar 05 2010 - 16:11:40 PST)
- Anna Dejardin (Fri Mar 05 2010 - 06:30:37 PST)
[AMBER] Amber: heme atom identification
- Bill Ross (Mon Mar 22 2010 - 15:19:14 PDT)
- Jason Swails (Mon Mar 22 2010 - 15:16:01 PDT)
- SimonKao (Mon Mar 22 2010 - 09:05:40 PDT)
[AMBER] Amber:antechamber & heme(metal?) problems
- Shaikh Abdul R S Ramaju (Sun Mar 28 2010 - 23:00:11 PDT)
- case (Sat Mar 27 2010 - 11:49:47 PDT)
- SimonKao (Fri Mar 26 2010 - 13:40:36 PDT)
[AMBER] AmberTools1.3 installation error
- Anna Dejardin (Thu Mar 04 2010 - 02:43:54 PST)
- Bill Ross (Wed Mar 03 2010 - 10:02:21 PST)
- case (Wed Mar 03 2010 - 06:57:08 PST)
- Anna Dejardin (Wed Mar 03 2010 - 06:20:09 PST)
- case (Wed Mar 03 2010 - 05:21:05 PST)
- Anna Dejardin (Wed Mar 03 2010 - 03:47:28 PST)
[AMBER] angular velocity trajectory
- Madhurima Jana (Mon Mar 29 2010 - 21:48:37 PDT)
[AMBER] antechamber changing atom name case, is it right?
- Alan (Thu Mar 18 2010 - 10:03:36 PDT)
[AMBER] antechamber problems
- Steve Seibold (Thu Mar 25 2010 - 11:15:34 PDT)
[AMBER] Antechamber problems.
- Bill Ross (Thu Mar 25 2010 - 11:05:36 PDT)
- case (Thu Mar 25 2010 - 10:52:31 PDT)
- Steve Seibold (Thu Mar 25 2010 - 10:44:18 PDT)
[AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type.
- Dean Cuebas (Fri Mar 12 2010 - 14:44:17 PST)
- Jason Swails (Fri Mar 12 2010 - 13:16:56 PST)
- Bill Ross (Fri Mar 12 2010 - 12:57:40 PST)
- Denny Bromley (Fri Mar 12 2010 - 12:40:12 PST)
- Dean Cuebas (Fri Mar 12 2010 - 10:07:21 PST)
- Denny Bromley (Fri Mar 12 2010 - 09:50:27 PST)
- Dean Cuebas (Fri Mar 12 2010 - 09:39:54 PST)
- case (Fri Mar 12 2010 - 04:47:28 PST)
- Denny Bromley (Thu Mar 11 2010 - 20:33:05 PST)
[AMBER] atom-type cz ???
- case (Wed Mar 03 2010 - 18:56:47 PST)
- Barbault Florent (Wed Mar 03 2010 - 07:59:58 PST)
- case (Wed Mar 03 2010 - 07:26:18 PST)
- Barbault Florent (Wed Mar 03 2010 - 05:30:59 PST)
[AMBER] ATP charge convergence
- Eric Pettersen (Fri Mar 19 2010 - 09:50:20 PDT)
- Alan (Fri Mar 19 2010 - 09:34:22 PDT)
- Eric Pettersen (Thu Mar 18 2010 - 17:17:58 PDT)
- Eric Pettersen (Thu Mar 18 2010 - 17:11:18 PDT)
- Eric Pettersen (Thu Mar 18 2010 - 17:07:10 PDT)
[AMBER] ATP force field
- aneesh cna (Tue Mar 09 2010 - 01:11:36 PST)
- deepti nayar (Mon Mar 08 2010 - 23:14:53 PST)
[AMBER] Average structure
- Bill Ross (Fri Mar 26 2010 - 09:58:02 PDT)
- Billy Miller III (Fri Mar 26 2010 - 05:44:29 PDT)
- waleed zalloum (Fri Mar 26 2010 - 04:55:17 PDT)
[AMBER] Bad atom type Br
- pandb09.lzu.cn (Thu Mar 25 2010 - 02:05:04 PDT)
[AMBER] Binding cooprativety and binding order of ligands
- Sushil Mishra (Thu Mar 25 2010 - 10:53:41 PDT)
[AMBER] Binding Energy Calculation by QM/MM method
- Kshatresh Dutta Dubey (Sun Mar 14 2010 - 11:52:49 PDT)
- Ross Walker (Sun Mar 14 2010 - 11:13:40 PDT)
- Billy Miller III (Sun Mar 14 2010 - 07:40:19 PDT)
- Kshatresh Dutta Dubey (Sat Mar 13 2010 - 21:45:17 PST)
- Kshatresh Dutta Dubey (Fri Mar 12 2010 - 21:31:27 PST)
[AMBER] box of spc water
- Ganesh Kamath (Fri Mar 12 2010 - 09:19:08 PST)
[AMBER] Calculating Amber Force fields from Wikipedia
- Carlos Simmerling (Tue Mar 16 2010 - 18:12:07 PDT)
- whimsica.aol.com (Tue Mar 16 2010 - 17:43:41 PDT)
- Kevin Hauser (Tue Mar 16 2010 - 17:41:08 PDT)
- whimsica.aol.com (Tue Mar 16 2010 - 17:32:02 PDT)
- Carlos Simmerling (Tue Mar 16 2010 - 16:09:24 PDT)
- M. L. Dodson (Tue Mar 16 2010 - 14:58:00 PDT)
- Whimsica.aol.com (Tue Mar 16 2010 - 14:30:34 PDT)
- M. L. Dodson (Mon Mar 15 2010 - 20:45:26 PDT)
- whimsica.aol.com (Mon Mar 15 2010 - 19:42:50 PDT)
- Ross Walker (Mon Mar 15 2010 - 19:16:29 PDT)
- Carlos Simmerling (Mon Mar 15 2010 - 08:38:05 PDT)
- Whimsica.aol.com (Mon Mar 15 2010 - 08:32:57 PDT)
- Carlos Simmerling (Mon Mar 15 2010 - 07:47:36 PDT)
- whimsica.aol.com (Mon Mar 15 2010 - 06:46:22 PDT)
[AMBER] Can anyone tell me what the parm99.dat values correspond to?
- M. L. Dodson (Mon Mar 15 2010 - 20:20:31 PDT)
- whimsica.aol.com (Mon Mar 15 2010 - 18:52:39 PDT)
- Bill Ross (Mon Mar 15 2010 - 18:45:12 PDT)
- Bill Ross (Mon Mar 15 2010 - 18:37:43 PDT)
- M. L. Dodson (Mon Mar 15 2010 - 18:31:31 PDT)
- Carlos Simmerling (Mon Mar 15 2010 - 18:04:59 PDT)
- whimsica.aol.com (Mon Mar 15 2010 - 17:32:03 PDT)
- Carlos Simmerling (Mon Mar 15 2010 - 17:21:38 PDT)
- Bill Ross (Mon Mar 15 2010 - 17:13:35 PDT)
- whimsica.aol.com (Mon Mar 15 2010 - 17:10:26 PDT)
- Bill Ross (Mon Mar 15 2010 - 17:05:50 PDT)
- whimsica.aol.com (Mon Mar 15 2010 - 17:00:34 PDT)
- M. L. Dodson (Mon Mar 15 2010 - 14:24:38 PDT)
- Bill Ross (Mon Mar 15 2010 - 14:11:34 PDT)
- whimsica.aol.com (Mon Mar 15 2010 - 13:58:28 PDT)
[AMBER] Can you give me some suggestion on how to use NetCDF to obtain a binary formate trajectory with AMBER
- Jason Swails (Tue Mar 16 2010 - 19:05:21 PDT)
- Nancy (Tue Mar 16 2010 - 18:51:25 PDT)
[AMBER] can't get the final "snapshot_statistics.out" file
- Billy Miller III (Mon Mar 15 2010 - 05:42:11 PDT)
- Rama krishnan (Mon Mar 15 2010 - 05:23:54 PDT)
- Alexander Metz (Mon Mar 15 2010 - 04:52:50 PDT)
- geyan (Mon Mar 15 2010 - 01:35:50 PDT)
- Billy Miller III (Sun Mar 14 2010 - 07:21:40 PDT)
- geyan (Sat Mar 13 2010 - 19:25:52 PST)
[AMBER] CASP
- Shaandar Nyamtulga (Sun Mar 28 2010 - 23:47:50 PDT)
[AMBER] chamber error message
- Mark Williamson (Tue Mar 09 2010 - 13:10:09 PST)
- Hannes Loeffler (Tue Mar 09 2010 - 05:46:00 PST)
[AMBER] Charge protocol for OLP, HYP
- Emmanuel Baribefe Naziga (Mon Mar 15 2010 - 08:53:20 PDT)
- Lachele Foley (Lists) (Mon Mar 15 2010 - 08:39:31 PDT)
[AMBER] Check overlap
- John S (Thu Mar 18 2010 - 18:41:09 PDT)
[AMBER] CIS proline
- Carlos Simmerling (Tue Mar 09 2010 - 04:46:35 PST)
- Francesca Cantini (Tue Mar 09 2010 - 04:31:08 PST)
[AMBER] CITATION PROBLEM ABOUT i-APBS
- Robert Konecny (Tue Mar 02 2010 - 11:08:29 PST)
- Rilei Yu (Tue Mar 02 2010 - 04:12:55 PST)
[AMBER] combining coordinate and velocity files into one
- Bill Ross (Tue Mar 09 2010 - 15:39:37 PST)
- Jason Swails (Tue Mar 09 2010 - 15:15:31 PST)
- Amire-Brahimi Benjamin (Tue Mar 09 2010 - 15:02:06 PST)
- Jason Swails (Sun Mar 07 2010 - 14:48:23 PST)
- Amire-Brahimi Benjamin (Sun Mar 07 2010 - 13:42:57 PST)
[AMBER] Confirm compiling Amber10/Tools1.3 breaks with intel v 11.1?
- case (Wed Mar 17 2010 - 09:01:13 PDT)
- Trevor Gokey (Tue Mar 16 2010 - 23:04:58 PDT)
- Ross Walker (Tue Mar 16 2010 - 22:48:30 PDT)
- Trevor Gokey (Tue Mar 16 2010 - 21:34:26 PDT)
[AMBER] COOH group:extra undesired bond
- Jio M (Wed Mar 31 2010 - 09:41:06 PDT)
[AMBER] CPU Load for Amber Running In Parallel
- Ross Walker (Fri Mar 05 2010 - 20:47:27 PST)
- Imtiaz Shafiq (Fri Mar 05 2010 - 19:37:27 PST)
[AMBER] crdgrow
- case (Thu Mar 25 2010 - 10:48:08 PDT)
- Steve Seibold (Wed Mar 24 2010 - 09:15:58 PDT)
[AMBER] crdgrow AMBER 8
- Bill Ross (Wed Mar 24 2010 - 13:01:45 PDT)
- Steve Seibold (Wed Mar 24 2010 - 12:45:57 PDT)
[AMBER] Cyclic compounds
- Jason Swails (Tue Mar 02 2010 - 10:50:53 PST)
- Bill Ross (Tue Mar 02 2010 - 10:46:32 PST)
- John S (Tue Mar 02 2010 - 10:39:50 PST)
- Jason Swails (Mon Mar 01 2010 - 21:24:08 PST)
- John S (Mon Mar 01 2010 - 20:50:35 PST)
[AMBER] DEBIAN: cannot get rid of xleap
- case (Wed Mar 31 2010 - 11:09:00 PDT)
- Amedeo Capobianco (Wed Mar 31 2010 - 10:31:54 PDT)
[AMBER] DEBIAN: cannot get rid of xleap SOLVED
- Amedeo Capobianco (Wed Mar 31 2010 - 12:01:35 PDT)
[AMBER] difference in output from bnda and fd_helix functions
- Igor Sizov (Thu Mar 25 2010 - 12:07:07 PDT)
- case (Thu Mar 25 2010 - 10:26:18 PDT)
- Igor Sizov (Wed Mar 24 2010 - 11:19:08 PDT)
[AMBER] Difference of ff99 and ff03 in building DNA duplex
- Kevin Hauser (Thu Mar 11 2010 - 21:05:42 PST)
- Ilyas Yildirim (Thu Mar 11 2010 - 21:03:32 PST)
- Ross Walker (Thu Mar 11 2010 - 20:49:40 PST)
- Jason Swails (Thu Mar 11 2010 - 20:49:16 PST)
- Asfa Ali (Thu Mar 11 2010 - 20:40:37 PST)
- Thomas Cheatham (Thu Mar 11 2010 - 19:21:51 PST)
- case (Thu Mar 11 2010 - 19:21:12 PST)
- Qinqin Ji (Thu Mar 11 2010 - 19:08:14 PST)
[AMBER] Distance between two atoms vs time
- Bill Ross (Mon Mar 22 2010 - 10:03:15 PDT)
- Billy Miller III (Mon Mar 22 2010 - 05:57:13 PDT)
- imtiaz shafiq (Mon Mar 22 2010 - 05:24:26 PDT)
[AMBER] Distortions
- Carlos Simmerling (Tue Mar 09 2010 - 06:01:14 PST)
- Asfa Ali (Tue Mar 09 2010 - 05:03:08 PST)
- Asfa Ali (Mon Mar 08 2010 - 01:22:26 PST)
[AMBER] disulfide bonds?
- case (Wed Mar 31 2010 - 06:46:07 PDT)
- Carlos Simmerling (Wed Mar 31 2010 - 06:44:01 PDT)
- xuemeiwang1103 (Wed Mar 31 2010 - 06:32:02 PDT)
[AMBER] DUMPAVE
- lee lior (Wed Mar 24 2010 - 13:58:32 PDT)
[AMBER] electric fields
- Ganesh Kamath (Thu Mar 04 2010 - 14:44:04 PST)
[AMBER] Energy and Density Unites
- Christine Baranski (Fri Mar 19 2010 - 06:17:57 PDT)
[AMBER] energy calculation
- Dwight McGee (Fri Mar 12 2010 - 13:33:04 PST)
- Jason Swails (Fri Mar 12 2010 - 09:25:21 PST)
- Jason Swails (Tue Mar 09 2010 - 11:01:55 PST)
- rui (Tue Mar 09 2010 - 10:37:22 PST)
[AMBER] Energy units in mm-pbsa calculations
- moitrayee.mbu.iisc.ernet.in (Tue Mar 30 2010 - 03:34:05 PDT)
- moitrayee.mbu.iisc.ernet.in (Sat Mar 27 2010 - 10:21:39 PDT)
- Billy Miller III (Sat Mar 27 2010 - 07:00:03 PDT)
- moitrayee.mbu.iisc.ernet.in (Fri Mar 26 2010 - 23:59:40 PDT)
- moitrayee.mbu.iisc.ernet.in (Fri Mar 26 2010 - 07:41:37 PDT)
- Billy Miller III (Fri Mar 26 2010 - 06:32:22 PDT)
- moitrayee.mbu.iisc.ernet.in (Fri Mar 26 2010 - 05:34:41 PDT)
- Billy Miller III (Thu Mar 25 2010 - 19:31:34 PDT)
- moitrayee.mbu.iisc.ernet.in (Thu Mar 25 2010 - 09:42:10 PDT)
- Billy Miller III (Thu Mar 25 2010 - 06:51:13 PDT)
- moitrayee.mbu.iisc.ernet.in (Thu Mar 25 2010 - 03:44:59 PDT)
- Ray Luo (Wed Mar 24 2010 - 10:48:28 PDT)
- Billy Miller III (Tue Mar 23 2010 - 06:40:07 PDT)
- moitrayee.mbu.iisc.ernet.in (Tue Mar 23 2010 - 05:57:30 PDT)
[AMBER] Enquiry regarding MD run
- Bill Ross (Mon Mar 15 2010 - 11:45:51 PDT)
- Pallavi Mohanty (Mon Mar 15 2010 - 10:59:17 PDT)
- Bill Ross (Mon Mar 15 2010 - 10:51:49 PDT)
- Sushil Mishra (Mon Mar 15 2010 - 02:00:19 PDT)
- Pallavi Mohanty (Mon Mar 15 2010 - 01:07:16 PDT)
- Sushil Mishra (Mon Mar 15 2010 - 00:44:22 PDT)
- Pallavi Mohanty (Mon Mar 15 2010 - 00:29:58 PDT)
- Carlos Simmerling (Wed Mar 10 2010 - 06:06:30 PST)
- Pallavi Mohanty (Wed Mar 10 2010 - 06:02:21 PST)
- Carlos Simmerling (Wed Mar 10 2010 - 03:36:07 PST)
- Pallavi Mohanty (Wed Mar 10 2010 - 02:11:51 PST)
- Carlos Simmerling (Tue Mar 09 2010 - 03:31:00 PST)
- Pallavi Mohanty (Mon Mar 08 2010 - 20:42:32 PST)
- Bill Ross (Wed Mar 03 2010 - 09:47:21 PST)
- Jason Swails (Tue Mar 02 2010 - 22:04:23 PST)
- bharat lakhani (Tue Mar 02 2010 - 21:42:10 PST)
[AMBER] Enquiry regarding Minimisation
- Carlos Simmerling (Sat Mar 13 2010 - 03:48:10 PST)
- Pallavi Mohanty (Sat Mar 13 2010 - 02:50:22 PST)
[AMBER] error - during minimization in AMBER10
- Jason Swails (Fri Mar 05 2010 - 20:45:12 PST)
- Jason Swails (Fri Mar 05 2010 - 20:39:21 PST)
- Imtiaz Shafiq (Fri Mar 05 2010 - 20:06:13 PST)
- kureeckal ramesh (Fri Mar 05 2010 - 19:54:13 PST)
[AMBER] Error decoding variable
- case (Thu Mar 11 2010 - 07:56:53 PST)
- Fernando Martín García (Mon Mar 08 2010 - 03:34:55 PST)
[AMBER] Error during MMPBSA calc.
- Jagan Mohan (Sat Mar 20 2010 - 01:59:12 PDT)
- David Watson (Fri Mar 19 2010 - 09:16:42 PDT)
- Jagan Mohan (Fri Mar 19 2010 - 08:55:27 PDT)
- Billy Miller III (Fri Mar 19 2010 - 07:15:39 PDT)
- Jagan Mohan (Fri Mar 19 2010 - 07:02:13 PDT)
[AMBER] Error in MMPBSA
- pandb09.lzu.cn (Sun Mar 28 2010 - 17:14:44 PDT)
[AMBER] error in parallel md run
- Nicee (Fri Mar 26 2010 - 01:17:13 PDT)
- Jason Swails (Thu Mar 25 2010 - 22:54:26 PDT)
- Nicee (Thu Mar 25 2010 - 22:43:22 PDT)
[AMBER] error in save prmtop
- Bill Ross (Tue Mar 23 2010 - 10:37:37 PDT)
- geyan (Tue Mar 23 2010 - 07:44:12 PDT)
- Carlos Simmerling (Tue Mar 23 2010 - 07:32:51 PDT)
- geyan (Tue Mar 23 2010 - 07:30:07 PDT)
- Carlos Simmerling (Tue Mar 23 2010 - 07:08:10 PDT)
- geyan (Tue Mar 23 2010 - 07:04:34 PDT)
[AMBER] error when doing MMPBSA
- pxq (Tue Mar 23 2010 - 17:43:18 PDT)
- Ray Luo, Ph.D. (Mon Mar 22 2010 - 21:43:10 PDT)
- pxq (Mon Mar 22 2010 - 17:32:42 PDT)
- Ray Luo (Mon Mar 22 2010 - 09:54:40 PDT)
- pxq (Mon Mar 22 2010 - 01:51:44 PDT)
- Ray Luo (Sun Mar 21 2010 - 12:06:29 PDT)
- pxq (Sun Mar 21 2010 - 07:52:29 PDT)
- Jason Swails (Sun Mar 21 2010 - 07:43:45 PDT)
- pxq (Sun Mar 21 2010 - 00:27:59 PDT)
[AMBER] ERROR: PGFIO-F-239/namelist read/unit=5/entity name is not member of group.
- case (Wed Mar 10 2010 - 07:35:01 PST)
- lee lior (Tue Mar 09 2010 - 13:41:51 PST)
[AMBER] Errors while running Amber
- Ross Walker (Fri Mar 05 2010 - 08:51:32 PST)
- Nkwe Monama (Fri Mar 05 2010 - 06:46:59 PST)
- Robert Duke (Fri Mar 05 2010 - 05:37:00 PST)
- Nkwe Monama (Fri Mar 05 2010 - 01:17:03 PST)
- Carlos Simmerling (Thu Mar 04 2010 - 05:24:59 PST)
- Nkwe Monama (Thu Mar 04 2010 - 05:17:50 PST)
- Carlos Simmerling (Thu Mar 04 2010 - 05:00:50 PST)
- Nkwe Monama (Thu Mar 04 2010 - 04:56:52 PST)
- Carlos Simmerling (Thu Mar 04 2010 - 04:22:59 PST)
- Nkwe Monama (Thu Mar 04 2010 - 03:05:10 PST)
[AMBER] Extract coordinate residues form mdcrd
- Carlos Simmerling (Wed Mar 10 2010 - 06:40:17 PST)
- Silvia Carlotto (Wed Mar 10 2010 - 06:38:47 PST)
[AMBER] Extract potential energy from ptraj?
- Adrian Roitberg (Tue Mar 09 2010 - 20:18:04 PST)
- Lili Peng (Tue Mar 09 2010 - 20:05:56 PST)
[AMBER] force field parameters for isopropanol
- Karl Kirschner (Thu Mar 04 2010 - 00:36:16 PST)
- Ganesh Kamath (Wed Mar 03 2010 - 07:27:13 PST)
[AMBER] force field with neutral terminal
- Ramya Narasimhan (Thu Mar 18 2010 - 23:24:34 PDT)
- Ramya Narasimhan (Thu Mar 18 2010 - 22:07:34 PDT)
- Carlos Simmerling (Wed Mar 17 2010 - 08:20:56 PDT)
- Jason Swails (Wed Mar 17 2010 - 08:16:40 PDT)
- Ramya Narasimhan (Tue Mar 16 2010 - 23:59:04 PDT)
- Carlos Simmerling (Tue Mar 16 2010 - 03:36:36 PDT)
- Ramya Narasimhan (Tue Mar 16 2010 - 00:56:21 PDT)
[AMBER] Fortran run time error
- Asfa Ali (Tue Mar 09 2010 - 20:25:29 PST)
- Jason Swails (Tue Mar 09 2010 - 06:50:01 PST)
- Tom Joseph (Tue Mar 09 2010 - 06:49:22 PST)
- Asfa Ali (Tue Mar 09 2010 - 06:30:54 PST)
[AMBER] free energy contribution of water
- Hyma vathi (Wed Mar 31 2010 - 04:30:57 PDT)
[AMBER] Fwd: understanding AMBER FORCES parm files?
- case (Sat Mar 13 2010 - 10:59:50 PST)
- whimsica.aol.com (Sat Mar 13 2010 - 10:18:37 PST)
[AMBER] Fwd: Xleap : Improper torsions applied
- Sushil Mishra (Mon Mar 08 2010 - 08:32:44 PST)
[AMBER] G03: ONIOM
- Jason Swails (Fri Mar 12 2010 - 07:33:22 PST)
- Arash Farahmand (Fri Mar 12 2010 - 06:59:33 PST)
[AMBER] general query:RMSD
- Jio M (Sat Mar 27 2010 - 03:38:03 PDT)
- Jio M (Sun Mar 21 2010 - 02:01:04 PDT)
- Carlos Simmerling (Sat Mar 20 2010 - 09:41:57 PDT)
- Jio M (Fri Mar 19 2010 - 13:21:57 PDT)
[AMBER] Generating cpin file for constant pH in Amber9
- Jamie Romnes (Wed Mar 03 2010 - 12:39:05 PST)
- Jason Swails (Wed Mar 03 2010 - 11:52:18 PST)
- Bill Ross (Wed Mar 03 2010 - 11:47:12 PST)
- Jamie Romnes (Wed Mar 03 2010 - 11:41:09 PST)
- Jason Swails (Wed Mar 03 2010 - 11:30:36 PST)
- Jamie Romnes (Wed Mar 03 2010 - 11:11:41 PST)
[AMBER] help for restraint minimization
- Carlos Simmerling (Wed Mar 24 2010 - 06:18:52 PDT)
- jacky zhao (Wed Mar 24 2010 - 02:23:38 PDT)
[AMBER] how to achieve the 2D periodic boundary
- kecy_w.sina.com (Tue Mar 23 2010 - 18:45:24 PDT)
[AMBER] How to apply extra dihedrals
- Jason Swails (Tue Mar 16 2010 - 21:22:06 PDT)
- Lekpa Duukori (Tue Mar 16 2010 - 21:19:52 PDT)
- Bill Ross (Tue Mar 16 2010 - 20:57:03 PDT)
- Jason Swails (Tue Mar 16 2010 - 20:29:20 PDT)
- InSuk Joung (Tue Mar 16 2010 - 18:03:06 PDT)
- Lekpa Duukori (Tue Mar 16 2010 - 08:19:18 PDT)
[AMBER] how to convert to standard Amber PDB input
- case (Tue Mar 30 2010 - 05:24:14 PDT)
- geyan (Mon Mar 29 2010 - 20:26:17 PDT)
[AMBER] how to deal with the system with negative charge ?
- Bill Ross (Tue Mar 30 2010 - 10:19:37 PDT)
- case (Tue Mar 30 2010 - 05:33:20 PDT)
- sculiujl (Tue Mar 30 2010 - 04:10:13 PDT)
- Dmitry Mukha (Tue Mar 30 2010 - 01:47:57 PDT)
- sculiujl (Tue Mar 30 2010 - 01:20:18 PDT)
[AMBER] how to do analysis of the local structure
- Carlos Simmerling (Thu Mar 11 2010 - 03:31:38 PST)
- Nancy (Wed Mar 10 2010 - 23:13:30 PST)
- Dwight McGee (Wed Mar 10 2010 - 22:45:37 PST)
- Nancy (Wed Mar 10 2010 - 21:17:29 PST)
[AMBER] How to find conserved coordinated waters?
- Thomas Cheatham III (Mon Mar 29 2010 - 14:57:48 PDT)
- Sasha Buzko (Mon Mar 29 2010 - 14:51:30 PDT)
[AMBER] how to get the hydrophobic area for a particlar region
- Balazs Jojart (Sat Mar 27 2010 - 05:28:13 PDT)
- Billy Miller III (Fri Mar 26 2010 - 19:44:40 PDT)
- Jason Swails (Fri Mar 26 2010 - 19:42:04 PDT)
- qiaoyan (Fri Mar 26 2010 - 19:26:02 PDT)
- Ray Luo (Thu Mar 25 2010 - 11:36:39 PDT)
- Balazs Jojart (Thu Mar 25 2010 - 11:14:33 PDT)
- Ray Luo (Thu Mar 25 2010 - 09:49:27 PDT)
- qiaoyan (Wed Mar 24 2010 - 19:59:14 PDT)
[AMBER] How to obtain an ideal helix structure of Alanine 5 peptide (ACE-Ala5-NME) ?
- Carlos Simmerling (Fri Mar 19 2010 - 10:24:14 PDT)
- Dongshan Wei (Fri Mar 19 2010 - 09:39:33 PDT)
- M. L. Dodson (Thu Mar 18 2010 - 17:49:14 PDT)
- Adrian Roitberg (Thu Mar 18 2010 - 14:36:06 PDT)
- Dongshan Wei (Thu Mar 18 2010 - 14:28:54 PDT)
[AMBER] IMPROPER TERM CONTRIBUTION
- Alan (Thu Mar 18 2010 - 08:47:57 PDT)
- case (Thu Mar 18 2010 - 08:12:07 PDT)
- Alan (Thu Mar 18 2010 - 08:04:15 PDT)
- Bill Ross (Wed Mar 17 2010 - 09:45:48 PDT)
- Carlos Simmerling (Wed Mar 17 2010 - 05:26:43 PDT)
- Alan (Wed Mar 17 2010 - 05:17:16 PDT)
- case (Wed Mar 17 2010 - 04:49:19 PDT)
- Peter Charles Kahuna (Wed Mar 17 2010 - 02:43:30 PDT)
[AMBER] Installation error of amber10 after compile Ambertools1.3
- albert albert (Mon Mar 01 2010 - 03:43:31 PST)
[AMBER] Installing AmberTools
- Thomas Stockner (Sun Mar 28 2010 - 11:00:57 PDT)
- Jason Swails (Sun Mar 28 2010 - 08:43:01 PDT)
- Thomas Stockner (Sun Mar 28 2010 - 06:39:38 PDT)
[AMBER] is iwrap=1 a key parameter?
- Nancy (Mon Mar 29 2010 - 22:11:17 PDT)
- case (Mon Mar 29 2010 - 07:19:26 PDT)
- Ben Roberts (Mon Mar 29 2010 - 06:40:06 PDT)
- Nancy (Mon Mar 29 2010 - 05:49:24 PDT)
[AMBER] issues with pmemd
- Bill Ross (Tue Mar 30 2010 - 14:10:16 PDT)
- Ross Walker (Tue Mar 30 2010 - 14:05:04 PDT)
- Ganesh Kamath (Tue Mar 30 2010 - 12:14:54 PDT)
- case (Tue Mar 30 2010 - 11:23:19 PDT)
- Robert Duke (Tue Mar 30 2010 - 11:18:43 PDT)
- Ganesh Kamath (Tue Mar 30 2010 - 10:57:48 PDT)
[AMBER] Large FIle
- Jason Swails (Wed Mar 17 2010 - 12:49:53 PDT)
- Bill Ross (Wed Mar 17 2010 - 10:09:24 PDT)
- Gannett, Peter (Wed Mar 17 2010 - 09:27:40 PDT)
- Jason Swails (Wed Mar 17 2010 - 09:12:38 PDT)
- Jason Swails (Wed Mar 17 2010 - 09:08:19 PDT)
- Beale, John (Wed Mar 17 2010 - 08:54:14 PDT)
[AMBER] Lennard Jones potential
- Antonios Samiotakis (Thu Mar 18 2010 - 16:50:51 PDT)
[AMBER] ligand parameterization
- Dean Cuebas (Wed Mar 24 2010 - 11:33:45 PDT)
- Dean Cuebas (Wed Mar 24 2010 - 10:46:41 PDT)
- gurunath katagi (Tue Mar 23 2010 - 23:05:24 PDT)
[AMBER] ligand-protein complex parametrization problems
- case (Fri Mar 12 2010 - 05:08:57 PST)
- Andrew Voronkov (Fri Mar 12 2010 - 04:17:16 PST)
- Billy Miller III (Thu Mar 11 2010 - 07:50:26 PST)
- Andrew Voronkov (Thu Mar 11 2010 - 07:39:52 PST)
[AMBER] Lone Pair
- Carlos Simmerling (Thu Mar 25 2010 - 10:29:21 PDT)
- s. Bill (Thu Mar 25 2010 - 06:29:39 PDT)
[AMBER] Mask selection
- John S (Fri Mar 12 2010 - 14:44:10 PST)
- Thomas Cheatham III (Fri Mar 12 2010 - 14:23:30 PST)
- John S (Fri Mar 12 2010 - 14:21:12 PST)
[AMBER] mbonbi and mbondi2
- Carlos Simmerling (Sun Mar 21 2010 - 14:01:54 PDT)
- Kevin Hauser (Sun Mar 21 2010 - 13:29:44 PDT)
- s. Bill (Sun Mar 21 2010 - 12:55:58 PDT)
[AMBER] MD simulation in gas phase-AMBER 10
- Carlos Simmerling (Fri Mar 26 2010 - 08:40:01 PDT)
- Dian Jiao (Thu Mar 25 2010 - 11:02:15 PDT)
- case (Thu Mar 25 2010 - 10:50:10 PDT)
- Dian Jiao (Thu Mar 25 2010 - 10:45:59 PDT)
- case (Thu Mar 25 2010 - 10:41:14 PDT)
- Carlos Simmerling (Thu Mar 25 2010 - 10:34:55 PDT)
- Dian Jiao (Thu Mar 25 2010 - 10:30:45 PDT)
[AMBER] mdinfor error
- Bill Ross (Thu Mar 11 2010 - 10:04:20 PST)
- Bill Ross (Thu Mar 11 2010 - 10:03:22 PST)
- Chinh Su Tran To (Thu Mar 11 2010 - 03:43:08 PST)
- Carlos Simmerling (Thu Mar 11 2010 - 03:37:35 PST)
- Chinh Su Tran To (Thu Mar 11 2010 - 03:31:23 PST)
- Carlos Simmerling (Thu Mar 11 2010 - 03:27:51 PST)
- Chinh Su Tran To (Thu Mar 11 2010 - 02:34:23 PST)
[AMBER] membranes
- Balazs Jojart (Wed Mar 31 2010 - 09:00:26 PDT)
- Hannes Loeffler (Wed Mar 31 2010 - 09:00:11 PDT)
- Vlad Cojocaru (Wed Mar 31 2010 - 08:44:26 PDT)
- Gould, Ian R (Wed Mar 31 2010 - 08:32:49 PDT)
- Adrian Roitberg (Wed Mar 31 2010 - 08:24:37 PDT)
- Matthew Tessier (Wed Mar 31 2010 - 08:22:58 PDT)
- Balazs Jojart (Wed Mar 31 2010 - 07:56:24 PDT)
- Adrian Roitberg (Wed Mar 31 2010 - 07:29:17 PDT)
[AMBER] Minimization Failure
- Taufik Al-Sarraj (Wed Mar 24 2010 - 12:39:21 PDT)
- Taufik Al-Sarraj (Tue Mar 16 2010 - 11:37:28 PDT)
- Bill Ross (Tue Mar 16 2010 - 11:36:17 PDT)
- Taufik Al-Sarraj (Tue Mar 16 2010 - 11:26:42 PDT)
- case (Tue Mar 16 2010 - 11:24:44 PDT)
- Bill Ross (Tue Mar 16 2010 - 11:18:29 PDT)
- Taufik Al-Sarraj (Tue Mar 16 2010 - 11:04:53 PDT)
[AMBER] minimization really make protein better?
- Carlos Simmerling (Tue Mar 30 2010 - 04:22:48 PDT)
- Dmitri Nilov (Tue Mar 30 2010 - 00:03:10 PDT)
- geyan (Mon Mar 29 2010 - 20:15:55 PDT)
- Carlos Simmerling (Mon Mar 29 2010 - 04:35:28 PDT)
- geyan (Sun Mar 28 2010 - 21:48:21 PDT)
[AMBER] minimization residues around the ligand
- Rilei Yu (Mon Mar 08 2010 - 17:56:21 PST)
[AMBER] Missing values for MM BGAS:error in mm-pbsa
- moitrayee.mbu.iisc.ernet.in (Thu Mar 25 2010 - 00:05:34 PDT)
- lidansa.mail.ustc.edu.cn (Wed Mar 24 2010 - 18:07:29 PDT)
- moitrayee.mbu.iisc.ernet.in (Wed Mar 24 2010 - 11:53:26 PDT)
[AMBER] MM-PBSA not generating snapshot_lig.all.out and snapshot_statistics.out files
- Billy Miller III (Sat Mar 27 2010 - 12:05:19 PDT)
- mish (Sat Mar 27 2010 - 11:25:49 PDT)
[AMBER] MMPBSA calculation
- Ray Luo (Thu Mar 18 2010 - 10:09:06 PDT)
- Billy Miller III (Thu Mar 18 2010 - 07:45:45 PDT)
- Jeffrey (Thu Mar 18 2010 - 05:23:36 PDT)
[AMBER] mmpbsa doesn't work
- Billy Miller III (Tue Mar 23 2010 - 06:22:55 PDT)
- qiaoyan (Mon Mar 22 2010 - 20:38:48 PDT)
[AMBER] MMPBSA err!
- Dwight McGee (Mon Mar 08 2010 - 10:29:19 PST)
- Aurum Bai (Mon Mar 08 2010 - 06:30:06 PST)
[AMBER] MMPBSA error
- Shulin Zhuang (Fri Mar 26 2010 - 14:32:08 PDT)
- Dwight McGee (Fri Mar 26 2010 - 06:45:57 PDT)
- Soumya Lipsa Rath (Fri Mar 26 2010 - 01:50:35 PDT)
- Soumya Lipsa Rath (Fri Mar 26 2010 - 01:48:35 PDT)
- Shulin Zhuang (Thu Mar 25 2010 - 23:22:02 PDT)
- Soumya Lipsa Rath (Thu Mar 25 2010 - 20:43:08 PDT)
- Dwight McGee (Thu Mar 25 2010 - 07:08:13 PDT)
- Jason Swails (Wed Mar 24 2010 - 22:41:06 PDT)
- Shulin Zhuang (Wed Mar 24 2010 - 21:57:32 PDT)
- Jason Swails (Wed Mar 24 2010 - 21:47:48 PDT)
- Soumya Lipsa Rath (Wed Mar 24 2010 - 19:52:46 PDT)
- Jason Swails (Tue Mar 23 2010 - 23:21:40 PDT)
- Soumya Lipsa Rath (Tue Mar 23 2010 - 21:51:30 PDT)
- Dwight McGee (Tue Mar 23 2010 - 07:32:47 PDT)
- Soumya Lipsa Rath (Tue Mar 23 2010 - 01:21:41 PDT)
[AMBER] MMPBSA in case of highly water accessible molecules ?
- Marek Maly (Tue Mar 09 2010 - 13:43:11 PST)
[AMBER] MMPBSA problems with Fe and Zn
- Cristina Sisu (Mon Mar 01 2010 - 09:20:28 PST)
- Billy Miller III (Mon Mar 01 2010 - 09:18:32 PST)
- Billy Miller III (Mon Mar 01 2010 - 09:11:01 PST)
- Cristina Sisu (Mon Mar 01 2010 - 09:05:23 PST)
- Billy Miller III (Mon Mar 01 2010 - 08:21:30 PST)
- Dwight McGee (Mon Mar 01 2010 - 08:14:43 PST)
- Cristina Sisu (Mon Mar 01 2010 - 08:04:05 PST)
- Jason Swails (Mon Mar 01 2010 - 06:07:53 PST)
- mattia (Mon Mar 01 2010 - 04:00:56 PST)
- Cristina Sisu (Mon Mar 01 2010 - 03:53:11 PST)
[AMBER] MMPBSA.py problem
- Billy Miller III (Mon Mar 15 2010 - 05:53:57 PDT)
- s. Bill (Mon Mar 15 2010 - 02:00:23 PDT)
- Jason Swails (Sun Mar 14 2010 - 09:47:40 PDT)
- Billy Miller III (Sun Mar 14 2010 - 07:18:20 PDT)
- s. Bill (Sun Mar 14 2010 - 03:56:25 PDT)
[AMBER] NAMD-parameter set up
- Rilei Yu (Fri Mar 26 2010 - 04:22:37 PDT)
[AMBER] neb/amber 10
- Carlos Simmerling (Fri Mar 26 2010 - 08:13:14 PDT)
- Carlos Simmerling (Sat Mar 13 2010 - 05:21:55 PST)
- Carlos Simmerling (Wed Mar 03 2010 - 12:57:13 PST)
- Guillermina Estiu (Wed Mar 03 2010 - 11:12:05 PST)
[AMBER] Neutral aminogroup of N-terminal residue: N3 atom type choice
- Dean Cuebas (Wed Mar 31 2010 - 13:57:42 PDT)
- Dmitri Nilov (Wed Mar 31 2010 - 07:12:14 PDT)
- M. L. Dodson (Wed Mar 31 2010 - 06:41:30 PDT)
- Dmitri Nilov (Wed Mar 31 2010 - 03:31:44 PDT)
[AMBER] NOT IN RESIDUE TEMPLATES
- Jason Swails (Thu Mar 25 2010 - 23:56:14 PDT)
- sikander azam (Thu Mar 25 2010 - 23:34:40 PDT)
- Bill Ross (Mon Mar 22 2010 - 10:16:47 PDT)
- Carlos Simmerling (Mon Mar 22 2010 - 09:15:41 PDT)
- sikander azam (Mon Mar 22 2010 - 09:11:17 PDT)
[AMBER] Nucgen
- Ross Walker (Tue Mar 16 2010 - 22:52:11 PDT)
- Jagdeesh C (Tue Mar 16 2010 - 22:11:05 PDT)
[AMBER] OMe fragment
- Lekpa Duukori (Wed Mar 03 2010 - 13:48:09 PST)
- FyD (Wed Mar 03 2010 - 12:51:02 PST)
- Lekpa Duukori (Wed Mar 03 2010 - 10:26:09 PST)
- FyD (Tue Mar 02 2010 - 21:58:23 PST)
- Lekpa Duukori (Tue Mar 02 2010 - 21:02:47 PST)
- FyD (Tue Mar 02 2010 - 20:44:00 PST)
- Lekpa Duukori (Tue Mar 02 2010 - 18:40:01 PST)
- Lekpa Duukori (Tue Mar 02 2010 - 07:03:43 PST)
- FyD (Tue Mar 02 2010 - 02:29:06 PST)
- Jason Swails (Mon Mar 01 2010 - 19:07:10 PST)
- Lachele Foley (Lists) (Mon Mar 01 2010 - 18:27:53 PST)
- Lekpa Duukori (Mon Mar 01 2010 - 18:08:55 PST)
- Jason Swails (Mon Mar 01 2010 - 18:02:44 PST)
- Jason Swails (Mon Mar 01 2010 - 17:55:45 PST)
- Lekpa Duukori (Mon Mar 01 2010 - 14:37:55 PST)
[AMBER] parameter file for modified nucleosides (O6-methyl guanine)
- Bill Ross (Tue Mar 09 2010 - 10:07:41 PST)
- N.R. Jena (Mon Mar 08 2010 - 23:04:22 PST)
- N.R. Jena (Thu Mar 04 2010 - 02:40:13 PST)
- Bill Ross (Wed Mar 03 2010 - 09:41:36 PST)
- N.R. Jena (Tue Mar 02 2010 - 20:20:21 PST)
- Bill Ross (Tue Mar 02 2010 - 10:20:12 PST)
- Jason Swails (Tue Mar 02 2010 - 09:37:19 PST)
- N.R. Jena (Tue Mar 02 2010 - 08:59:38 PST)
- case (Tue Mar 02 2010 - 05:11:16 PST)
- N.R. Jena (Tue Mar 02 2010 - 04:53:39 PST)
- N.R. Jena (Tue Mar 02 2010 - 04:24:59 PST)
[AMBER] Parameters for trimethylated Lysine?
- Carlos Simmerling (Wed Mar 03 2010 - 03:35:23 PST)
- Mannan (Wed Mar 03 2010 - 02:14:03 PST)
[AMBER] PARMSCAN
- Peter Charles Kahuna (Thu Mar 04 2010 - 05:39:13 PST)
[AMBER] Particle insertion and deletion
- Roman Osman (Sun Mar 14 2010 - 14:12:25 PDT)
- Carlos Simmerling (Sun Mar 14 2010 - 14:06:51 PDT)
- Dian Jiao (Sun Mar 14 2010 - 13:14:20 PDT)
[AMBER] PBC interactions
- Markus Kaukonen (Mon Mar 01 2010 - 23:35:19 PST)
- Jason Swails (Mon Mar 01 2010 - 17:37:15 PST)
- Ganesh Krishnan (Mon Mar 01 2010 - 13:51:14 PST)
[AMBER] PBSOL not equal to PBSUR + PBCAL?
- Ray Luo (Wed Mar 24 2010 - 14:00:44 PDT)
- Jeffrey (Thu Mar 18 2010 - 18:41:51 PDT)
- Ray Luo (Thu Mar 18 2010 - 09:59:40 PDT)
- Jeffrey (Thu Mar 18 2010 - 01:01:34 PDT)
[AMBER] PDB Database
- Sushil Mishra (Sun Mar 21 2010 - 03:29:02 PDT)
- s. Bill (Sun Mar 21 2010 - 03:08:07 PDT)
[AMBER] pKa Calculations Using Thermodynamic Integration
- Jason Swails (Wed Mar 31 2010 - 08:08:06 PDT)
- imtiaz shafiq (Wed Mar 31 2010 - 08:02:49 PDT)
[AMBER] Please help me out
- bharat lakhani (Thu Mar 04 2010 - 03:23:35 PST)
[AMBER] Polarization Scaling Down
- Ivan Gladich (Thu Mar 18 2010 - 07:02:52 PDT)
[AMBER] Post-processing with AMBER 10
- Dian Jiao (Fri Mar 26 2010 - 15:02:21 PDT)
- Daniel Roe (Fri Mar 26 2010 - 14:31:51 PDT)
- Dian Jiao (Fri Mar 26 2010 - 14:05:14 PDT)
[AMBER] problem in minimisation
- Bill Ross (Wed Mar 17 2010 - 09:58:37 PDT)
- Carlos Simmerling (Wed Mar 17 2010 - 08:22:16 PDT)
- Hyma vathi (Wed Mar 17 2010 - 08:04:12 PDT)
[AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine
- Bill Ross (Fri Mar 26 2010 - 09:42:06 PDT)
- N.R. Jena (Fri Mar 26 2010 - 05:59:06 PDT)
- Jason Swails (Thu Mar 25 2010 - 23:32:03 PDT)
- N.R. Jena (Thu Mar 25 2010 - 22:58:00 PDT)
- N.R. Jena (Thu Mar 25 2010 - 22:43:38 PDT)
[AMBER] problem to generate parameters files from NMR solved DNA structure
- case (Thu Mar 11 2010 - 06:04:44 PST)
- Ananya Paul (Thu Mar 11 2010 - 05:40:54 PST)
- case (Thu Mar 11 2010 - 04:46:58 PST)
- Ananya Paul (Wed Mar 10 2010 - 23:30:08 PST)
[AMBER] problem to generate parameters files of DNA
- case (Wed Mar 10 2010 - 07:12:27 PST)
- Ananya Paul (Wed Mar 10 2010 - 06:37:40 PST)
- case (Wed Mar 10 2010 - 05:09:47 PST)
- Ananya Paul (Wed Mar 10 2010 - 02:18:28 PST)
[AMBER] problem with antechamber for C60
- Dean Cuebas (Tue Mar 23 2010 - 13:13:37 PDT)
- Chun-Wei Pao (Tue Mar 23 2010 - 07:44:19 PDT)
- Chun-Wei Pao (Mon Mar 22 2010 - 23:10:59 PDT)
- Chun-Wei Pao (Mon Mar 22 2010 - 20:47:00 PDT)
[AMBER] problem with bugfix.all for amber10
- case (Mon Mar 08 2010 - 07:11:49 PST)
- Philipp Marquetand (Mon Mar 08 2010 - 04:43:47 PST)
[AMBER] Problem with solvationbox command
- pellegrini (Wed Mar 24 2010 - 03:26:43 PDT)
- Ross Walker (Tue Mar 23 2010 - 15:22:46 PDT)
- pellegrini (Tue Mar 23 2010 - 06:11:17 PDT)
[AMBER] problem with steered MD
- Dmitri Nilov (Mon Mar 29 2010 - 23:37:51 PDT)
- John Chuang莊曜遠 (Mon Mar 29 2010 - 20:25:21 PDT)
- nicholus bhattacharjee (Wed Mar 24 2010 - 21:37:37 PDT)
- Adrian Roitberg (Tue Mar 23 2010 - 15:50:19 PDT)
- nicholus bhattacharjee (Tue Mar 23 2010 - 08:34:52 PDT)
- Adrian Roitberg (Tue Mar 23 2010 - 07:16:35 PDT)
- nicholus bhattacharjee (Tue Mar 23 2010 - 05:41:26 PDT)
[AMBER] Problem with translate restrt file
- Ivan Gladich (Mon Mar 01 2010 - 11:47:18 PST)
- Jason Swails (Mon Mar 01 2010 - 10:24:28 PST)
- Ivan Gladich (Mon Mar 01 2010 - 10:00:06 PST)
[AMBER] Problems on Tutorial A8
- Ross Walker (Wed Mar 24 2010 - 11:22:10 PDT)
- tianyuan meng (Wed Mar 24 2010 - 00:15:58 PDT)
[AMBER] Protein + Bilayer Simulations: Role of salt
- Balazs Jojart (Tue Mar 02 2010 - 23:32:50 PST)
- Lalit Dubey (Mon Mar 01 2010 - 12:28:57 PST)
- Lalit Dubey (Mon Mar 01 2010 - 06:43:48 PST)
[AMBER] Protein Crystal Buried Waters and Amber Simulation ?
- Bill Ross (Thu Mar 04 2010 - 16:14:07 PST)
- Christine Baranski (Thu Mar 04 2010 - 16:04:16 PST)
[AMBER] Protein, Water and Amber
- steinbrt.rci.rutgers.edu (Mon Mar 08 2010 - 00:54:59 PST)
- Imtiaz Shafiq (Sun Mar 07 2010 - 15:15:40 PST)
[AMBER] ptraj hydrogen bond analysis error
- Daniel Roe (Wed Mar 17 2010 - 15:42:13 PDT)
- Jamie Romnes (Wed Mar 17 2010 - 14:47:53 PDT)
[AMBER] Ptraj problems
- Carlos Simmerling (Thu Mar 11 2010 - 10:56:31 PST)
- Ganesh Krishnan (Thu Mar 11 2010 - 10:55:07 PST)
- Bill Ross (Thu Mar 11 2010 - 10:27:56 PST)
- Ganesh Krishnan (Thu Mar 11 2010 - 09:43:05 PST)
[AMBER] ptraj rms
- s. Bill (Sat Mar 13 2010 - 08:08:41 PST)
- s. Bill (Sat Mar 13 2010 - 07:36:51 PST)
[AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency
- Adrian Roitberg (Wed Mar 31 2010 - 11:50:23 PDT)
- Markus Kaukonen (Wed Mar 31 2010 - 11:34:32 PDT)
- M. L. Dodson (Wed Mar 31 2010 - 06:36:05 PDT)
- Dmitri Nilov (Wed Mar 31 2010 - 01:10:21 PDT)
- Ross Walker (Tue Mar 30 2010 - 14:10:45 PDT)
- M. L. Dodson (Tue Mar 30 2010 - 08:09:27 PDT)
- Dmitri Nilov (Tue Mar 30 2010 - 07:41:00 PDT)
[AMBER] Quantifying Errors in PBSA
- D.J. Cole (Fri Mar 05 2010 - 11:47:45 PST)
[AMBER] Query on Minimization
- Bill Ross (Fri Mar 05 2010 - 09:26:28 PST)
- bharat lakhani (Fri Mar 05 2010 - 00:41:36 PST)
[AMBER] question about AMBER 9
- Carlos Simmerling (Tue Mar 09 2010 - 03:30:06 PST)
- Chinh Su Tran To (Tue Mar 09 2010 - 02:06:18 PST)
[AMBER] radgyr
- Carlos Simmerling (Tue Mar 23 2010 - 06:56:01 PDT)
- Beale, John (Tue Mar 23 2010 - 03:44:05 PDT)
[AMBER] Re :checkoverlap
- John S (Wed Mar 17 2010 - 20:45:37 PDT)
[AMBER] reg REMD
- Carlos Simmerling (Mon Mar 29 2010 - 05:02:16 PDT)
- maya maya (Mon Mar 29 2010 - 04:49:08 PDT)
[AMBER] reg-Generalized Born Approach
- case (Wed Mar 31 2010 - 11:42:39 PDT)
- Carlos Simmerling (Wed Mar 31 2010 - 11:21:35 PDT)
- maya maya (Wed Mar 31 2010 - 11:19:01 PDT)
- Bill Ross (Wed Mar 31 2010 - 10:13:29 PDT)
- maya maya (Wed Mar 31 2010 - 08:51:33 PDT)
[AMBER] Regarding amber molecular dynamics
- Bill Ross (Tue Mar 23 2010 - 21:38:20 PDT)
- PalaniMuthu M (Tue Mar 23 2010 - 21:01:55 PDT)
- Bill Ross (Tue Mar 23 2010 - 11:31:22 PDT)
- PalaniMuthu M (Tue Mar 23 2010 - 10:34:53 PDT)
- PalaniMuthu M (Tue Mar 23 2010 - 10:41:49 PDT)
[AMBER] regarding ambertools
- Asfa Ali (Sat Mar 20 2010 - 09:53:42 PDT)
- Jason Swails (Sat Mar 20 2010 - 07:51:54 PDT)
- Asfa Ali (Fri Mar 19 2010 - 10:52:40 PDT)
[AMBER] regarding compiling amber10
- Jason Swails (Tue Mar 09 2010 - 07:07:15 PST)
- jani vinod (Tue Mar 09 2010 - 03:54:50 PST)
[AMBER] Regarding energy in mdout file in SANDER
- Carlos Simmerling (Wed Mar 03 2010 - 03:34:54 PST)
- aneesh cna (Wed Mar 03 2010 - 02:19:33 PST)
[AMBER] regarding NMR structures
- Asfa Ali (Tue Mar 16 2010 - 23:51:41 PDT)
- case (Tue Mar 16 2010 - 10:05:50 PDT)
- case (Tue Mar 16 2010 - 09:41:28 PDT)
- Carlos Simmerling (Tue Mar 16 2010 - 06:25:30 PDT)
- Asfa Ali (Tue Mar 16 2010 - 06:08:20 PDT)
[AMBER] Regarding problem with self guided molecular dynamics
- Jason Swails (Tue Mar 23 2010 - 10:21:11 PDT)
- aneesh cna (Mon Mar 22 2010 - 23:02:18 PDT)
[AMBER] Regarding SGLD
- aneesh cna (Tue Mar 16 2010 - 06:40:02 PDT)
[AMBER] Regd:vlimit
- case (Sun Mar 21 2010 - 23:10:13 PDT)
- John S (Sun Mar 21 2010 - 21:03:18 PDT)
[AMBER] Removed proton in proteins
- case (Mon Mar 08 2010 - 07:25:20 PST)
- Francesca Cantini (Mon Mar 08 2010 - 06:32:04 PST)
[AMBER] residual dipolar couplings (RDC)
- case (Sat Mar 06 2010 - 06:41:09 PST)
- Carlos Simmerling (Fri Mar 05 2010 - 15:21:18 PST)
- Danny Xu (Fri Mar 05 2010 - 14:51:00 PST)
[AMBER] RESP, AM1BCC & geometries
- Aiko Matsumoto (Tue Mar 16 2010 - 06:34:55 PDT)
[AMBER] RMSD between two different proteins
- Jagan Mohan (Fri Mar 19 2010 - 02:16:36 PDT)
- nicholus bhattacharjee (Fri Mar 19 2010 - 01:17:42 PDT)
- Jagan Mohan (Fri Mar 19 2010 - 00:26:37 PDT)
- nicholus bhattacharjee (Fri Mar 19 2010 - 00:10:04 PDT)
[AMBER] RMSD of Specific Atoms
- Jason Swails (Sat Mar 27 2010 - 07:44:04 PDT)
- Jagdeesh C (Sat Mar 27 2010 - 00:29:45 PDT)
[AMBER] RMSF calculation is correct ?
- Sarra Geranil (Tue Mar 02 2010 - 09:35:07 PST)
[AMBER] Run.dip: Program Error during test run after Amber 10 installation
- case (Sun Mar 28 2010 - 06:48:03 PDT)
- Senthil Natesan (Fri Mar 26 2010 - 13:44:43 PDT)
[AMBER] Running several jobs under one script
- Jason Swails (Thu Mar 25 2010 - 09:27:45 PDT)
- Nkwe Monama (Thu Mar 25 2010 - 02:47:57 PDT)
[AMBER] Running without flex
- case (Tue Mar 30 2010 - 11:32:17 PDT)
[AMBER] sander bomb and maxpr question
- case (Fri Mar 26 2010 - 07:53:56 PDT)
- Andrew Olson (Wed Mar 24 2010 - 07:08:15 PDT)
- case (Wed Mar 17 2010 - 17:36:14 PDT)
- Andrew Olson (Wed Mar 17 2010 - 15:30:05 PDT)
- case (Wed Mar 17 2010 - 12:56:21 PDT)
- Andrew Olson (Wed Mar 17 2010 - 11:51:36 PDT)
[AMBER] sander bomb: volume of ucell too big
- Bill Ross (Mon Mar 08 2010 - 09:26:02 PST)
- Nancy (Sat Mar 06 2010 - 23:13:43 PST)
- case (Sat Mar 06 2010 - 06:50:56 PST)
- Nancy (Fri Mar 05 2010 - 23:25:35 PST)
[AMBER] savePdb in leap
- case (Sat Mar 06 2010 - 07:15:41 PST)
- Jason Swails (Fri Mar 05 2010 - 15:58:50 PST)
- Peter Schmidtke (Fri Mar 05 2010 - 05:47:34 PST)
[AMBER] schlegel diagram
- meandme meandme (Tue Mar 30 2010 - 03:22:45 PDT)
[AMBER] Script for creating topology files , running minimization and MD simulation in amber
- Jason Swails (Thu Mar 25 2010 - 23:22:33 PDT)
- Palanimuthu M (Thu Mar 25 2010 - 22:55:53 PDT)
- manoj singh (Thu Mar 25 2010 - 22:24:47 PDT)
- Palanimuthu M (Thu Mar 25 2010 - 22:23:07 PDT)
[AMBER] Script for creating topology files , running minimization and MD simulation using amoeba force field
- case (Thu Mar 25 2010 - 10:39:36 PDT)
- Workalemhu Berhanu (Thu Mar 25 2010 - 07:31:22 PDT)
[AMBER] Segmentation fault
- Bill Ross (Wed Mar 03 2010 - 10:11:02 PST)
- Asfa Ali (Wed Mar 03 2010 - 07:20:28 PST)
[AMBER] serial compilation of pmemd
- bbalta.itu.edu.tr (Mon Mar 22 2010 - 06:51:02 PDT)
[AMBER] Simulating a protein with nmr structure
- nicholus bhattacharjee (Thu Mar 11 2010 - 03:10:42 PST)
- Deepangi Pandit (Wed Mar 10 2010 - 10:45:12 PST)
- Carlos Simmerling (Wed Mar 10 2010 - 03:37:25 PST)
- nicholus bhattacharjee (Wed Mar 10 2010 - 01:50:23 PST)
[AMBER] simulation under pressure
- Marek Maly (Tue Mar 30 2010 - 02:53:25 PDT)
- Jason Swails (Mon Mar 29 2010 - 20:30:26 PDT)
- Daniel Roe (Mon Mar 29 2010 - 19:23:07 PDT)
- Yang Li (Mon Mar 29 2010 - 18:40:41 PDT)
- Carlos Simmerling (Mon Mar 29 2010 - 12:58:40 PDT)
- Yang Li (Mon Mar 29 2010 - 12:53:01 PDT)
- case (Fri Mar 26 2010 - 07:54:10 PDT)
- Yang Li (Mon Mar 22 2010 - 20:05:45 PDT)
[AMBER] sleap help
- InSuk Joung (Thu Mar 04 2010 - 13:55:15 PST)
[AMBER] sleap not built
- Wei Zhang (Mon Mar 15 2010 - 16:27:49 PDT)
- Robert Wohlhueter (Mon Mar 15 2010 - 15:51:24 PDT)
[AMBER] SMD of QM part in QMMM MD simulation
- M. L. Dodson (Sat Mar 27 2010 - 06:27:16 PDT)
- Dmitri Nilov (Sat Mar 27 2010 - 05:39:47 PDT)
[AMBER] Solvatebox on Amber8
- pellegrini (Tue Mar 23 2010 - 03:29:32 PDT)
[AMBER] Specification of solventCap causing atoms to collapse into each other
- Ben Roberts (Tue Mar 23 2010 - 11:42:44 PDT)
[AMBER] Spline order too small when using AMOEBA force field
- case (Sat Mar 13 2010 - 09:34:34 PST)
- Workalemhu Berhanu (Sat Mar 13 2010 - 04:42:55 PST)
[AMBER] start from scratch
- geyan (Tue Mar 16 2010 - 00:30:49 PDT)
[AMBER] swiss cheese water shell
- Bill Ross (Mon Mar 01 2010 - 09:26:30 PST)
[AMBER] The error information
- Bill Ross (Wed Mar 03 2010 - 17:47:04 PST)
- zhihong ke (Wed Mar 03 2010 - 17:38:08 PST)
[AMBER] tleap and xleap problem in loading mol2 files
- Jason Swails (Thu Mar 11 2010 - 21:10:02 PST)
- d96543015.ntu.edu.tw (Thu Mar 11 2010 - 20:51:41 PST)
[AMBER] tleap savepdb command and organic lignads in proteins
- imtiaz shafiq (Wed Mar 31 2010 - 06:43:46 PDT)
- Bill Ross (Tue Mar 30 2010 - 14:48:16 PDT)
- imtiaz shafiq (Tue Mar 30 2010 - 14:45:00 PDT)
- Jason Swails (Tue Mar 30 2010 - 10:51:11 PDT)
- imtiaz shafiq (Tue Mar 30 2010 - 10:50:11 PDT)
- Jason Swails (Tue Mar 30 2010 - 10:45:32 PDT)
- imtiaz shafiq (Tue Mar 30 2010 - 10:43:50 PDT)
[AMBER] trajectory momentum for a substructure
- Taufik Al-Sarraj (Mon Mar 08 2010 - 10:20:01 PST)
[AMBER] transforming Antechamber GAFF parameters into another force field
- Denny Bromley (Mon Mar 29 2010 - 09:40:31 PDT)
- Alan (Sun Mar 28 2010 - 04:51:11 PDT)
- Gustavo Seabra (Sat Mar 27 2010 - 21:30:54 PDT)
- Bill Ross (Fri Mar 26 2010 - 16:41:12 PDT)
- Denny Bromley (Fri Mar 26 2010 - 16:26:06 PDT)
- Nicholas Musolino (Fri Mar 26 2010 - 15:16:04 PDT)
- Denny Bromley (Fri Mar 26 2010 - 15:00:26 PDT)
[AMBER] unsubscribe
- whimsica.aol.com (Mon Mar 15 2010 - 00:40:54 PDT)
[AMBER] Using 6-12 / 10-12 potential in AMBER
- Jason Swails (Tue Mar 23 2010 - 10:12:09 PDT)
- Alessandro Nascimento (Tue Mar 23 2010 - 08:44:01 PDT)
[AMBER] Various Errors in Tests
- case (Fri Mar 12 2010 - 04:56:39 PST)
- Philipp Marquetand (Fri Mar 12 2010 - 03:19:08 PST)
- case (Tue Mar 09 2010 - 05:42:28 PST)
- Philipp Marquetand (Tue Mar 09 2010 - 02:52:24 PST)
- Philipp Marquetand (Tue Mar 09 2010 - 02:45:28 PST)
[AMBER] Vdw radii params in antechamber
- Denny Bromley (Wed Mar 03 2010 - 12:58:00 PST)
- Thomas Cheatham (Wed Mar 03 2010 - 11:55:39 PST)
- Jason Swails (Wed Mar 03 2010 - 11:53:26 PST)
- Bill Ross (Wed Mar 03 2010 - 11:32:20 PST)
- Dian Jiao (Wed Mar 03 2010 - 10:17:42 PST)
- Denny Bromley (Wed Mar 03 2010 - 10:00:55 PST)
- Jason Swails (Tue Mar 02 2010 - 21:40:17 PST)
- Denny Bromley (Tue Mar 02 2010 - 21:08:11 PST)
[AMBER] vlimit error during equilibration step
- Carlos Simmerling (Wed Mar 31 2010 - 04:12:38 PDT)
- Nicee (Wed Mar 31 2010 - 00:26:02 PDT)
- jani vinod (Wed Mar 31 2010 - 00:00:12 PDT)
- Nicee (Tue Mar 30 2010 - 21:04:21 PDT)
- Nicee (Tue Mar 30 2010 - 04:48:17 PDT)
- Carlos Simmerling (Tue Mar 30 2010 - 04:29:12 PDT)
- Nicee (Mon Mar 29 2010 - 21:37:28 PDT)
[AMBER] vlimit exceeded for step
- case (Thu Mar 18 2010 - 12:27:40 PDT)
- Jason Swails (Thu Mar 18 2010 - 09:07:34 PDT)
- Carlos Simmerling (Thu Mar 18 2010 - 07:42:08 PDT)
- Hyma vathi (Thu Mar 18 2010 - 07:35:10 PDT)
- Carlos Simmerling (Thu Mar 18 2010 - 07:29:49 PDT)
- Hyma vathi (Thu Mar 18 2010 - 07:28:29 PDT)
[AMBER] Which shake option to be used
- case (Sun Mar 28 2010 - 06:35:24 PDT)
- nicholus bhattacharjee (Sun Mar 28 2010 - 03:21:51 PDT)
[AMBER] wrong?
- steinbrt.rci.rutgers.edu (Mon Mar 15 2010 - 01:49:54 PDT)
- Hannes Loeffler (Mon Mar 15 2010 - 01:34:45 PDT)
- geyan (Mon Mar 15 2010 - 01:27:58 PDT)
[AMBER] Xleap : Improper torsions applied
- Sushil Mishra (Mon Mar 08 2010 - 06:55:26 PST)
About amber10 installation
- Ross Walker (Sat Mar 13 2010 - 10:22:44 PST)
Re :checkoverlap
- John S (Thu Mar 18 2010 - 12:55:55 PDT)
SOS for mmpbsa
- Jason Swails (Thu Mar 11 2010 - 08:25:18 PST)
- Ray Luo (Wed Mar 10 2010 - 10:17:07 PST)

Amber Archive Mar 2010 by subject