Amber Archive Aug 2010 by thread
712 messages
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Starting
Sat Jul 31 2010 - 13:00:03 PDT,
Ending
Tue Aug 31 2010 - 23:30:03 PDT
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[AMBER] obtain a .pdb file from a .prepin/.frcmod file
Ehsan Habibi
(Sat Jul 31 2010 - 12:42:29 PDT)
Re: [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests?
Thomas Zeiser
(Sun Aug 01 2010 - 00:32:04 PDT)
Re: [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests?
Scott Le Grand
(Mon Aug 02 2010 - 10:08:25 PDT)
[AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense?
Sasha Buzko
(Wed Aug 04 2010 - 20:57:37 PDT)
Re: [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense?
Ross Walker
(Thu Aug 05 2010 - 07:02:57 PDT)
Re: [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense?
Scott Le Grand
(Thu Aug 05 2010 - 08:03:42 PDT)
Re: [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense?
Sasha Buzko
(Thu Aug 05 2010 - 10:10:10 PDT)
Re: [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense?
Scott Le Grand
(Thu Aug 05 2010 - 10:17:58 PDT)
Re: [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense?
Ross Walker
(Thu Aug 05 2010 - 18:26:26 PDT)
[AMBER] Horrific pmemd.cuda performance on an 8-GPU system
Sasha Buzko
(Wed Aug 11 2010 - 12:15:59 PDT)
Re: [AMBER] Horrific pmemd.cuda performance on an 8-GPU system
Ross Walker
(Wed Aug 11 2010 - 13:04:25 PDT)
Re: [AMBER] Horrific pmemd.cuda performance on an 8-GPU system
Sasha Buzko
(Thu Aug 12 2010 - 09:23:50 PDT)
Re: [AMBER] Horrific pmemd.cuda performance on an 8-GPU system
michael
(Wed Aug 11 2010 - 14:48:36 PDT)
Re: [AMBER] how to generate porcupine plot
Jia Xu
(Sun Aug 01 2010 - 01:27:12 PDT)
[AMBER] how to extract temperatur and other data from mdout
setyanto tri wahyudi
(Sun Aug 01 2010 - 20:45:20 PDT)
Re: [AMBER] how to extract temperatur and other data from mdout
Bill Ross
(Sun Aug 01 2010 - 22:24:04 PDT)
Re: [AMBER] how to extract temperatur and other data from mdout
setyanto tri wahyudi
(Sun Aug 01 2010 - 23:06:10 PDT)
Re: [AMBER] how to extract temperatur and other data from mdout
Jason Swails
(Mon Aug 02 2010 - 05:27:55 PDT)
Re: [AMBER] how to extract temperatur and other data from mdout
Bill Ross
(Mon Aug 02 2010 - 09:52:08 PDT)
Re: [AMBER] how to extract temperatur and other data from mdout
setyanto tri wahyudi
(Mon Aug 02 2010 - 20:25:55 PDT)
Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs
Daniel Sindhikara
(Sun Aug 01 2010 - 21:12:52 PDT)
[AMBER] error in heating
rameshwar prajapati
(Sun Aug 01 2010 - 22:31:55 PDT)
Re: [AMBER] error in heating
Bill Ross
(Sun Aug 01 2010 - 22:48:40 PDT)
Re: [AMBER] error in heating
Bill Ross
(Sun Aug 01 2010 - 22:52:25 PDT)
[AMBER] errror in heating
rameshwar prajapati
(Sun Aug 01 2010 - 22:47:51 PDT)
Re: [AMBER] errror in heating
Bill Ross
(Sun Aug 01 2010 - 22:56:46 PDT)
Re: [AMBER] errror in heating
rameshwar prajapati
(Sun Aug 01 2010 - 23:22:37 PDT)
Re: [AMBER] errror in heating
Jason Swails
(Mon Aug 02 2010 - 04:37:25 PDT)
Re: [AMBER] errror in heating
Bill Ross
(Mon Aug 02 2010 - 08:28:21 PDT)
[AMBER] NVE
Philippe Pinard
(Sun Aug 01 2010 - 22:53:53 PDT)
Re: [AMBER] NVE
steinbrt.rci.rutgers.edu
(Mon Aug 02 2010 - 00:59:02 PDT)
Re: [AMBER] NVE
Jason Swails
(Mon Aug 02 2010 - 04:23:08 PDT)
[AMBER] antechamber
Philippe Pinard
(Mon Aug 02 2010 - 11:56:26 PDT)
[AMBER] RDPARM
Philippe Pinard
(Mon Aug 02 2010 - 16:12:20 PDT)
Re: [AMBER] RDPARM
Thomas Cheatham III
(Mon Aug 02 2010 - 16:24:40 PDT)
Re: [AMBER] RDPARM
Philippe Pinard
(Tue Aug 03 2010 - 08:41:54 PDT)
Re: [AMBER] RDPARM
Thomas Cheatham III
(Tue Aug 03 2010 - 14:11:58 PDT)
Re: [AMBER] RDPARM
Philippe Pinard
(Tue Aug 03 2010 - 14:32:10 PDT)
Re: [AMBER] RDPARM
Thomas Cheatham III
(Tue Aug 03 2010 - 15:00:07 PDT)
Re: [AMBER] RDPARM
case
(Tue Aug 03 2010 - 15:26:49 PDT)
Re: [AMBER] RDPARM
Philippe Pinard
(Wed Aug 04 2010 - 09:35:49 PDT)
Re: [AMBER] RDPARM
case
(Wed Aug 04 2010 - 14:48:36 PDT)
Re: [AMBER] RDPARM
Philippe Pinard
(Wed Aug 04 2010 - 17:24:56 PDT)
Re: [AMBER] RDPARM
case
(Wed Aug 04 2010 - 17:37:18 PDT)
Re: [AMBER] RDPARM
Philippe Pinard
(Tue Aug 03 2010 - 14:40:03 PDT)
Re: [AMBER] antechamber
case
(Mon Aug 02 2010 - 18:30:33 PDT)
[AMBER] Problem with running PMEMD on a cluster
ali naserian nik
(Mon Aug 02 2010 - 00:37:12 PDT)
Re: [AMBER] minimization segmentation fault
Jorgen Simonsen
(Mon Aug 02 2010 - 00:59:46 PDT)
Re: [AMBER] minimization segmentation fault
Bill Ross
(Mon Aug 02 2010 - 09:50:34 PDT)
[AMBER] Gradually Compress Volume to Increase Density
Shubhra Gupta
(Mon Aug 02 2010 - 01:59:45 PDT)
Re: [AMBER] Gradually Compress Volume to Increase Density
Jason Swails
(Mon Aug 02 2010 - 04:17:55 PDT)
Re: [AMBER] Gradually Compress Volume to Increase Density
Shubhra Gupta
(Mon Aug 02 2010 - 05:19:34 PDT)
Re: [AMBER] Gradually Compress Volume to Increase Density
Jason Swails
(Mon Aug 02 2010 - 05:33:46 PDT)
Re: [AMBER] Gradually Compress Volume to Increase Density
Bill Ross
(Mon Aug 02 2010 - 08:21:10 PDT)
[AMBER] Writing trajectory for C-alpha atoms
Ibrahim Moustafa
(Mon Aug 02 2010 - 08:31:33 PDT)
Re: [AMBER] Writing trajectory for C-alpha atoms
Daniel Roe
(Mon Aug 02 2010 - 08:43:59 PDT)
Re: [AMBER] Writing trajectory for C-alpha atoms
Ibrahim Moustafa
(Mon Aug 02 2010 - 10:38:25 PDT)
Re: [AMBER] Writing trajectory for C-alpha atoms
Jason Swails
(Mon Aug 02 2010 - 11:35:47 PDT)
Re: [AMBER] Writing trajectory for C-alpha atoms
Ibrahim Moustafa
(Mon Aug 02 2010 - 11:56:57 PDT)
Re: [AMBER] Writing trajectory for C-alpha atoms
Bill Ross
(Mon Aug 02 2010 - 11:54:57 PDT)
Re: [AMBER] Writing trajectory for C-alpha atoms
Ibrahim Moustafa
(Mon Aug 02 2010 - 12:16:48 PDT)
[AMBER] conversion of the CYANA upl into amber format: QE, QD of Tyr and Phe
Francesca Cantini
(Mon Aug 02 2010 - 09:35:31 PDT)
Re: [AMBER] conversion of the CYANA upl into amber format: QE, QD of Tyr and Phe
case
(Mon Aug 02 2010 - 16:52:43 PDT)
[AMBER] restraining only heavy atoms in PMEMD
Senthil Natesan
(Mon Aug 02 2010 - 11:37:33 PDT)
[AMBER] Mistake in using amber
Rilei Yu
(Mon Aug 02 2010 - 17:55:47 PDT)
Re: [AMBER] Mistake in using amber
Gustavo Seabra
(Mon Aug 02 2010 - 18:01:41 PDT)
Re: [AMBER] Mistake in using amber
Bill Ross
(Mon Aug 02 2010 - 18:02:42 PDT)
Re: [AMBER] Mistake in using amber
Rilei Yu
(Mon Aug 02 2010 - 18:10:40 PDT)
Re: [AMBER] Mistake in using amber
steinbrt.rci.rutgers.edu
(Tue Aug 03 2010 - 00:32:53 PDT)
[AMBER] questions about installing pmend.cuda
宋德寿
(Mon Aug 02 2010 - 21:45:49 PDT)
Re: [AMBER] questions about installing pmend.cuda
maluyao
(Mon Aug 02 2010 - 21:55:06 PDT)
Re: [AMBER] questions about installing pmend.cuda
宋德寿
(Mon Aug 02 2010 - 22:26:25 PDT)
Re: [AMBER] questions about installing pmend.cuda
宋德寿
(Mon Aug 02 2010 - 23:39:45 PDT)
Re: [AMBER] questions about installing pmend.cuda
Jason Swails
(Tue Aug 03 2010 - 04:26:21 PDT)
Re: [AMBER] questions about installing pmend.cuda
宋德寿
(Tue Aug 03 2010 - 05:07:32 PDT)
Re: [AMBER] questions about installing pmend.cuda
宋德寿
(Tue Aug 03 2010 - 20:03:24 PDT)
Re: [AMBER] questions about installing pmend.cuda
case
(Tue Aug 03 2010 - 06:20:09 PDT)
Re: [AMBER] questions about installing pmend.cuda
Ross Walker
(Tue Aug 03 2010 - 11:04:15 PDT)
Re: [AMBER] questions about installing pmend.cuda
宋德寿
(Tue Aug 03 2010 - 19:59:02 PDT)
[AMBER] how to run entropy calculation using pmemd
fancy2012
(Tue Aug 03 2010 - 02:50:13 PDT)
Re: [AMBER] how to run entropy calculation using pmemd
Jason Swails
(Tue Aug 03 2010 - 04:29:47 PDT)
Re: [AMBER] how to run entropy calculation using pmemd
fancy2012
(Tue Aug 03 2010 - 04:36:05 PDT)
[AMBER] ptraj and image
Thomas Exner
(Tue Aug 03 2010 - 04:08:11 PDT)
Re: [AMBER] ptraj and image
steinbrt.rci.rutgers.edu
(Tue Aug 03 2010 - 04:13:13 PDT)
Re: [AMBER] No solvent overlap
Thomas Exner
(Tue Aug 03 2010 - 04:12:31 PDT)
Re: [AMBER] No solvent overlap
case
(Wed Aug 04 2010 - 04:23:44 PDT)
[AMBER] How to parametrize ligand using AMOEBA polarizable potential
sunita gupta
(Tue Aug 03 2010 - 04:43:25 PDT)
[AMBER] PTRAJ: problem with image command
Xioling Chuang
(Tue Aug 03 2010 - 07:30:46 PDT)
Re: [AMBER] PTRAJ: problem with image command
InSuk Joung
(Tue Aug 03 2010 - 08:20:13 PDT)
Re: [AMBER] PTRAJ: problem with image command
Xioling Chuang
(Tue Aug 03 2010 - 09:17:02 PDT)
Re: [AMBER] PTRAJ: problem with image command
InSuk Joung
(Tue Aug 03 2010 - 11:04:32 PDT)
Re: [AMBER] PTRAJ: problem with image command
InSuk Joung
(Tue Aug 03 2010 - 11:05:56 PDT)
Re: [AMBER] PTRAJ: problem with image command
Xioling Chuang
(Tue Aug 03 2010 - 20:43:39 PDT)
[AMBER] Solid surface simulation in Amber - the recommended approach ?
Marek Maly
(Tue Aug 03 2010 - 11:35:28 PDT)
Re: [AMBER] Solid surface simulation in Amber - the recommended approach ?
Marek Maly
(Fri Aug 06 2010 - 18:26:22 PDT)
Re: [AMBER] Solid surface simulation in Amber
Bill Ross
(Tue Aug 03 2010 - 12:14:57 PDT)
Re: [AMBER] Solid surface simulation in Amber
Marek Maly
(Tue Aug 03 2010 - 15:23:34 PDT)
Re: [AMBER] Solid surface simulation in Amber
Bill Ross
(Tue Aug 03 2010 - 16:03:49 PDT)
Re: [AMBER] Solid surface simulation in Amber
Bill Ross
(Tue Aug 03 2010 - 16:08:20 PDT)
Re: [AMBER] Solid surface simulation in Amber
Marek Maly
(Tue Aug 03 2010 - 16:00:24 PDT)
Re: [AMBER] Solid surface simulation in Amber
Tom Williams
(Tue Aug 03 2010 - 23:06:47 PDT)
Re: [AMBER] Solid surface simulation in Amber
case
(Wed Aug 04 2010 - 04:23:11 PDT)
Re: [AMBER] Solid surface simulation in Amber
Marek Maly
(Wed Aug 04 2010 - 08:03:54 PDT)
Re: [AMBER] Solid surface simulation in Amber
Tom Williams
(Wed Aug 04 2010 - 09:35:57 PDT)
[AMBER] ptraj question
Jia Xu
(Tue Aug 03 2010 - 15:29:36 PDT)
Re: [AMBER] ptraj question
Jason Swails
(Tue Aug 03 2010 - 17:27:16 PDT)
[AMBER] How to define putative reaction coordinates in AMBER?
Catein Catherine
(Tue Aug 03 2010 - 23:09:01 PDT)
[AMBER] Error message in runing Steered MD in AMBER 10 (tutorial A10)
Catein Catherine
(Wed Aug 04 2010 - 02:59:40 PDT)
Re: [AMBER] Error message in runing Steered MD in AMBER 10 (tutorial A10)
Jason Swails
(Wed Aug 04 2010 - 06:17:34 PDT)
Re: [AMBER] How to define putative reaction coordinates in AMBER?
Jason Swails
(Wed Aug 04 2010 - 05:29:45 PDT)
[AMBER] analysis of mm_pbsa
Asfa Ali
(Tue Aug 03 2010 - 23:50:33 PDT)
Re: [AMBER] analysis of mm_pbsa
Jason Swails
(Wed Aug 04 2010 - 05:36:32 PDT)
Re: [AMBER] analysis of mm_pbsa
Asfa Ali
(Wed Aug 04 2010 - 06:19:02 PDT)
Re: [AMBER] analysis of mm_pbsa
Jason Swails
(Wed Aug 04 2010 - 06:27:18 PDT)
Re: [AMBER] analysis of mm_pbsa
Asfa Ali
(Wed Aug 04 2010 - 06:36:46 PDT)
[AMBER] entropy calculation using nmode
Asfa Ali
(Wed Aug 04 2010 - 03:46:59 PDT)
[AMBER] simulation with multiple docked ligand
Ashutosh Shandilya
(Wed Aug 04 2010 - 05:47:07 PDT)
Re: [AMBER] simulation with multiple docked ligand
steinbrt.rci.rutgers.edu
(Wed Aug 04 2010 - 05:55:10 PDT)
[AMBER] Energy abrupt rise in Energy minimization
Jiang Yusheng
(Wed Aug 04 2010 - 10:37:32 PDT)
Re: [AMBER] Energy abrupt rise in Energy minimization
Bill Ross
(Wed Aug 04 2010 - 11:33:21 PDT)
Re: [AMBER] Energy abrupt rise in Energy minimization
Jiang Yusheng
(Wed Aug 04 2010 - 11:49:16 PDT)
Re: [AMBER] Energy abrupt rise in Energy minimization
Bill Ross
(Wed Aug 04 2010 - 12:10:48 PDT)
Re: [AMBER] Energy abrupt rise in Energy minimization
Jiang Yusheng
(Wed Aug 04 2010 - 12:31:15 PDT)
Re: [AMBER] Energy abrupt rise in Energy minimization
Bill Ross
(Wed Aug 04 2010 - 13:25:40 PDT)
Re: [AMBER] Energy abrupt rise in Energy minimization
Jiang Yusheng
(Thu Aug 05 2010 - 07:00:04 PDT)
Re: [AMBER] Permission to post Admin processes?
Marc Moreau
(Wed Aug 04 2010 - 10:49:42 PDT)
[AMBER] How to make parameter files of GTP from PDB file.
kurisaki ikuo
(Wed Aug 04 2010 - 20:12:59 PDT)
Re: [AMBER] How to make parameter files of GTP from PDB file.
kurisaki ikuo
(Wed Aug 04 2010 - 20:43:37 PDT)
Re: [AMBER] How to make parameter files of GTP from PDB file.
Bill Ross
(Thu Aug 05 2010 - 10:28:45 PDT)
[AMBER] Parametrization of Ligand using AMOEBA potential
sunita gupta
(Thu Aug 05 2010 - 00:32:55 PDT)
Re: [AMBER] Parametrization of Ligand using AMOEBA potential
Dian Jiao
(Thu Aug 05 2010 - 07:15:05 PDT)
[AMBER] Tutorial3
George Tzotzos
(Thu Aug 05 2010 - 09:52:37 PDT)
[AMBER] Tutorial3
George Tzotzos
(Thu Aug 05 2010 - 10:22:02 PDT)
[AMBER] error message about memory in antechamber
Guoxiong Su
(Thu Aug 05 2010 - 11:16:27 PDT)
Re: [AMBER] error message about memory in antechamber
case
(Thu Aug 05 2010 - 12:48:26 PDT)
[AMBER] Can I use LCOD command for umbrella sampling PMF calculation?
Catein Catherine
(Fri Aug 06 2010 - 00:46:58 PDT)
Re: [AMBER] Can I use LCOD command for umbrella sampling PMF calculation?
Jason Swails
(Fri Aug 06 2010 - 05:52:43 PDT)
Re: [AMBER] error message about memory in antechamber
Guoxiong Su
(Mon Aug 09 2010 - 08:47:52 PDT)
Re: [AMBER] error message about memory in antechamber
case
(Mon Aug 09 2010 - 11:47:52 PDT)
Re: [AMBER] error message about memory in antechamber
Guoxiong Su
(Tue Aug 10 2010 - 12:26:20 PDT)
Re: [AMBER] error message about memory in antechamber
case
(Wed Aug 11 2010 - 09:03:54 PDT)
[AMBER] Post-processing error
arikcohen
(Thu Aug 05 2010 - 17:15:54 PDT)
Re: [AMBER] Post-processing error - NO NEED TO ANSWER, PROBLEM SOLVED
arikcohen
(Fri Aug 06 2010 - 16:41:45 PDT)
Re: [AMBER] Post-processing error - NO NEED TO ANSWER, PROBLEM SOLVED
Bill Ross
(Fri Aug 06 2010 - 16:50:17 PDT)
Re: [AMBER] Post-processing error - NO NEED TO ANSWER, PROBLEM SOLVED
arikcohen
(Fri Aug 06 2010 - 18:02:09 PDT)
[AMBER] H-bonding analysis
Asfa Ali
(Thu Aug 05 2010 - 23:19:19 PDT)
[AMBER] Can I convert the umberlla sampling results to LCOD for 1D-PMF analysis?
Catein Catherine
(Fri Aug 06 2010 - 00:57:17 PDT)
[AMBER] Error message when doing A10 tutorial (SMD with LCOD) with AMBER 10.
Catein Catherine
(Fri Aug 06 2010 - 01:11:15 PDT)
[AMBER] How to run LCOD in AMBER 10?
Catein Catherine
(Sun Aug 08 2010 - 21:26:17 PDT)
[AMBER] Where to apply find computer resources to run AMBER?
Catein Catherine
(Sun Aug 08 2010 - 21:55:33 PDT)
[AMBER] How can I run Random Acceleration Molecular Dynamics with AMBER10?
Catein Catherine
(Sun Aug 08 2010 - 22:58:09 PDT)
Re: [AMBER] How can I run Random Acceleration Molecular Dynamics with AMBER10?
Jason Swails
(Mon Aug 09 2010 - 05:51:42 PDT)
Re: [AMBER] How can I run Random Acceleration Molecular Dynamics with AMBER10?
Vlad Cojocaru
(Mon Aug 09 2010 - 06:51:15 PDT)
Re: [AMBER] Where to apply find computer resources to run AMBER?
Ross Walker
(Mon Aug 09 2010 - 06:20:15 PDT)
Re: [AMBER] Where to apply find computer resources to run AMBER?
Catein Catherine
(Mon Aug 09 2010 - 07:21:04 PDT)
Re: [AMBER] How to run LCOD in AMBER 10?
Jason Swails
(Mon Aug 09 2010 - 06:10:37 PDT)
Re: [AMBER] How to run LCOD in AMBER 10?
Catein Catherine
(Mon Aug 09 2010 - 07:14:37 PDT)
Re: [AMBER] How to run LCOD in AMBER 10?
M. L. Dodson
(Mon Aug 09 2010 - 08:30:40 PDT)
Re: [AMBER] Can I convert the umberlla sampling results to LCOD for 1D-PMF analysis?
Jason Swails
(Fri Aug 06 2010 - 06:02:21 PDT)
Re: [AMBER] H-bonding analysis
Bill Ross
(Fri Aug 06 2010 - 09:52:37 PDT)
[AMBER] peptides not folding in remd with changing sequence of D and L isomer
Jorgen Simonsen
(Sun Aug 08 2010 - 09:44:35 PDT)
Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer
Jason Swails
(Sun Aug 08 2010 - 10:47:53 PDT)
Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer
Daniel Sindhikara
(Sun Aug 08 2010 - 23:54:52 PDT)
Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer
Jorgen Simonsen
(Mon Aug 09 2010 - 00:02:03 PDT)
Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer
Carlos Simmerling
(Mon Aug 09 2010 - 04:21:22 PDT)
Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer
Jorgen Simonsen
(Mon Aug 09 2010 - 04:52:25 PDT)
Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer
Carlos Simmerling
(Mon Aug 09 2010 - 04:54:07 PDT)
Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer
Jorgen Simonsen
(Mon Aug 09 2010 - 05:02:05 PDT)
Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer
Carlos Simmerling
(Mon Aug 09 2010 - 07:20:43 PDT)
Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer
Jorgen Simonsen
(Mon Aug 09 2010 - 08:12:50 PDT)
Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer
Carlos Simmerling
(Mon Aug 09 2010 - 08:18:16 PDT)
[AMBER] dear sir
selva raj
(Sun Aug 08 2010 - 10:42:59 PDT)
Re: [AMBER] dear sir
Sushil Mishra
(Sun Aug 08 2010 - 10:50:50 PDT)
Re: [AMBER] dear sir
Sushil Mishra
(Sun Aug 08 2010 - 10:52:11 PDT)
[AMBER] The Result of PARMCHK
setyanto tri wahyudi
(Sun Aug 08 2010 - 23:32:47 PDT)
Re: [AMBER] The Result of PARMCHK
case
(Mon Aug 09 2010 - 04:57:37 PDT)
Re: [AMBER] The Result of PARMCHK
setyanto tri wahyudi
(Mon Aug 09 2010 - 20:09:34 PDT)
Re: [AMBER] The Result of PARMCHK
case
(Tue Aug 10 2010 - 04:33:20 PDT)
Re: [AMBER] The Result of PARMCHK
setyanto tri wahyudi
(Wed Aug 11 2010 - 19:41:19 PDT)
[AMBER] Soft-core Coulomb potential
Samuel Genheden
(Mon Aug 09 2010 - 00:52:31 PDT)
Re: [AMBER] Soft-core Coulomb potential
case
(Mon Aug 09 2010 - 04:58:59 PDT)
[AMBER] error when compiling pmemd
Jorgen Simonsen
(Mon Aug 09 2010 - 03:56:13 PDT)
Re: [AMBER] error when compiling pmemd
case
(Mon Aug 09 2010 - 05:05:36 PDT)
Re: [AMBER] error when compiling pmemd
Jorgen Simonsen
(Mon Aug 09 2010 - 05:15:08 PDT)
Re: [AMBER] error when compiling pmemd
Ross Walker
(Mon Aug 09 2010 - 06:06:44 PDT)
Re: [AMBER] error when compiling pmemd
Jorgen Simonsen
(Mon Aug 09 2010 - 09:20:42 PDT)
Re: [AMBER] error when compiling pmemd
Jason Swails
(Mon Aug 09 2010 - 12:57:40 PDT)
Re: [AMBER] error when compiling pmemd
Jorgen Simonsen
(Mon Aug 09 2010 - 23:55:56 PDT)
Re: [AMBER] error when compiling pmemd
Jason Swails
(Tue Aug 10 2010 - 06:05:14 PDT)
Re: [AMBER] error when compiling pmemd
Jorgen Simonsen
(Tue Aug 10 2010 - 09:37:08 PDT)
Re: [AMBER] error when compiling pmemd
Ross Walker
(Tue Aug 10 2010 - 10:35:28 PDT)
Re: [AMBER] error when compiling pmemd
Jorgen Simonsen
(Tue Aug 10 2010 - 11:14:43 PDT)
Re: [AMBER] error when compiling pmemd
Daniel Roe
(Tue Aug 10 2010 - 11:21:32 PDT)
Re: [AMBER] error when compiling pmemd
Ross Walker
(Tue Aug 10 2010 - 11:32:07 PDT)
Re: [AMBER] error when compiling pmemd
Jorgen Simonsen
(Tue Aug 10 2010 - 11:37:19 PDT)
[AMBER] question about empirical valence bond theory
Ganesh Kamath
(Mon Aug 09 2010 - 07:06:38 PDT)
[AMBER] using nab to create peptides and minimise
Alan
(Mon Aug 09 2010 - 07:32:33 PDT)
Re: [AMBER] using nab to create peptides and minimise
case
(Mon Aug 09 2010 - 07:54:15 PDT)
[AMBER] SASA over trajectory
Beale, John
(Mon Aug 09 2010 - 07:58:22 PDT)
Re: [AMBER] SASA over trajectory
Carlos Simmerling
(Mon Aug 09 2010 - 08:01:06 PDT)
[AMBER] Amber: saveamberparm error
Karan Mehra
(Mon Aug 09 2010 - 11:49:16 PDT)
Re: [AMBER] Amber: saveamberparm error
Bill Ross
(Mon Aug 09 2010 - 12:04:43 PDT)
Re: [AMBER] Amber: saveamberparm error
case
(Tue Aug 10 2010 - 04:48:24 PDT)
Re: [AMBER] Amber: saveamberparm error
Karan Mehra
(Wed Aug 11 2010 - 12:38:11 PDT)
Re: [AMBER] Amber: saveamberparm error
case
(Wed Aug 11 2010 - 12:47:49 PDT)
[AMBER] Name for Glucosamine
Shubhra Gupta
(Mon Aug 09 2010 - 22:39:17 PDT)
Re: [AMBER] Name for Glucosamine
Shubhra Gupta
(Tue Aug 10 2010 - 05:21:52 PDT)
Re: [AMBER] Name for Glucosamine
Lachele Foley (Lists)
(Tue Aug 10 2010 - 08:16:42 PDT)
[AMBER] AMBER ff02 r1
Neha Gandhi
(Tue Aug 10 2010 - 02:14:08 PDT)
[AMBER] Resource for trying out various GPU setups with AMBER
Ross Walker
(Tue Aug 10 2010 - 08:26:20 PDT)
[AMBER] restrain group specification for GPU
Qizhi Cui
(Tue Aug 10 2010 - 08:40:11 PDT)
Re: [AMBER] restrain group specification for GPU
Scott Le Grand
(Tue Aug 10 2010 - 09:33:08 PDT)
Re: [AMBER] restrain group specification for GPU
Bill Ross
(Tue Aug 10 2010 - 09:59:08 PDT)
Re: [AMBER] restrain group specification for GPU
Qizhi Cui
(Tue Aug 10 2010 - 12:59:37 PDT)
Re: [AMBER] restrain group specification for GPU
Ross Walker
(Tue Aug 10 2010 - 10:30:02 PDT)
Re: [AMBER] restrain group specification for GPU
Qizhi Cui
(Tue Aug 10 2010 - 15:26:39 PDT)
Re: [AMBER] restrain group specification for GPU
Scott Le Grand
(Tue Aug 10 2010 - 17:15:20 PDT)
Re: [AMBER] restrain group specification for GPU
Scott Le Grand
(Wed Aug 11 2010 - 08:32:30 PDT)
[AMBER] determining closest water molecules
Beale, John
(Tue Aug 10 2010 - 08:51:53 PDT)
Re: [AMBER] determining closest water molecules
Thomas Cheatham III
(Tue Aug 10 2010 - 09:26:05 PDT)
[AMBER] simulation output for explicit and implicit model
Yan Gao
(Tue Aug 10 2010 - 15:32:27 PDT)
Re: [AMBER] simulation output for explicit and implicit model
Jason Swails
(Tue Aug 10 2010 - 15:45:17 PDT)
[AMBER] simulation output for explicit and implicit model--please disregard the previous message
Yan Gao
(Tue Aug 10 2010 - 15:43:57 PDT)
Re: [AMBER] simulation output for explicit and implicit model--please disregard the previous message
Bill Ross
(Tue Aug 10 2010 - 16:11:48 PDT)
[AMBER] nonbond interactions
Philippe Pinard
(Tue Aug 10 2010 - 15:46:17 PDT)
Re: [AMBER] nonbond interactions
Jason Swails
(Tue Aug 10 2010 - 17:34:52 PDT)
[AMBER] BUG and FIX: pmemd crashes when vlimit exceeded
Don.Bashford.stjude.org
(Tue Aug 10 2010 - 17:46:58 PDT)
Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded
Robert Duke
(Tue Aug 10 2010 - 18:15:32 PDT)
Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. .
Don.Bashford.stjude.org
(Wed Aug 11 2010 - 14:29:48 PDT)
Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. .
Jason Swails
(Wed Aug 11 2010 - 14:45:41 PDT)
Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. .. .
Don.Bashford.stjude.org
(Thu Aug 12 2010 - 12:19:11 PDT)
Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. .. .
Jason Swails
(Thu Aug 12 2010 - 12:27:51 PDT)
Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. .
Robert Duke
(Thu Aug 12 2010 - 07:03:53 PDT)
[AMBER] How to change temperature in mm_pbsa.pl script
pxq
(Tue Aug 10 2010 - 18:28:29 PDT)
Re: [AMBER] How to change temperature in mm_pbsa.pl script
Jason Swails
(Wed Aug 11 2010 - 08:03:06 PDT)
Re: [AMBER] How to change temperature in mm_pbsa.pl script
pxq
(Thu Aug 12 2010 - 07:52:49 PDT)
Re: [AMBER] How to change temperature in mm_pbsa.pl script
Bill Miller III
(Thu Aug 12 2010 - 08:04:01 PDT)
[AMBER] constant volume
Jorgen Simonsen
(Wed Aug 11 2010 - 01:06:26 PDT)
[AMBER] How to define "generalized distance coordinate restraint" in AMBER10?
Catein Catherine
(Wed Aug 11 2010 - 02:55:02 PDT)
Re: [AMBER] How to define "generalized distance coordinate restraint" in AMBER10?
Jason Swails
(Wed Aug 11 2010 - 05:46:42 PDT)
Re: [AMBER] How to define "generalized distance coordinate restraint" in AMBER10?
Catein Catherine
(Thu Aug 12 2010 - 02:57:55 PDT)
Re: [AMBER] How to define "generalized distance coordinate restraint" in AMBER10?
Jason Swails
(Thu Aug 12 2010 - 04:40:00 PDT)
Re: [AMBER] constant volume
case
(Wed Aug 11 2010 - 04:41:39 PDT)
Re: [AMBER] constant volume
Andrew Purkiss-Trew
(Wed Aug 11 2010 - 05:30:56 PDT)
Re: [AMBER] constant volume
Jorgen Simonsen
(Wed Aug 11 2010 - 05:34:02 PDT)
Re: [AMBER] constant volume
Jorgen Simonsen
(Wed Aug 11 2010 - 05:45:27 PDT)
[AMBER] test $AMBERHOME/AmberTools/test/sqm/nma/Run: check_slko_files.x should be executable
Alan
(Wed Aug 11 2010 - 02:52:49 PDT)
Re: [AMBER] test $AMBERHOME/AmberTools/test/sqm/nma/Run: check_slko_files.x should be executable
Andreas Goetz
(Wed Aug 11 2010 - 03:03:28 PDT)
[AMBER] query on invoking ff99SB and ff99
Bala subramanian
(Wed Aug 11 2010 - 08:35:00 PDT)
Re: [AMBER] query on invoking ff99SB and ff99
Jason Swails
(Wed Aug 11 2010 - 09:00:05 PDT)
Re: [AMBER] query on invoking ff99SB and ff99
case
(Wed Aug 11 2010 - 09:12:30 PDT)
Re: [AMBER] query on invoking ff99SB and ff99
Alan
(Thu Aug 12 2010 - 03:11:52 PDT)
Re: [AMBER] query on invoking ff99SB and ff99
case
(Thu Aug 12 2010 - 04:51:44 PDT)
Re: [AMBER] query on invoking ff99SB and ff99
Alan
(Thu Aug 12 2010 - 05:23:44 PDT)
Re: [AMBER] query on invoking ff99SB and ff99
case
(Thu Aug 12 2010 - 06:49:25 PDT)
Re: [AMBER] query on invoking ff99SB and ff99
Bill Ross
(Wed Aug 11 2010 - 10:26:50 PDT)
[AMBER] NMR refinement = increase in RMSD
Andrew Olson
(Wed Aug 11 2010 - 08:59:55 PDT)
Re: [AMBER] NMR refinement = increase in RMSD
case
(Fri Aug 13 2010 - 04:39:28 PDT)
[AMBER] drawing sphere in each frame and update
Sun, Yufang
(Wed Aug 11 2010 - 13:31:20 PDT)
Re: [AMBER] drawing sphere in each frame and update
steinbrt.rci.rutgers.edu
(Thu Aug 12 2010 - 00:10:15 PDT)
[AMBER] snapshots
Philippe Pinard
(Wed Aug 11 2010 - 15:30:48 PDT)
Re: [AMBER] snapshots
arikcohen
(Wed Aug 11 2010 - 15:33:47 PDT)
Re: [AMBER] snapshots
Jason Swails
(Wed Aug 11 2010 - 16:27:41 PDT)
[AMBER] Bug in MMPBSA.py.MPI
Matthias Negri
(Wed Aug 11 2010 - 17:05:36 PDT)
Re: [AMBER] Bug in MMPBSA.py.MPI
Jason Swails
(Wed Aug 11 2010 - 18:53:01 PDT)
[AMBER] Ionic Strength Limits for MMPBSA
Hopkins, Robert
(Wed Aug 11 2010 - 15:33:28 PDT)
[AMBER] How to change fillratio in mm_pbsa.pl
pxq
(Thu Aug 12 2010 - 07:59:13 PDT)
Re: [AMBER] How to change fillratio in mm_pbsa.pl
Jason Swails
(Thu Aug 12 2010 - 08:04:04 PDT)
Re: [AMBER] Installation_problem_Ambertools1.4_in Mac OSX
Raman Parkesh
(Thu Aug 12 2010 - 11:18:39 PDT)
Re: [AMBER] Installation_problem_Ambertools1.4_in Mac OSX
Jason Swails
(Thu Aug 12 2010 - 11:32:26 PDT)
Re: [AMBER] Installation_problem_Ambertools1.4_in Mac OSX
Raman Parkesh
(Thu Aug 12 2010 - 11:39:49 PDT)
[AMBER] gbsa in pmemd
Yi Xue
(Thu Aug 12 2010 - 14:00:57 PDT)
Re: [AMBER] gbsa in pmemd
Ross Walker
(Thu Aug 12 2010 - 16:48:12 PDT)
[AMBER] How to define center of mass for two separate residues in the restraint file?
Catein Catherine
(Thu Aug 12 2010 - 20:04:09 PDT)
Re: [AMBER] How to define center of mass for two separate residues in the restraint file?
Jason Swails
(Thu Aug 12 2010 - 20:18:19 PDT)
[AMBER] Double bonds ?
Marek Maly
(Tue Aug 17 2010 - 10:15:14 PDT)
Re: [AMBER] Double bonds ?
case
(Tue Aug 17 2010 - 15:18:00 PDT)
Re: [AMBER] Double bonds ?
Marek Maly
(Wed Aug 18 2010 - 04:55:29 PDT)
[AMBER] Trivial syntax problem ?
Marek Maly
(Wed Aug 18 2010 - 13:29:43 PDT)
Re: [AMBER] Trivial syntax problem ?
case
(Wed Aug 18 2010 - 18:33:27 PDT)
[AMBER] How to define twist angle with DOC?
Catein Catherine
(Wed Aug 18 2010 - 21:26:44 PDT)
[AMBER] Extremely high activation energy was found for a PMF. Any potential source of errors?
Catein Catherine
(Wed Aug 18 2010 - 21:32:46 PDT)
Re: [AMBER] Extremely high activation energy was found for a PMF. Any potential source of errors?
Jason Swails
(Wed Aug 18 2010 - 23:13:05 PDT)
Re: [AMBER] Trivial syntax problem ?
Marek Maly
(Thu Aug 19 2010 - 09:50:05 PDT)
[AMBER] mm_pbsa analysis failure
Sangita Kachhap
(Fri Aug 13 2010 - 04:36:49 PDT)
Re: [AMBER] mm_pbsa analysis failure
Anselm Horn
(Fri Aug 13 2010 - 05:17:26 PDT)
[AMBER] Query regarding radius of H atoms of TIP3 water model
sunita gupta
(Fri Aug 13 2010 - 05:52:02 PDT)
Re: [AMBER] Query regarding radius of H atoms of TIP3 water model
case
(Fri Aug 13 2010 - 06:53:41 PDT)
[AMBER] problem of NM calculations
fancy2012
(Fri Aug 13 2010 - 06:01:27 PDT)
Re: [AMBER] problem of NM calculations
Jason Swails
(Fri Aug 13 2010 - 12:50:29 PDT)
Re: [AMBER] problem of NM calculations
fancy2012
(Sat Aug 14 2010 - 01:31:01 PDT)
Re: [AMBER] problem of NM calculations
fancy2012
(Sun Aug 15 2010 - 02:37:52 PDT)
[AMBER] makeCHIR_RST and proline
Jorgen Simonsen
(Fri Aug 13 2010 - 06:53:37 PDT)
[AMBER] Deleting bonds in sleap
Ben Roberts
(Fri Aug 13 2010 - 12:29:33 PDT)
Re: [AMBER] Deleting bonds in sleap
case
(Fri Aug 13 2010 - 12:51:47 PDT)
Re: [AMBER] Deleting bonds in sleap
Ben Roberts
(Fri Aug 13 2010 - 13:08:54 PDT)
Re: [AMBER] Deleting bonds in sleap
Andreas Goetz
(Fri Aug 13 2010 - 13:13:49 PDT)
Re: [AMBER] Deleting bonds in sleap
Ben Roberts
(Fri Aug 13 2010 - 13:40:02 PDT)
Re: [AMBER] Deleting bonds in sleap
case
(Sat Aug 14 2010 - 06:20:09 PDT)
[AMBER] How to include parmbsc0 force field in preparing prmtop/inpcrd files?
Catein Catherine
(Sat Aug 14 2010 - 20:52:09 PDT)
Re: [AMBER] How to include parmbsc0 force field in preparing prmtop/inpcrd files?
Paul S. Nerenberg
(Sat Aug 14 2010 - 23:39:45 PDT)
Re: [AMBER] How to include parmbsc0 force field in preparing prmtop/inpcrd files?
Catein Catherine
(Sun Aug 15 2010 - 22:44:22 PDT)
[AMBER] how to overcome the memory issues in mm-gbsa calculation for DS analysis?
Catein Catherine
(Mon Aug 16 2010 - 02:36:11 PDT)
Re: [AMBER] Deleting bonds in sleap
Ben Roberts
(Mon Aug 16 2010 - 15:13:43 PDT)
Re: [AMBER] Deleting bonds in sleap
Bill Ross
(Fri Aug 13 2010 - 13:19:03 PDT)
Re: [AMBER] Deleting bonds in sleap
Ben Roberts
(Fri Aug 13 2010 - 15:45:41 PDT)
Re: [AMBER] random number seed - range
Hopkins, Robert
(Fri Aug 13 2010 - 14:03:53 PDT)
Re: [AMBER] random number seed - range
Robert Duke
(Fri Aug 13 2010 - 14:40:35 PDT)
Re: [AMBER] random number seed - range
Paul S. Nerenberg
(Fri Aug 13 2010 - 14:58:55 PDT)
Re: [AMBER] random number seed - range
Ross Walker
(Fri Aug 13 2010 - 14:55:20 PDT)
Re: [AMBER] random number seed - range
Robert Duke
(Fri Aug 13 2010 - 14:59:42 PDT)
Re: [AMBER] random number seed - range
Ross Walker
(Fri Aug 13 2010 - 15:08:39 PDT)
Re: [AMBER] random number seed - range
Robert Duke
(Fri Aug 13 2010 - 15:05:34 PDT)
Re: [AMBER] random number seed - range
Dean Cuebas
(Fri Aug 13 2010 - 15:16:27 PDT)
Re: [AMBER] random number seed - range
Ross Walker
(Fri Aug 13 2010 - 15:22:11 PDT)
Re: [AMBER] random number seed - range
Ross Walker
(Fri Aug 13 2010 - 15:16:43 PDT)
[AMBER] regarding random number generator
Sangita Kachhap
(Sat Aug 14 2010 - 09:07:41 PDT)
Re: [AMBER] regarding random number generator
Ross Walker
(Sat Aug 14 2010 - 11:28:22 PDT)
Re: [AMBER] regarding random number generator
Sangita Kachhap
(Sat Aug 14 2010 - 12:22:34 PDT)
[AMBER] AmberTools and OS X
John McGuigan
(Sat Aug 14 2010 - 22:04:53 PDT)
Re: [AMBER] AmberTools and OS X
Paul S. Nerenberg
(Sat Aug 14 2010 - 23:45:46 PDT)
Re: [AMBER] AmberTools and OS X
John McGuigan
(Sun Aug 15 2010 - 13:44:40 PDT)
[AMBER] How to identify water molecules at the interface ?
Amor San Juan
(Sun Aug 15 2010 - 20:51:47 PDT)
Re: [AMBER] How to identify water molecules at the interface ?
Jason Swails
(Mon Aug 16 2010 - 05:59:25 PDT)
Re: [AMBER] How to identify water molecules at the interface ? follow up ....
Amor San Juan
(Sun Aug 15 2010 - 23:19:59 PDT)
Re: [AMBER] How to identify water molecules at the interface ? follow up ....
Jason Swails
(Mon Aug 16 2010 - 06:03:42 PDT)
[AMBER] Creating new topology file from close.mdcrd file
Amor San Juan
(Tue Aug 17 2010 - 02:42:40 PDT)
[AMBER] How to find the most important drug dissociation pathway theoretically? PMF?
Catein Catherine
(Tue Aug 17 2010 - 04:00:31 PDT)
Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF?
Jason Swails
(Tue Aug 17 2010 - 05:56:29 PDT)
Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF?
Catein Catherine
(Tue Aug 17 2010 - 08:36:35 PDT)
Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF?
Jason Swails
(Tue Aug 17 2010 - 09:04:01 PDT)
Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF?
Daniel Sindhikara
(Tue Aug 17 2010 - 09:04:53 PDT)
Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF?
Jason Swails
(Tue Aug 17 2010 - 10:49:53 PDT)
Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF?
Balazs Jojart
(Tue Aug 17 2010 - 12:49:42 PDT)
Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF?
danglena1411.gmail.com
(Wed Aug 18 2010 - 00:40:55 PDT)
Re: [AMBER] Creating new topology file from close.mdcrd file
Jason Swails
(Tue Aug 17 2010 - 05:52:18 PDT)
[AMBER] Cut-off distance "in Closest" command of ptraj
Amor San Juan
(Tue Aug 17 2010 - 22:35:36 PDT)
Re: [AMBER] Cut-off distance "in Closest" command of ptraj
Jason Swails
(Wed Aug 18 2010 - 06:43:32 PDT)
Re: [AMBER] Cut-off distance "in Closest" command of ptraj
Amor San Juan
(Thu Aug 19 2010 - 00:14:28 PDT)
Re: [AMBER] Cut-off distance "in Closest" command of ptraj
Jason Swails
(Thu Aug 19 2010 - 07:04:56 PDT)
[AMBER] PTRAJ: closest & strip in one script or separate
Amor San Juan
(Fri Aug 20 2010 - 02:33:50 PDT)
Re: [AMBER] PTRAJ: closest & strip in one script or separate
Jason Swails
(Fri Aug 20 2010 - 05:03:24 PDT)
[AMBER] protonate
kamlesh sahu
(Mon Aug 16 2010 - 00:43:21 PDT)
Re: [AMBER] protonate
case
(Mon Aug 16 2010 - 04:41:15 PDT)
Re: [AMBER] protonate
kamlesh sahu
(Mon Aug 16 2010 - 08:21:02 PDT)
[AMBER] segmentation fault - ptrajin image familiar
Jorgen Simonsen
(Mon Aug 16 2010 - 01:01:25 PDT)
Re: [AMBER] segmentation fault - ptrajin image familiar
manikanthan bhavaraju
(Mon Aug 16 2010 - 01:56:33 PDT)
Re: [AMBER] segmentation fault - ptrajin image familiar
case
(Mon Aug 16 2010 - 04:45:06 PDT)
Re: [AMBER] segmentation fault - ptrajin image familiar
Daniel Roe
(Mon Aug 16 2010 - 05:18:12 PDT)
Re: [AMBER] segmentation fault - ptrajin image familiar
Jorgen Simonsen
(Mon Aug 16 2010 - 06:00:10 PDT)
Re: [AMBER] segmentation fault - ptrajin image familiar
Jason Swails
(Mon Aug 16 2010 - 06:06:18 PDT)
[AMBER] Configure gnu
P Bhattacharya
(Mon Aug 16 2010 - 07:03:01 PDT)
Re: [AMBER] Configure gnu
Daniel Roe
(Mon Aug 16 2010 - 07:18:16 PDT)
Re: [AMBER] Configure gnu
P Bhattacharya
(Mon Aug 16 2010 - 07:55:59 PDT)
[AMBER] Unit for Van der Waals and Electrostatic Eq.
Hector Chang
(Mon Aug 16 2010 - 08:26:55 PDT)
Re: [AMBER] Unit for Van der Waals and Electrostatic Eq.
Paul S. Nerenberg
(Mon Aug 16 2010 - 08:32:56 PDT)
Re: [AMBER] Unit for Van der Waals and Electrostatic Eq.
case
(Mon Aug 16 2010 - 08:37:15 PDT)
Re: [AMBER] Unit for Van der Waals and Electrostatic Eq.
Jason Swails
(Mon Aug 16 2010 - 11:48:32 PDT)
[AMBER] Adding lambda points less than 0.1 and greater than 0.9 in TI calculations
g t
(Mon Aug 16 2010 - 11:56:23 PDT)
Re: [AMBER] Adding lambda points less than 0.1 and greater than 0.9 in TI calculations
steinbrt.rci.rutgers.edu
(Mon Aug 16 2010 - 12:13:52 PDT)
Re: [AMBER] Adding lambda points less than 0.1 and greater than 0.9 in TI calculations
g t
(Thu Aug 19 2010 - 08:58:23 PDT)
[AMBER] single-point energy calculation on selected atoms
Yi Xue
(Mon Aug 16 2010 - 17:43:36 PDT)
Re: [AMBER] Creating new topology file from close.mdcrd file : SOLUTION found
Amor San Juan
(Tue Aug 17 2010 - 03:58:40 PDT)
[AMBER] Created a new atom named: H within residue: .R<NASP 1>
Jorgen Simonsen
(Tue Aug 17 2010 - 05:47:32 PDT)
Re: [AMBER] Created a new atom named: H within residue: .R<NASP 1>
case
(Tue Aug 17 2010 - 07:34:43 PDT)
[AMBER] Question about mdinfo file.
Mayank Daga
(Tue Aug 17 2010 - 08:10:26 PDT)
Re: [AMBER] Question about mdinfo file.
Jason Swails
(Tue Aug 17 2010 - 08:31:11 PDT)
Re: [AMBER] Question about mdinfo file.
Mayank Daga
(Tue Aug 17 2010 - 08:55:11 PDT)
Re: [AMBER] Question about mdinfo file.
Jason Swails
(Tue Aug 17 2010 - 09:00:16 PDT)
Re: [AMBER] Question about mdinfo file.
Mayank Daga
(Tue Aug 17 2010 - 09:42:21 PDT)
Re: [AMBER] Question about mdinfo file.
Ross Walker
(Tue Aug 17 2010 - 10:04:23 PDT)
Re: [AMBER] Question about mdinfo file.
Mayank Daga
(Tue Aug 17 2010 - 10:19:11 PDT)
Re: [AMBER] Question about mdinfo file.
Ross Walker
(Tue Aug 17 2010 - 10:39:18 PDT)
Re: [AMBER] Question about mdinfo file.
Mayank Daga
(Tue Aug 17 2010 - 11:41:02 PDT)
Re: [AMBER] Question about mdinfo file.
Ross Walker
(Tue Aug 17 2010 - 11:56:31 PDT)
Re: [AMBER] Question about mdinfo file.
Mayank Daga
(Tue Aug 17 2010 - 12:51:46 PDT)
Re: [AMBER] Question about mdinfo file.
Jason Swails
(Tue Aug 17 2010 - 13:02:52 PDT)
Re: [AMBER] Question about mdinfo file.
Ross Walker
(Tue Aug 17 2010 - 09:52:19 PDT)
Re: [AMBER] Question about mdinfo file.
Robert Duke
(Tue Aug 17 2010 - 08:49:38 PDT)
Re: [AMBER] Question about mdinfo file.
Robert Duke
(Tue Aug 17 2010 - 08:58:42 PDT)
Re: [AMBER] Question about mdinfo file.
Robert Duke
(Tue Aug 17 2010 - 10:08:06 PDT)
Re: [AMBER] Question about mdinfo file.
Robert Duke
(Tue Aug 17 2010 - 10:25:17 PDT)
[AMBER] amber ：FAD parameters and RESP charge
xqkong
(Tue Aug 17 2010 - 08:14:57 PDT)
[AMBER] parmbsc0
Jason Swails
(Tue Aug 17 2010 - 12:25:23 PDT)
Re: [AMBER] parmbsc0
case
(Tue Aug 17 2010 - 15:21:31 PDT)
[AMBER] Diffusion coefficient in PTRAJ.
Hoshin Kim
(Tue Aug 17 2010 - 00:52:41 PDT)
Re: [AMBER] entropy calculations MMPBSA.py.MPI
Matthias Negri
(Tue Aug 17 2010 - 15:45:34 PDT)
[AMBER] combination of CPU + GPU for Amber 11
CHAMI F.
(Tue Aug 17 2010 - 16:39:10 PDT)
Re: [AMBER] combination of CPU + GPU for Amber 11
Ross Walker
(Tue Aug 17 2010 - 17:36:51 PDT)
Re: [AMBER] combination of CPU + GPU for Amber 11
CHAMI F.
(Wed Aug 18 2010 - 02:53:42 PDT)
Re: [AMBER] combination of CPU + GPU for Amber 11
CHAMI F.
(Wed Aug 18 2010 - 02:58:01 PDT)
[AMBER] (no subject)
xqkong
(Tue Aug 17 2010 - 17:47:28 PDT)
[AMBER] Error in snader execution
arikcohen
(Tue Aug 17 2010 - 18:53:00 PDT)
Re: [AMBER] Error in snader execution
Jason Swails
(Tue Aug 17 2010 - 19:11:40 PDT)
Re: [AMBER] Error in snader execution
arikcohen
(Wed Aug 18 2010 - 11:03:11 PDT)
[AMBER] MMPBSA Warnings
George Tzotzos
(Wed Aug 18 2010 - 00:56:45 PDT)
Re: [AMBER] MMPBSA Warnings
Bill Miller III
(Wed Aug 18 2010 - 04:28:08 PDT)
Re: [AMBER] MMPBSA Warnings
Jason Swails
(Wed Aug 18 2010 - 07:15:48 PDT)
[AMBER] Defining restraint by distance
Olotu Odunayo
(Wed Aug 18 2010 - 01:19:26 PDT)
[AMBER] antechamber issue with gasteiger
Alan
(Wed Aug 18 2010 - 01:41:20 PDT)
Re: [AMBER] antechamber issue with gasteiger
Jason Swails
(Wed Aug 18 2010 - 07:12:37 PDT)
Re: [AMBER] antechamber issue with gasteiger
Alan
(Wed Aug 18 2010 - 08:55:16 PDT)
Re: [AMBER] antechamber issue with gasteiger
Alan
(Tue Aug 24 2010 - 08:33:23 PDT)
Re: [AMBER] antechamber issue with gasteiger
Jason Swails
(Tue Aug 24 2010 - 08:39:54 PDT)
[AMBER] Calculating diffusion coefficient in PTRAJ
Hoshin Kim
(Tue Aug 17 2010 - 22:10:13 PDT)
[AMBER] FAD parameters and RESP charge
xqkong
(Wed Aug 18 2010 - 17:36:45 PDT)
Re: [AMBER] FAD parameters and RESP charge
Jason Swails
(Wed Aug 18 2010 - 17:54:28 PDT)
Re: [AMBER] FAD parameters and RESP charge
xqkong
(Wed Aug 18 2010 - 18:40:20 PDT)
[AMBER] MMPBSA.py error message.
Wookyung Yu
(Wed Aug 18 2010 - 21:55:25 PDT)
Re: [AMBER] MMPBSA.py error message.
Jason Swails
(Wed Aug 18 2010 - 23:07:35 PDT)
[AMBER] restart reimage
manikanthan bhavaraju
(Wed Aug 18 2010 - 23:24:01 PDT)
Re: [AMBER] restart reimage
Jason Swails
(Thu Aug 19 2010 - 07:07:32 PDT)
[AMBER] O2'methyl RNA
waleed zalloum
(Thu Aug 19 2010 - 05:37:25 PDT)
Re: [AMBER] O2'methyl RNA
Jason Swails
(Thu Aug 19 2010 - 07:23:41 PDT)
Re: [AMBER] O2'methyl RNA
waleed zalloum
(Thu Aug 19 2010 - 07:34:26 PDT)
Re: [AMBER] O2'methyl RNA
Jason Swails
(Thu Aug 19 2010 - 08:04:14 PDT)
Re: [AMBER] O2'methyl RNA
waleed zalloum
(Fri Aug 20 2010 - 07:05:08 PDT)
[AMBER] Unit for Van der Waals and Electrostatic Eq.
Hector Chang
(Thu Aug 19 2010 - 09:34:20 PDT)
Re: [AMBER] Unit for Van der Waals and Electrostatic Eq.
Bill Ross
(Thu Aug 19 2010 - 09:42:04 PDT)
[AMBER] Basic question: is protonation of receptor amino acid recidues needed for MD calculations?
George Tzotzos
(Thu Aug 19 2010 - 09:45:33 PDT)
Re: [AMBER] Basic question: is protonation of receptor amino acid recidues needed for MD calculations?
Jason Swails
(Thu Aug 19 2010 - 09:51:21 PDT)
Re: [AMBER] Basic question: is protonation of receptor amino acid recidues needed for MD calculations?
Hegazy,Lamees
(Thu Aug 19 2010 - 09:59:22 PDT)
[AMBER] MM-PBSA fails with a division by zero error
Sasha Buzko
(Thu Aug 19 2010 - 11:32:54 PDT)
Re: [AMBER] MM-PBSA fails with a division by zero error
Jason Swails
(Thu Aug 19 2010 - 12:19:52 PDT)
[AMBER] Syntax for using RRES and LRES to turn on per residue decomposition (idecomp = 2) in a TI calculation
g t
(Thu Aug 19 2010 - 12:05:59 PDT)
Re: [AMBER] Syntax for using RRES and LRES to turn on per residue decomposition (idecomp = 2) in a TI calculation
Jason Swails
(Thu Aug 19 2010 - 12:29:09 PDT)
Re: [AMBER] Syntax for using RRES and LRES to turn on per residue decomposition (idecomp = 2) in a TI calculation
g t
(Thu Aug 19 2010 - 12:45:24 PDT)
[AMBER] How to run NED in amber10? PIMD or MPI or LES.MPI?
Catein Catherine
(Fri Aug 20 2010 - 02:39:44 PDT)
Re: [AMBER] How to run NED in amber10? PIMD or MPI or LES.MPI?
Jason Swails
(Fri Aug 20 2010 - 05:06:35 PDT)
Re: [AMBER] How to run NED in amber10? PIMD or MPI or LES.MPI?
Carlos Simmerling
(Fri Aug 20 2010 - 09:25:05 PDT)
[AMBER] PBC
arikcohen
(Thu Aug 19 2010 - 17:35:21 PDT)
Re: [AMBER] PBC
Jason Swails
(Fri Aug 20 2010 - 04:31:52 PDT)
Re: [AMBER] PBC
arikcohen
(Fri Aug 20 2010 - 12:43:24 PDT)
Re: [AMBER] PBC
Jason Swails
(Fri Aug 20 2010 - 12:49:21 PDT)
Re: [AMBER] PBC
arikcohen
(Fri Aug 20 2010 - 14:36:50 PDT)
Re: [AMBER] PBC
case
(Fri Aug 20 2010 - 13:38:01 PDT)
Re: [AMBER] PBC
arikcohen
(Fri Aug 20 2010 - 14:38:18 PDT)
[AMBER] bond energy spikes in conjugent gradient minimization
Vickie Roberts
(Fri Aug 20 2010 - 00:55:21 PDT)
Re: [AMBER] bond energy spikes in conjugent gradient minimization
case
(Fri Aug 20 2010 - 04:48:47 PDT)
Re: [AMBER] bond energy spikes in conjugent gradient minimization
Jason Swails
(Fri Aug 20 2010 - 04:56:37 PDT)
[AMBER] mm_pbsa failure
Sangita Kachhap
(Fri Aug 20 2010 - 03:58:34 PDT)
[AMBER] sander.MPI error
George Tzotzos
(Fri Aug 20 2010 - 06:43:41 PDT)
Re: [AMBER] sander.MPI error
case
(Fri Aug 20 2010 - 07:03:19 PDT)
Re: [AMBER] sander.MPI error
George Tzotzos
(Fri Aug 20 2010 - 07:31:40 PDT)
Re: [AMBER] sander.MPI error
Jason Swails
(Fri Aug 20 2010 - 08:37:20 PDT)
[AMBER] exchange probability in remd
Lekpa Duukori
(Fri Aug 20 2010 - 10:14:40 PDT)
Re: [AMBER] exchange probability in remd
Carlos Simmerling
(Fri Aug 20 2010 - 10:18:19 PDT)
Re: [AMBER] exchange probability in remd
Lekpa Duukori
(Fri Aug 20 2010 - 10:25:58 PDT)
[AMBER] too many titratable groups
piotrek.vega.umcs.lublin.pl
(Fri Aug 20 2010 - 11:26:42 PDT)
Re: [AMBER] too many titratable groups
Jason Swails
(Fri Aug 20 2010 - 11:43:20 PDT)
[AMBER] Implicit Solvent Equation
Hector Chang
(Fri Aug 20 2010 - 13:17:44 PDT)
Re: [AMBER] Implicit Solvent Equation
case
(Sun Aug 22 2010 - 05:58:17 PDT)
[AMBER] About dipoles
hong-bin Xie
(Fri Aug 20 2010 - 14:32:59 PDT)
Re: [AMBER] About dipoles
Ross Walker
(Mon Aug 23 2010 - 08:46:31 PDT)
Re: [AMBER] About dipoles
hong-bin Xie
(Mon Aug 23 2010 - 09:08:47 PDT)
Re: [AMBER] About dipoles
Ross Walker
(Mon Aug 23 2010 - 09:19:37 PDT)
Re: [AMBER] About dipoles
hong-bin Xie
(Mon Aug 23 2010 - 09:25:44 PDT)
Re: [AMBER] About dipoles
Ross Walker
(Mon Aug 23 2010 - 12:16:19 PDT)
Re: [AMBER] About dipoles
Ross Walker
(Mon Aug 23 2010 - 11:32:55 PDT)
Re: [AMBER] About dipoles
Adrian Roitberg
(Mon Aug 23 2010 - 11:38:12 PDT)
[AMBER] FEP help
William Flak
(Fri Aug 20 2010 - 21:50:14 PDT)
Re: [AMBER] FEP help
case
(Sat Aug 21 2010 - 06:19:02 PDT)
[AMBER] protein protein interaction
manikanthan bhavaraju
(Fri Aug 20 2010 - 22:28:58 PDT)
Re: [AMBER] protein protein interaction
case
(Sat Aug 21 2010 - 06:20:29 PDT)
Re: [AMBER] protein protein interaction
manikanthan bhavaraju
(Sun Aug 22 2010 - 12:46:43 PDT)
Re: [AMBER] protein protein interaction
Carlos Simmerling
(Sun Aug 22 2010 - 13:08:41 PDT)
Re: [AMBER] protein protein interaction
manikanthan bhavaraju
(Sun Aug 22 2010 - 15:13:34 PDT)
Re: [AMBER] protein protein interaction
Carlos Simmerling
(Sun Aug 22 2010 - 15:33:02 PDT)
[AMBER] hydration status
monica.imtech.res.in
(Sat Aug 21 2010 - 07:14:33 PDT)
[AMBER] volume in a cavity
Ganesh Kamath
(Sat Aug 21 2010 - 07:21:19 PDT)
[AMBER] questions for the different atom style and resp charge
xqkong
(Sun Aug 22 2010 - 01:59:48 PDT)
Re: [AMBER] questions for the different atom style and resp charge
xqkong
(Sun Aug 22 2010 - 03:11:50 PDT)
Re: [AMBER] questions for the different atom style and resp charge
FyD
(Mon Aug 23 2010 - 00:28:37 PDT)
Re: [AMBER] questions for the different atom style and resp charge
xqkong
(Mon Aug 23 2010 - 08:00:11 PDT)
Re: [AMBER] questions for the different atom style and resp charge
FyD
(Mon Aug 23 2010 - 12:22:06 PDT)
Re: [AMBER] questions for the different atom style and resp charge
xqkong
(Mon Aug 23 2010 - 18:31:21 PDT)
Re: [AMBER] questions for the different atom style and resp charge
FyD
(Mon Aug 23 2010 - 23:08:36 PDT)
Re: [AMBER] questions for the different atom style and resp charge
xqkong
(Mon Aug 23 2010 - 18:46:38 PDT)
Re: [AMBER] questions for the different atom style and resp charge
xqkong
(Mon Aug 23 2010 - 23:44:10 PDT)
Re: [AMBER] questions for the different atom style and resp charge
FyD
(Tue Aug 24 2010 - 12:01:05 PDT)
Re: [AMBER] questions for the different atom style and resp charge
xqkong
(Wed Aug 25 2010 - 02:53:30 PDT)
[AMBER] mm_pbsa ERROR
Sangita Kachhap
(Sun Aug 22 2010 - 03:52:49 PDT)
Re: [AMBER] AMBER question
Ross Walker
(Sun Aug 22 2010 - 07:52:32 PDT)
[AMBER] Dipole moment in QM/MM
hong-bin Xie
(Sun Aug 22 2010 - 10:14:48 PDT)
[AMBER] entropies from nmode in MMPBSA
Cristina Sisu
(Sun Aug 22 2010 - 17:28:24 PDT)
Re: [AMBER] entropies from nmode in MMPBSA
Bill Miller III
(Mon Aug 23 2010 - 03:48:22 PDT)
Re: [AMBER] entropies from nmode in MMPBSA
Cristina Sisu
(Mon Aug 23 2010 - 04:14:03 PDT)
[AMBER] Equilibration
M. Reza Ganjalikhany
(Mon Aug 23 2010 - 02:01:39 PDT)
Re: [AMBER] Equilibration
Gustavo Seabra
(Mon Aug 23 2010 - 07:26:59 PDT)
Re: [AMBER] Equilibration
M. Reza Ganjalikhany
(Mon Aug 23 2010 - 13:03:15 PDT)
Re: [AMBER] Equilibration
manikanthan bhavaraju
(Mon Aug 23 2010 - 15:18:36 PDT)
Re: [AMBER] Equilibration
Gustavo Seabra
(Mon Aug 23 2010 - 18:28:29 PDT)
Re: [AMBER] Equilibration
M. Reza Ganjalikhany
(Tue Aug 24 2010 - 00:48:38 PDT)
Re: [AMBER] Equilibration
Gustavo Seabra
(Tue Aug 24 2010 - 06:40:35 PDT)
[AMBER] how we increase the number of sugar molecule in a system
subrata paul
(Mon Aug 23 2010 - 02:02:50 PDT)
Re: [AMBER] how we increase the number of sugar molecule in a system
Sushil Mishra
(Mon Aug 23 2010 - 02:10:39 PDT)
Re: [AMBER] how we increase the number of sugar molecule in a system
subrata paul
(Mon Aug 23 2010 - 02:46:11 PDT)
[AMBER] Dipole moment calculation from ptraj
Siddharth Rastogi
(Mon Aug 23 2010 - 02:33:46 PDT)
Re: [AMBER] Dipole moment calculation from ptraj
case
(Mon Aug 23 2010 - 05:17:16 PDT)
[AMBER] Interaction energy_mm_pbsa
moitrayee.mbu.iisc.ernet.in
(Mon Aug 23 2010 - 03:17:52 PDT)
Re: [AMBER] Interaction energy_mm_pbsa
Bill Miller III
(Mon Aug 23 2010 - 03:58:44 PDT)
Re: [AMBER] Interaction energy_mm_pbsa
moitrayee.mbu.iisc.ernet.in
(Mon Aug 23 2010 - 04:15:07 PDT)
Re: [AMBER] Interaction energy_mm_pbsa
Bill Miller III
(Mon Aug 23 2010 - 04:20:51 PDT)
Re: [AMBER] Interaction energy_mm_pbsa
moitrayee.mbu.iisc.ernet.in
(Mon Aug 23 2010 - 04:33:13 PDT)
[AMBER] amber11: Applying restraint weights
George Tzotzos
(Mon Aug 23 2010 - 03:57:50 PDT)
Re: [AMBER] amber11: Applying restraint weights
Carlos Simmerling
(Mon Aug 23 2010 - 04:30:26 PDT)
Re: [AMBER] amber11: Applying restraint weights
case
(Mon Aug 23 2010 - 05:24:55 PDT)
[AMBER] ptraj "closest"
Amor San Juan
(Mon Aug 23 2010 - 04:10:11 PDT)
Re: [AMBER] ptraj "closest"
Daniel Roe
(Mon Aug 23 2010 - 07:07:17 PDT)
Re: [AMBER] ptraj "closest"
Amor San Juan
(Tue Aug 24 2010 - 04:32:30 PDT)
[AMBER] MMPBSA.py indexError
Amor San Juan
(Tue Aug 24 2010 - 04:53:30 PDT)
Re: [AMBER] MMPBSA.py indexError
Bill Miller III
(Tue Aug 24 2010 - 04:59:55 PDT)
Re: [AMBER] MMPBSA.py indexError
Jason Swails
(Tue Aug 24 2010 - 05:30:57 PDT)
Re: [AMBER] MMPBSA.py indexError
Amor San Juan
(Wed Aug 25 2010 - 02:09:53 PDT)
[AMBER] Water deeply buried for MMPBSA calculations
Amor San Juan
(Wed Aug 25 2010 - 03:54:54 PDT)
Re: [AMBER] Water deeply buried for MMPBSA calculations
Jason Swails
(Wed Aug 25 2010 - 04:19:55 PDT)
Re: [AMBER] Water deeply buried for MMPBSA calculations
Amor San Juan
(Thu Aug 26 2010 - 04:05:43 PDT)
[AMBER] [Fwd: Re: Interaction energy_mm_pbsa]
moitrayee.mbu.iisc.ernet.in
(Mon Aug 23 2010 - 04:35:40 PDT)
Re: [AMBER] [Fwd: Re: Interaction energy_mm_pbsa]
Bill Miller III
(Mon Aug 23 2010 - 04:37:31 PDT)
Re: [AMBER] [Fwd: Re: Interaction energy_mm_pbsa]
moitrayee.mbu.iisc.ernet.in
(Mon Aug 23 2010 - 04:47:21 PDT)
Re: [AMBER] [Fwd: Re: Interaction energy_mm_pbsa]
Jason Swails
(Mon Aug 23 2010 - 06:27:50 PDT)
Re: [AMBER] [Fwd: Re: Interaction energy_mm_pbsa]
moitrayee.mbu.iisc.ernet.in
(Tue Aug 24 2010 - 02:11:05 PDT)
[AMBER] slowly releasing restraint_wt force
Sangita Kachhap
(Mon Aug 23 2010 - 08:29:13 PDT)
[AMBER] calculation of volume of active site
Ganesh Kamath
(Mon Aug 23 2010 - 09:30:38 PDT)
Re: [AMBER] calculation of volume of active site
Jia Xu
(Mon Aug 23 2010 - 10:08:48 PDT)
Re: [AMBER] calculation of volume of active site
Peter Schmidtke
(Mon Aug 23 2010 - 10:15:41 PDT)
Re: [AMBER] calculation of volume of active site
Ganesh Kamath
(Mon Aug 23 2010 - 10:20:58 PDT)
Re: [AMBER] calculation of volume of active site
Peter Schmidtke
(Tue Aug 24 2010 - 03:03:14 PDT)
[AMBER] ACS Division of Computers in Chemistry: award applications due October 15
Carlos Simmerling
(Mon Aug 23 2010 - 10:06:16 PDT)
Re: [AMBER] ACS Division of Computers in Chemistry: award applications due October 15
Carlos Simmerling
(Mon Aug 23 2010 - 10:10:32 PDT)
Re: [AMBER] ACS Division of Computers in Chemistry: award applications due October 15
Carlos Simmerling
(Mon Aug 23 2010 - 10:33:01 PDT)
Re: [AMBER] ACS Division of Computers in Chemistry: award applications due October 15
Dima A Sabbah
(Mon Aug 23 2010 - 11:01:24 PDT)
[AMBER] Installing Amber9 on Ubuntu platform
Arun Gupta
(Mon Aug 23 2010 - 11:57:30 PDT)
Re: [AMBER] Installing Amber9 on Ubuntu platform
Jason Swails
(Mon Aug 23 2010 - 12:22:55 PDT)
Re: [AMBER] Installing Amber9 on Ubuntu platform
Bill Ross
(Mon Aug 23 2010 - 12:25:41 PDT)
Re: [AMBER] Installing Amber9 on Ubuntu platform
case
(Mon Aug 23 2010 - 12:27:59 PDT)
[AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails
Shulin Zhuang
(Mon Aug 23 2010 - 18:06:43 PDT)
Re: [AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails
Gustavo Seabra
(Mon Aug 23 2010 - 18:17:24 PDT)
Re: [AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails
Shulin Zhuang
(Mon Aug 23 2010 - 18:20:43 PDT)
Re: [AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails
case
(Tue Aug 24 2010 - 04:21:56 PDT)
Re: [AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails
Shulin Zhuang
(Tue Aug 24 2010 - 05:32:19 PDT)
[AMBER] solvateBox - what is the suitable value for distance?
colvin
(Mon Aug 23 2010 - 18:23:43 PDT)
Re: [AMBER] solvateBox - what is the suitable value for distance?
case
(Tue Aug 24 2010 - 09:40:23 PDT)
Re: [AMBER] solvateBox - what is the suitable value for distance?
Brent Krueger
(Tue Aug 24 2010 - 10:07:10 PDT)
[AMBER] Running AMBER on a GPU Cluster.
Mayank Daga
(Mon Aug 23 2010 - 18:35:30 PDT)
Re: [AMBER] Running AMBER on a GPU Cluster.
Sasha Buzko
(Tue Aug 24 2010 - 10:13:40 PDT)
Re: [AMBER] Running AMBER on a GPU Cluster.
Ross Walker
(Tue Aug 24 2010 - 10:34:15 PDT)
Re: [AMBER] Running AMBER on a GPU Cluster.
Mayank Daga
(Tue Aug 24 2010 - 10:56:39 PDT)
[AMBER] flying out
William Flak
(Mon Aug 23 2010 - 21:02:38 PDT)
Re: [AMBER] flying out
manikanthan bhavaraju
(Mon Aug 23 2010 - 21:14:43 PDT)
Re: [AMBER] flying out
case
(Tue Aug 24 2010 - 04:28:20 PDT)
[AMBER] acceptance ration in rem.log
Toshifumi Yui
(Mon Aug 23 2010 - 22:12:35 PDT)
Re: [AMBER] acceptance ration in rem.log
Carlos Simmerling
(Tue Aug 24 2010 - 05:47:18 PDT)
[AMBER] Quantifying Hydrophobic interaction
aneesh cna
(Mon Aug 23 2010 - 22:16:28 PDT)
Re: [AMBER] Quantifying Hydrophobic interaction
case
(Tue Aug 24 2010 - 04:32:17 PDT)
Re: [AMBER] Quantifying Hydrophobic interaction
aneesh cna
(Tue Aug 24 2010 - 06:23:53 PDT)
Re: [AMBER] Quantifying Hydrophobic interaction
case
(Tue Aug 24 2010 - 09:35:52 PDT)
[AMBER] loading MG.off (./MG.off is not a valid database)
Ehsan Habibi
(Tue Aug 24 2010 - 01:16:48 PDT)
Re: [AMBER] loading MG.off (./MG.off is not a valid database)
case
(Tue Aug 24 2010 - 04:37:54 PDT)
[AMBER] Packmol file cannot minimized
setyanto tri wahyudi
(Tue Aug 24 2010 - 03:34:10 PDT)
Re: [AMBER] Packmol file cannot minimized
Jason Swails
(Tue Aug 24 2010 - 04:39:50 PDT)
Re: [AMBER] Packmol file cannot minimized
case
(Tue Aug 24 2010 - 04:42:25 PDT)
Re: [AMBER] Packmol file cannot minimized
setyanto tri wahyudi
(Thu Aug 26 2010 - 00:02:17 PDT)
Re: [AMBER] Packmol file cannot minimized
case
(Thu Aug 26 2010 - 04:34:35 PDT)
Re: [AMBER] Packmol file cannot minimized
Jason Swails
(Thu Aug 26 2010 - 05:24:49 PDT)
[AMBER] Dipole moment calculation from ptraj
v.satish.iitg.ernet.in
(Tue Aug 24 2010 - 05:50:52 PDT)
Re: [AMBER] Dipole moment calculation from ptraj
Thomas Cheatham III
(Wed Aug 25 2010 - 09:09:12 PDT)
[AMBER] question on improper dihedrals
Jason Swails
(Tue Aug 24 2010 - 12:19:07 PDT)
Re: [AMBER] question on improper dihedrals
case
(Tue Aug 24 2010 - 12:55:57 PDT)
Re: [AMBER] question on improper dihedrals
Jason Swails
(Tue Aug 24 2010 - 13:04:10 PDT)
[AMBER] simulation of a restrained protein fragment + pmemd.cuda issues
Sasha Buzko
(Tue Aug 24 2010 - 17:09:06 PDT)
Re: [AMBER] simulation of a restrained protein fragment + pmemd.cuda issues
Ross Walker
(Wed Aug 25 2010 - 11:29:26 PDT)
Re: [AMBER] simulation of a restrained protein fragment +pmemd.cuda issues
Paul Mortenson
(Thu Aug 26 2010 - 02:33:09 PDT)
Re: [AMBER] simulation of a restrained protein fragment +pmemd.cuda issues
Ross Walker
(Thu Aug 26 2010 - 04:40:26 PDT)
[AMBER] average structre
William Flak
(Tue Aug 24 2010 - 18:58:48 PDT)
[AMBER] Tutorial 3: MM-PBSA
George Tzotzos
(Tue Aug 24 2010 - 23:46:29 PDT)
[AMBER] MMPBSA.py nmode
Amor San Juan
(Wed Aug 25 2010 - 02:40:02 PDT)
Re: [AMBER] MMPBSA.py nmode
Bill Miller III
(Wed Aug 25 2010 - 04:05:13 PDT)
Re: [AMBER] MMPBSA.py nmode
Amor San Juan
(Thu Aug 26 2010 - 03:36:39 PDT)
Re: [AMBER] MMPBSA.py nmode
Bill Miller III
(Thu Aug 26 2010 - 03:51:51 PDT)
Re: [AMBER] MMPBSA.py nmode
Amor San Juan
(Thu Aug 26 2010 - 04:18:57 PDT)
Re: [AMBER] MMPBSA.py nmode
Bill Miller III
(Thu Aug 26 2010 - 04:22:24 PDT)
Re: [AMBER] Tutorial 3: MM-PBSA
Jason Swails
(Wed Aug 25 2010 - 04:27:22 PDT)
[AMBER] To obtain academic license of AMBER 11 program package
sonali dhindwal
(Tue Aug 24 2010 - 23:57:25 PDT)
[AMBER] how we increase the number of sugar molecule in a system
subrata paul
(Wed Aug 25 2010 - 00:22:19 PDT)
Re: [AMBER] how we increase the number of sugar molecule in a system
Lachele Foley (Lists)
(Wed Aug 25 2010 - 06:42:37 PDT)
Re: [AMBER] how we increase the number of sugar molecule in a system
subrata paul
(Thu Aug 26 2010 - 01:50:59 PDT)
Re: [AMBER] how we increase the number of sugar molecule in a system
case
(Thu Aug 26 2010 - 04:38:04 PDT)
Re: [AMBER] how we increase the number of sugar molecule in a system
ros
(Thu Aug 26 2010 - 08:21:44 PDT)
Re: [AMBER] how we increase the number of sugar molecule in a system
Lachele Foley (Lists)
(Thu Aug 26 2010 - 09:16:53 PDT)
[AMBER] dipole moment of molecule of trans and cis azobenzene ?
Chih-Ying Lin
(Thu Aug 26 2010 - 10:01:58 PDT)
[AMBER] Enthalpy estimate
Lekpa Duukori
(Wed Aug 25 2010 - 12:39:35 PDT)
Re: [AMBER] Enthalpy estimate
Jason Swails
(Wed Aug 25 2010 - 13:40:08 PDT)
Re: [AMBER] Enthalpy estimate
Lekpa Duukori
(Wed Aug 25 2010 - 13:50:57 PDT)
Re: [AMBER] Enthalpy estimate
case
(Thu Aug 26 2010 - 04:48:37 PDT)
Re: [AMBER] Workaround for gfortran-4.1.2?
Richard Owczarzy
(Wed Aug 25 2010 - 12:51:15 PDT)
Re: [AMBER] Workaround for gfortran-4.1.2?
Jason Swails
(Wed Aug 25 2010 - 13:10:50 PDT)
Re: [AMBER] Workaround for gfortran-4.1.2?
Lachele Foley (Lists)
(Wed Aug 25 2010 - 15:18:11 PDT)
Re: [AMBER] Workaround for gfortran-4.1.2?
Marc Moreau
(Wed Aug 25 2010 - 21:23:49 PDT)
[AMBER] Parameter extraction
arikcohen
(Wed Aug 25 2010 - 13:01:14 PDT)
Re: [AMBER] Parameter extraction
Jason Swails
(Wed Aug 25 2010 - 13:16:07 PDT)
Re: [AMBER] Parameter extraction
arikcohen
(Wed Aug 25 2010 - 14:25:17 PDT)
[AMBER] To obtain academic license of AMBER 11 program package
sonali dhindwal
(Thu Aug 26 2010 - 03:47:59 PDT)
Re: [AMBER] To obtain academic license of AMBER 11 program package
case
(Thu Aug 26 2010 - 04:40:59 PDT)
Re: [AMBER] To obtain academic license of AMBER 11 program package
sonali dhindwal
(Thu Aug 26 2010 - 06:45:28 PDT)
[AMBER] Antechamber issue
P Bhattacharya
(Thu Aug 26 2010 - 09:07:59 PDT)
Re: [AMBER] Antechamber issue
case
(Thu Aug 26 2010 - 10:00:39 PDT)
Re: [AMBER] Antechamber issue
P Bhattacharya
(Thu Aug 26 2010 - 14:51:40 PDT)
Re: [AMBER] Antechamber issue
Jason Swails
(Thu Aug 26 2010 - 16:38:51 PDT)
Re: [AMBER] Antechamber issue
P Bhattacharya
(Fri Aug 27 2010 - 14:57:53 PDT)
Re: [AMBER] Antechamber issue
case
(Fri Aug 27 2010 - 18:34:31 PDT)
Re: [AMBER] Antechamber issue
P Bhattacharya
(Mon Aug 30 2010 - 08:58:38 PDT)
Re: [AMBER] Antechamber issue
Jason Swails
(Mon Aug 30 2010 - 09:21:16 PDT)
Re: [AMBER] Antechamber issue
P Bhattacharya
(Mon Aug 30 2010 - 10:12:12 PDT)
Re: [AMBER] Antechamber issue
P Bhattacharya
(Mon Aug 30 2010 - 14:22:29 PDT)
Re: [AMBER] Antechamber issue
David A. Case
(Mon Aug 30 2010 - 14:28:37 PDT)
Re: [AMBER] how we increase the number of sugar molecule in a system
FyD
(Thu Aug 26 2010 - 10:18:38 PDT)
[AMBER] vlimit and shake
manikanthan bhavaraju
(Thu Aug 26 2010 - 13:25:30 PDT)
Re: [AMBER] vlimit and shake
manikanthan bhavaraju
(Thu Aug 26 2010 - 13:45:50 PDT)
Re: [AMBER] vlimit and shake
Jason Swails
(Thu Aug 26 2010 - 18:31:00 PDT)
Re: [AMBER] vlimit and shake
manikanthan bhavaraju
(Thu Aug 26 2010 - 19:32:25 PDT)
Re: [AMBER] vlimit and shake
Daniel Roe
(Thu Aug 26 2010 - 22:31:56 PDT)
[AMBER] ptraj help
William Flak
(Thu Aug 26 2010 - 16:58:48 PDT)
Re: [AMBER] ptraj help
Jason Swails
(Thu Aug 26 2010 - 17:39:26 PDT)
Re: [AMBER] ptraj help
William Flak
(Thu Aug 26 2010 - 19:45:40 PDT)
[AMBER] cuda lauch time out error in Amber 11
Sergio R Aragon
(Thu Aug 26 2010 - 17:01:43 PDT)
Re: [AMBER] cuda lauch time out error in Amber 11
Sasha Buzko
(Thu Aug 26 2010 - 17:26:15 PDT)
Re: [AMBER] cuda lauch time out error in Amber 11
Sergio R Aragon
(Thu Aug 26 2010 - 17:45:05 PDT)
Re: [AMBER] cuda lauch time out error in Amber 11
Sasha Buzko
(Thu Aug 26 2010 - 18:07:36 PDT)
Re: [AMBER] cuda lauch time out error in Amber 11
Scott Le Grand
(Thu Aug 26 2010 - 18:20:50 PDT)
Re: [AMBER] cuda launch time out error in Amber 11
Sergio R Aragon
(Thu Aug 26 2010 - 23:23:19 PDT)
Re: [AMBER] cuda launch time out error in Amber 11
Ross Walker
(Fri Aug 27 2010 - 06:12:54 PDT)
Re: [AMBER] cuda launch time out error in Amber 11
Sasha Buzko
(Fri Aug 27 2010 - 10:26:25 PDT)
Re: [AMBER] cuda lauch time out error in Amber 11
Scott Le Grand
(Thu Aug 26 2010 - 18:21:29 PDT)
Re: [AMBER] cuda lauch time out error in Amber 11
Ross Walker
(Fri Aug 27 2010 - 06:01:31 PDT)
Re: [AMBER] cuda lauch time out error in Amber 11
Ross Walker
(Fri Aug 27 2010 - 05:57:45 PDT)
Re: [AMBER] cuda launch time out error in Amber 11
Sergio R Aragon
(Fri Aug 27 2010 - 11:06:42 PDT)
Re: [AMBER] cuda launch time out error in Amber 11
Scott Le Grand
(Fri Aug 27 2010 - 21:29:24 PDT)
Re: [AMBER] cuda launch time out error in Amber 11
Sergio R Aragon
(Fri Aug 27 2010 - 22:46:59 PDT)
[AMBER] error in mmpbsa
Asfa Ali
(Fri Aug 27 2010 - 02:20:40 PDT)
Re: [AMBER] error in mmpbsa
Amor San Juan
(Fri Aug 27 2010 - 03:02:14 PDT)
Re: [AMBER] error in mmpbsa
Asfa Ali
(Fri Aug 27 2010 - 04:16:00 PDT)
Re: [AMBER] error in mmpbsa
Ray Luo
(Fri Aug 27 2010 - 10:04:56 PDT)
[AMBER] very slow work of ptraj on cluster
Andrew Voronkov
(Fri Aug 27 2010 - 09:33:09 PDT)
Re: [AMBER] very slow work of ptraj on cluster
Daniel Roe
(Fri Aug 27 2010 - 13:08:26 PDT)
Re: [AMBER] very slow work of ptraj on cluster
Andrew Voronkov
(Sat Aug 28 2010 - 04:33:06 PDT)
Re: [AMBER] very slow work of ptraj on cluster
Daniel Roe
(Sat Aug 28 2010 - 05:54:54 PDT)
Re: [AMBER] very slow work of ptraj on cluster
Andrew Voronkov
(Sat Aug 28 2010 - 09:36:31 PDT)
Re: [AMBER] very slow work of ptraj on cluster
Daniel Roe
(Sat Aug 28 2010 - 15:47:30 PDT)
Re: [AMBER] very slow work of ptraj on cluster
Andrew Voronkov
(Mon Aug 30 2010 - 02:10:24 PDT)
[AMBER] Latest Na+ and Cl- ion parameters
Ilyas Yildirim
(Fri Aug 27 2010 - 13:08:41 PDT)
Re: [AMBER] Latest Na+ and Cl- ion parameters
Dean Cuebas
(Fri Aug 27 2010 - 14:12:23 PDT)
[AMBER] Binary trajectory format in Amber8
Anselm Horn
(Sat Aug 28 2010 - 01:32:23 PDT)
Re: [AMBER] Binary trajectory format in Amber8
case
(Sat Aug 28 2010 - 06:32:05 PDT)
Re: [AMBER] Binary trajectory format in Amber8
Anselm Horn
(Sat Aug 28 2010 - 08:40:06 PDT)
[AMBER] force field parameters for ionic liquids
Ganesh Kamath
(Sat Aug 28 2010 - 06:27:55 PDT)
[AMBER] FEP with EP
William Flak
(Sat Aug 28 2010 - 18:53:51 PDT)
[AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1>
Majid Taghdir
(Sun Aug 29 2010 - 02:17:48 PDT)
Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1>
Jason Swails
(Sun Aug 29 2010 - 07:52:23 PDT)
[AMBER] How to define an unbiased reaction coordinate for potential of mean force calculations?
Catein Catherine
(Sun Aug 29 2010 - 23:09:31 PDT)
Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1>
Majid Taghdir
(Mon Aug 30 2010 - 03:43:05 PDT)
Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1>
Jason Swails
(Mon Aug 30 2010 - 05:15:59 PDT)
Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1>
Majid Taghdir
(Mon Aug 30 2010 - 06:26:29 PDT)
Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1>
Jason Swails
(Mon Aug 30 2010 - 07:12:09 PDT)
[AMBER] How to calculate the equilbrium constant for a protein-drug binding reaction
Catein Catherine
(Mon Aug 30 2010 - 07:44:27 PDT)
Re: [AMBER] How to calculate the equilbrium constant for a protein-drug binding reaction
Jason Swails
(Mon Aug 30 2010 - 08:50:03 PDT)
[AMBER] Is there any training program in Europe in the future?
albert
(Mon Aug 30 2010 - 00:22:33 PDT)
[AMBER] Regarding protein diffusion
aneesh cna
(Mon Aug 30 2010 - 01:24:12 PDT)
[AMBER] RE : Regarding protein diffusion
ABEL Stephane 175950
(Mon Aug 30 2010 - 07:04:33 PDT)
[AMBER] Free energy using MMPBSA
shenna shearin
(Mon Aug 30 2010 - 07:12:35 PDT)
Re: [AMBER] Free energy using MMPBSA
Bill Miller III
(Mon Aug 30 2010 - 08:29:04 PDT)
Re: [AMBER] Free energy using MMPBSA
Jason Swails
(Mon Aug 30 2010 - 08:39:40 PDT)
[AMBER] parameters for ionic liquids
Ganesh Kamath
(Mon Aug 30 2010 - 07:14:07 PDT)
[AMBER] amber11: segmentation fault error
George Tzotzos
(Mon Aug 30 2010 - 08:50:19 PDT)
Re: [AMBER] amber11: segmentation fault error
Jason Swails
(Mon Aug 30 2010 - 09:07:30 PDT)
[AMBER] the modified Bondi radii
zhihong ke
(Mon Aug 30 2010 - 10:15:24 PDT)
Re: [AMBER] the modified Bondi radii
Jason Swails
(Mon Aug 30 2010 - 10:20:16 PDT)
Re: [AMBER] the modified Bondi radii
zhihong ke
(Mon Aug 30 2010 - 10:30:29 PDT)
Re: [AMBER] the modified Bondi radii
Jason Swails
(Mon Aug 30 2010 - 15:55:34 PDT)
Re: [AMBER] the modified Bondi radii
Asfa Ali
(Tue Aug 31 2010 - 05:36:31 PDT)
[AMBER] How to solvate a molecule in a water spherocylinder in leap?
Guoxiong Su
(Mon Aug 30 2010 - 14:07:29 PDT)
Re: [AMBER] How to solvate a molecule in a water spherocylinder in leap?
David A. Case
(Mon Aug 30 2010 - 14:31:11 PDT)
Re: [AMBER] How to solvate a molecule in a water spherocylinder in leap?
Guoxiong Su
(Tue Aug 31 2010 - 07:12:30 PDT)
[AMBER] pmemd installation problem
Carra, Claudio (JSC-SK)[Universities Space Research Association]
(Mon Aug 30 2010 - 16:09:50 PDT)
Re: [AMBER] pmemd installation problem
Jason Swails
(Mon Aug 30 2010 - 21:30:42 PDT)
Re: [AMBER] pmemd installation problem
Ross Walker
(Tue Aug 31 2010 - 01:33:38 PDT)
Re: [AMBER] pmemd installation problem
Carra, Claudio (JSC-SK)[Universities Space Research Association]
(Tue Aug 31 2010 - 16:21:21 PDT)
[AMBER] addions2 function missing from sleap
Ben Roberts
(Mon Aug 30 2010 - 17:15:14 PDT)
[AMBER] Another missing sleap command: check
Ben Roberts
(Mon Aug 30 2010 - 17:28:36 PDT)
Re: [AMBER] Another missing sleap command: check
Ben Roberts
(Tue Aug 31 2010 - 07:49:36 PDT)
[AMBER] addions causes "assertion failed" in sleap
Ben Roberts
(Mon Aug 30 2010 - 18:26:41 PDT)
Re: [AMBER] addions causes "assertion failed" in sleap
Jason Swails
(Tue Aug 31 2010 - 06:39:55 PDT)
[AMBER] Amber9 compilation/Westmere platform
eric henon
(Tue Aug 31 2010 - 01:11:29 PDT)
Re: [AMBER] Amber9 compilation/Westmere platform
Jason Swails
(Tue Aug 31 2010 - 06:12:06 PDT)
[AMBER] Amber9 compilation/Westmere platform
eric henon
(Tue Aug 31 2010 - 06:41:43 PDT)
[AMBER] MMPBSA.py: minimization issue with nmode
Nicolas SAPAY
(Tue Aug 31 2010 - 05:14:47 PDT)
Re: [AMBER] MMPBSA.py: minimization issue with nmode
Bill Miller III
(Tue Aug 31 2010 - 05:31:05 PDT)
Re: [AMBER] MMPBSA.py: minimization issue with nmode
Jason Swails
(Tue Aug 31 2010 - 05:55:43 PDT)
Re: [AMBER] MMPBSA.py: minimization issue with nmode
Jason Swails
(Tue Aug 31 2010 - 06:04:33 PDT)
Re: [AMBER] MMPBSA.py: minimization issue with nmode
Nicolas SAPAY
(Tue Aug 31 2010 - 06:24:56 PDT)
Re: [AMBER] MMPBSA.py: minimization issue with nmode
Nicolas SAPAY
(Tue Aug 31 2010 - 06:21:13 PDT)
[AMBER] regarding trap simulation
Jorgen Simonsen
(Tue Aug 31 2010 - 06:27:26 PDT)
Re: [AMBER] regarding trap simulation
Jason Swails
(Tue Aug 31 2010 - 06:30:45 PDT)
Re: [AMBER] regarding trap simulation
Jorgen Simonsen
(Tue Aug 31 2010 - 06:44:43 PDT)
Re: [AMBER] regarding trap simulation
Jason Swails
(Tue Aug 31 2010 - 06:49:51 PDT)
[AMBER] phenylalanine amide
Francesco Pietra
(Tue Aug 31 2010 - 09:31:49 PDT)
Re: [AMBER] phenylalanine amide
Paul S. Nerenberg
(Tue Aug 31 2010 - 09:40:14 PDT)
Re: [AMBER] phenylalanine amide
Francesco Pietra
(Tue Aug 31 2010 - 09:59:05 PDT)
Re: [AMBER] phenylalanine amide
Paul S. Nerenberg
(Tue Aug 31 2010 - 10:34:05 PDT)
Re: [AMBER] phenylalanine amide
Francesco Pietra
(Tue Aug 31 2010 - 14:12:24 PDT)
[AMBER] Residue name problem in PTRAJ
Hoshin Kim
(Tue Aug 31 2010 - 15:32:19 PDT)
[AMBER] MD and LES
Computational Chemist
(Tue Aug 31 2010 - 23:13:45 PDT)
Last message date
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Tue Aug 31 2010 - 23:30:03 PDT
Archived on
: Fri Nov 15 2024 - 05:54:11 PST
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