Amber Archive Sep 2012: by subject

[AMBER] [q4md-fft] Problem related to the installation of RED
- FyD (Thu Sep 27 2012 - 03:24:13 PDT)
- Sindrila Dutta banik (Thu Sep 27 2012 - 02:56:45 PDT)
- FyD (Wed Sep 26 2012 - 06:42:12 PDT)
[AMBER] About error of min_qmmm.out
- Andreas Goetz (Tue Sep 11 2012 - 10:04:19 PDT)
- JiYuan Liu (Mon Sep 10 2012 - 23:08:51 PDT)
[AMBER] About Langevin dynamics algarithm
- Brian Radak (Thu Sep 20 2012 - 13:19:55 PDT)
- Mo Chen (Thu Sep 20 2012 - 12:49:50 PDT)
- Brian Radak (Thu Sep 20 2012 - 11:06:34 PDT)
- Mo Chen (Thu Sep 20 2012 - 10:17:09 PDT)
- Brian Radak (Thu Sep 20 2012 - 10:03:32 PDT)
- Mo Chen (Thu Sep 20 2012 - 09:40:09 PDT)
- Mo Chen (Thu Sep 20 2012 - 09:10:22 PDT)
- David A Case (Thu Sep 20 2012 - 05:56:11 PDT)
- Brian Radak (Tue Sep 18 2012 - 12:50:21 PDT)
- Mo Chen (Tue Sep 18 2012 - 12:28:44 PDT)
[AMBER] about md.out file thank you
- zhouhaibin2008.ok (Mon Sep 10 2012 - 20:51:42 PDT)
- 黎永秀 (Mon Sep 10 2012 - 19:33:27 PDT)
[AMBER] Adding a ROH to a oligosaccharide
- Lachele Foley (Lists) (Thu Sep 06 2012 - 09:51:08 PDT)
- Pedro Swagger (Thu Sep 06 2012 - 09:48:59 PDT)
- Pedro Swagger (Thu Sep 06 2012 - 09:44:15 PDT)
- Lachele Foley (Lists) (Thu Sep 06 2012 - 09:18:47 PDT)
- Pedro Swagger (Thu Sep 06 2012 - 08:49:12 PDT)
- Lachele Foley (Lists) (Wed Sep 05 2012 - 14:44:10 PDT)
- Pedro Swagger (Wed Sep 05 2012 - 13:36:57 PDT)
- Lachele Foley (Lists) (Wed Sep 05 2012 - 13:30:40 PDT)
- Pedro Swagger (Wed Sep 05 2012 - 13:28:01 PDT)
- Lachele Foley (Lists) (Wed Sep 05 2012 - 13:24:52 PDT)
- David A Case (Wed Sep 05 2012 - 13:15:38 PDT)
- Lachele Foley (Lists) (Wed Sep 05 2012 - 12:58:05 PDT)
- Pedro Swagger (Wed Sep 05 2012 - 12:44:56 PDT)
[AMBER] amber 12 installation
- Ross Walker (Tue Sep 18 2012 - 19:21:01 PDT)
- bmartini (Tue Sep 18 2012 - 19:00:29 PDT)
[AMBER] Amber : System must be very inhomogeneous.
- Dr. Vitaly Chaban (Tue Sep 04 2012 - 06:57:35 PDT)
- najmul arfin (Tue Sep 04 2012 - 06:46:38 PDT)
- Dr. Vitaly Chaban (Tue Sep 04 2012 - 05:52:37 PDT)
- najmul arfin (Tue Sep 04 2012 - 04:12:52 PDT)
[AMBER] AMBER Digest, Vol 274, Issue 1
- Jason Swails (Sat Sep 15 2012 - 05:48:37 PDT)
- Dilraj LAMA (Sat Sep 15 2012 - 02:10:56 PDT)
[AMBER] Amber tutorial
- Jason Swails (Wed Sep 19 2012 - 05:20:34 PDT)
- Chiara Pallara (Wed Sep 19 2012 - 05:03:17 PDT)
[AMBER] AMBER weird performance
- marawan hussain (Mon Sep 03 2012 - 18:22:59 PDT)
[AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland
- Adrian Roitberg (Mon Sep 17 2012 - 14:32:56 PDT)
- Jonathan Gough (Mon Sep 17 2012 - 10:35:36 PDT)
[AMBER] AMBER-Gaussian QM/MM
- Andreas Goetz (Wed Sep 26 2012 - 11:16:38 PDT)
- marawan hussain (Tue Sep 25 2012 - 23:48:52 PDT)
[AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang
- Yu Chen (Sat Sep 01 2012 - 20:30:25 PDT)
[AMBER] AMBER12 Manual: igb=8 in pmemd
- Jason Swails (Mon Sep 17 2012 - 09:03:02 PDT)
- Marc van der Kamp (Mon Sep 17 2012 - 03:16:20 PDT)
[AMBER] amber12 new installation issue
- Su, Shiquan (Fri Sep 14 2012 - 15:15:26 PDT)
- Robin Betz (Fri Sep 14 2012 - 14:11:35 PDT)
- Ross Walker (Wed Sep 12 2012 - 12:52:44 PDT)
- Su, Shiquan (Wed Sep 12 2012 - 12:38:28 PDT)
[AMBER] Amber12 Question
- David A. Case (Fri Sep 07 2012 - 07:14:28 PDT)
- Buback, Clayton (S&T-Student) (Thu Sep 06 2012 - 17:15:13 PDT)
[AMBER] Angle parameters not going after tleap
- Fabrício Bracht (Sun Sep 16 2012 - 07:25:08 PDT)
- Ben Roberts (Fri Sep 14 2012 - 17:06:53 PDT)
- Fabrício Bracht (Fri Sep 14 2012 - 15:14:15 PDT)
- Fabrício Bracht (Fri Sep 14 2012 - 14:09:47 PDT)
- Fabrício Bracht (Fri Sep 14 2012 - 13:51:14 PDT)
- Ben Roberts (Fri Sep 14 2012 - 13:35:53 PDT)
- Jason Swails (Fri Sep 14 2012 - 13:35:33 PDT)
- Fabrício Bracht (Fri Sep 14 2012 - 13:16:54 PDT)
- Fabrício Bracht (Fri Sep 14 2012 - 13:13:21 PDT)
- Fabrício Bracht (Fri Sep 14 2012 - 13:10:38 PDT)
- Ross Walker (Fri Sep 14 2012 - 12:59:39 PDT)
- Fabrício Bracht (Fri Sep 14 2012 - 12:49:47 PDT)
[AMBER] Announcement: Major GPU Update
- Ross Walker (Mon Sep 03 2012 - 14:23:16 PDT)
- Ye MEI (Mon Sep 03 2012 - 06:13:18 PDT)
- Jason Swails (Mon Sep 03 2012 - 06:00:54 PDT)
- Ross Walker (Mon Sep 03 2012 - 13:52:58 PDT)
[AMBER] Antechamber
- David A Case (Wed Sep 26 2012 - 15:08:20 PDT)
- Buback, Clayton (S&T-Student) (Wed Sep 26 2012 - 12:24:57 PDT)
- David A Case (Thu Sep 20 2012 - 05:54:42 PDT)
- Buback, Clayton (S&T-Student) (Tue Sep 18 2012 - 10:34:07 PDT)
- David A Case (Sat Sep 15 2012 - 08:45:44 PDT)
- Buback, Clayton (S&T-Student) (Fri Sep 14 2012 - 13:52:34 PDT)
- David A Case (Thu Sep 13 2012 - 05:56:37 PDT)
- Buback, Clayton (S&T-Student) (Wed Sep 12 2012 - 12:25:39 PDT)
[AMBER] Antechamber: generating prep file
- Rajeswari A. (Tue Sep 18 2012 - 00:30:17 PDT)
- David A Case (Mon Sep 17 2012 - 09:19:19 PDT)
- Rajeswari A. (Mon Sep 17 2012 - 06:38:57 PDT)
[AMBER] Antibiotics Parameters
- FyD (Sat Sep 15 2012 - 05:51:35 PDT)
- Shahoei, Seyyedehrezvan (Fri Sep 14 2012 - 09:39:02 PDT)
- FyD (Sat Sep 08 2012 - 08:10:22 PDT)
- Shahoei, Seyyedehrezvan (Fri Sep 07 2012 - 18:38:03 PDT)
- David A Case (Wed Sep 05 2012 - 05:35:45 PDT)
- FyD (Wed Sep 05 2012 - 00:15:48 PDT)
- Shahoei, Seyyedehrezvan (Tue Sep 04 2012 - 17:14:00 PDT)
[AMBER] assigning FFT grids
- Matthew Zwier (Tue Sep 18 2012 - 12:54:41 PDT)
- Brian Radak (Tue Sep 18 2012 - 07:25:11 PDT)
[AMBER] Atomtype for negatively charged O
- Jesper Sørensen (Fri Sep 14 2012 - 16:37:06 PDT)
[AMBER] Atomtype for negatively charged O, part 2
- FyD (Wed Sep 19 2012 - 22:03:19 PDT)
- Jesper Sørensen (Wed Sep 19 2012 - 12:56:37 PDT)
- FyD (Wed Sep 19 2012 - 12:39:39 PDT)
- Jesper Sørensen (Tue Sep 18 2012 - 15:44:40 PDT)
- Brent Krueger (Tue Sep 18 2012 - 04:22:10 PDT)
- FyD (Mon Sep 17 2012 - 23:26:59 PDT)
- Jesper Sørensen (Mon Sep 17 2012 - 09:47:59 PDT)
[AMBER] bugfix9
- Jason Swails (Mon Sep 24 2012 - 14:33:23 PDT)
- Nadeem A. Vellore (Mon Sep 24 2012 - 13:15:25 PDT)
[AMBER] can DSSP program give more information
- vaibhav dixit (Mon Sep 24 2012 - 04:48:45 PDT)
- Daniel Roe (Thu Sep 20 2012 - 07:17:51 PDT)
- vaibhav dixit (Wed Sep 19 2012 - 23:19:24 PDT)
- vaibhav dixit (Wed Sep 19 2012 - 23:14:48 PDT)
- Daniel Roe (Tue Sep 18 2012 - 06:04:19 PDT)
- vaibhav dixit (Mon Sep 17 2012 - 20:41:30 PDT)
- Daniel Roe (Mon Sep 17 2012 - 05:38:23 PDT)
- vaibhav dixit (Mon Sep 17 2012 - 00:04:08 PDT)
[AMBER] cannot open input file during analysis
- Jason Swails (Wed Sep 12 2012 - 05:33:42 PDT)
- Zalikha Ibrahim (Mon Sep 10 2012 - 15:12:31 PDT)
[AMBER] Centering a multimeric protein with solvateOct
- Jonathan Sheehan (Tue Sep 25 2012 - 12:39:10 PDT)
[AMBER] changing isotope in QM/MM simulation
- Andreas Goetz (Mon Sep 10 2012 - 13:32:59 PDT)
- Hakansson P. (Fri Sep 07 2012 - 08:49:48 PDT)
[AMBER] Compiling ptraj in parallel
- Gustavo Seabra (Thu Sep 06 2012 - 03:44:32 PDT)
- Daniel Roe (Wed Sep 05 2012 - 21:03:31 PDT)
- Gustavo Seabra (Wed Sep 05 2012 - 19:36:15 PDT)
- David A Case (Tue Sep 04 2012 - 11:16:05 PDT)
- Gustavo Seabra (Tue Sep 04 2012 - 10:12:55 PDT)
[AMBER] constant-pH REMD
- Jason Swails (Thu Sep 13 2012 - 07:38:21 PDT)
- Cheng-I Lee (Thu Sep 13 2012 - 06:36:17 PDT)
[AMBER] Could not open mdcrd file with mode (r)
- Zalikha Ibrahim (Sun Sep 30 2012 - 01:14:33 PDT)
- Bill Ross (Thu Sep 27 2012 - 15:08:53 PDT)
- Jason Swails (Thu Sep 27 2012 - 04:27:48 PDT)
- Zalikha Ibrahim (Wed Sep 26 2012 - 19:53:24 PDT)
- Daniel Roe (Wed Sep 26 2012 - 07:36:54 PDT)
- Zalikha Ibrahim (Wed Sep 26 2012 - 02:30:22 PDT)
- Zalikha Ibrahim (Wed Sep 26 2012 - 02:24:16 PDT)
- Zalikha Ibrahim (Wed Sep 26 2012 - 02:19:04 PDT)
- Gannett, Peter (Tue Sep 25 2012 - 17:34:42 PDT)
- Bill Ross (Tue Sep 25 2012 - 16:56:29 PDT)
- Bill Ross (Tue Sep 25 2012 - 16:48:22 PDT)
- Jason Swails (Tue Sep 25 2012 - 04:24:20 PDT)
- Zalikha Ibrahim (Tue Sep 25 2012 - 01:31:19 PDT)
- Bill Ross (Mon Sep 24 2012 - 20:13:27 PDT)
- Daniel Roe (Mon Sep 24 2012 - 19:56:17 PDT)
- Zalikha Ibrahim (Mon Sep 24 2012 - 16:56:40 PDT)
[AMBER] Cpptraj - Autoimage
- Thomas Cheatham III (Thu Sep 13 2012 - 12:17:55 PDT)
- Fernando Martín García (Wed Sep 12 2012 - 23:28:45 PDT)
- Daniel Roe (Wed Sep 12 2012 - 08:14:36 PDT)
- Fernando Martín García (Wed Sep 12 2012 - 06:11:14 PDT)
[AMBER] Create a solution
- David A Case (Thu Sep 20 2012 - 13:23:02 PDT)
- Jason Swails (Thu Sep 20 2012 - 12:33:00 PDT)
- davide.savy.unina.it (Thu Sep 20 2012 - 12:24:03 PDT)
[AMBER] cuda
- Mary Varughese (Fri Sep 28 2012 - 09:22:49 PDT)
- Jason Swails (Tue Sep 25 2012 - 04:30:15 PDT)
- Mary Varughese (Mon Sep 24 2012 - 21:48:23 PDT)
- Robert Crovella (Mon Sep 24 2012 - 15:17:42 PDT)
- Daniel Roe (Mon Sep 24 2012 - 11:56:35 PDT)
- Mary Varughese (Mon Sep 24 2012 - 10:52:24 PDT)
- Ross Walker (Mon Sep 24 2012 - 09:08:06 PDT)
- Deák Robert (Mon Sep 24 2012 - 07:57:13 PDT)
- Mary Varughese (Mon Sep 24 2012 - 07:41:35 PDT)
- Deák Robert (Mon Sep 24 2012 - 01:24:42 PDT)
- filip fratev (Sun Sep 23 2012 - 22:38:54 PDT)
- Mary Varughese (Sun Sep 23 2012 - 21:03:07 PDT)
[AMBER] CUDA-SPFP code and Hardware Version 1.3?
- Thomas Zeiser (Wed Sep 12 2012 - 01:57:38 PDT)
- Ross Walker (Thu Sep 06 2012 - 16:45:12 PDT)
- Thomas Zeiser (Wed Sep 05 2012 - 13:25:24 PDT)
- Jason Swails (Wed Sep 05 2012 - 05:07:08 PDT)
- Thomas Zeiser (Wed Sep 05 2012 - 03:58:53 PDT)
[AMBER] cudaMemcpy GpuBuffer error in pmemd.cuda
- Fabrício Bracht (Thu Sep 20 2012 - 15:04:53 PDT)
- Ross Walker (Thu Sep 20 2012 - 14:45:22 PDT)
- Fabrício Bracht (Thu Sep 20 2012 - 14:36:13 PDT)
- Ross Walker (Thu Sep 20 2012 - 10:08:57 PDT)
- Fabrício Bracht (Thu Sep 20 2012 - 08:39:43 PDT)
- Fabrício Bracht (Tue Sep 18 2012 - 10:37:59 PDT)
- Fabrício Bracht (Mon Sep 17 2012 - 14:55:02 PDT)
- M. L. Dodson (Mon Sep 17 2012 - 14:28:09 PDT)
- Fabrício Bracht (Mon Sep 17 2012 - 13:46:27 PDT)
[AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure
- Gerald Monard (Thu Sep 27 2012 - 14:45:32 PDT)
[AMBER] Difference of results between MMPBSA.py and NAB.
- Jason Swails (Thu Sep 20 2012 - 06:39:49 PDT)
- Sangmin Lee (Thu Sep 20 2012 - 06:17:30 PDT)
[AMBER] Difference of results between MMPBSA.py and NAB.(adjusted datas)
- Jason Swails (Thu Sep 20 2012 - 07:41:57 PDT)
- Sangmin Lee (Thu Sep 20 2012 - 07:13:45 PDT)
[AMBER] dipole printing in mdout file
- Sanjib Paul (Wed Sep 26 2012 - 06:46:35 PDT)
[AMBER] Error in converstion of pdb to mol2
- David A Case (Fri Sep 14 2012 - 06:59:50 PDT)
- Anogna (Thu Sep 13 2012 - 22:18:06 PDT)
- Jason Swails (Thu Sep 13 2012 - 04:47:24 PDT)
- Anogna (Wed Sep 12 2012 - 23:03:12 PDT)
- David A Case (Wed Sep 12 2012 - 05:48:31 PDT)
- Anogna (Wed Sep 12 2012 - 01:09:47 PDT)
[AMBER] Error while preparing Docked complex for Minimization
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Tue Sep 18 2012 - 06:05:49 PDT)
- Daniel Roe (Tue Sep 18 2012 - 04:56:56 PDT)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Tue Sep 18 2012 - 00:15:22 PDT)
[AMBER] error while using chamber (AmberTools1.5) to convert charmm psf and pdb to amber crd and top
- duanbg (Fri Sep 28 2012 - 17:37:28 PDT)
[AMBER] Error with umbrella sampling
- Fabrício Bracht (Wed Sep 19 2012 - 12:12:34 PDT)
- Jason Swails (Wed Sep 19 2012 - 10:47:30 PDT)
- Niel Henriksen (Wed Sep 19 2012 - 10:24:57 PDT)
- Fabrício Bracht (Wed Sep 19 2012 - 10:21:33 PDT)
- Jason Swails (Wed Sep 19 2012 - 06:53:36 PDT)
- Mo Chen (Tue Sep 18 2012 - 22:41:16 PDT)
- Fabrício Bracht (Tue Sep 18 2012 - 22:26:43 PDT)
- Jason Swails (Tue Sep 18 2012 - 19:55:20 PDT)
- Fabrício Bracht (Tue Sep 18 2012 - 19:25:37 PDT)
- David A Case (Tue Sep 18 2012 - 18:32:32 PDT)
- David A Case (Tue Sep 18 2012 - 15:32:07 PDT)
- Fabrício Bracht (Mon Sep 17 2012 - 13:54:23 PDT)
- Brian Radak (Mon Sep 17 2012 - 13:27:45 PDT)
- Fabrício Bracht (Mon Sep 17 2012 - 13:01:02 PDT)
[AMBER] Fermi and Kepler cards running in parallel
- Ross Walker (Sat Sep 22 2012 - 10:30:28 PDT)
- Jason Swails (Fri Sep 21 2012 - 22:00:21 PDT)
- Adam Jion (Fri Sep 21 2012 - 17:02:23 PDT)
[AMBER] finding global minimum
- Scott Le Grand (Sun Sep 02 2012 - 08:15:01 PDT)
- jit mukherjee (Sun Sep 02 2012 - 04:05:58 PDT)
[AMBER] forcefield for dipeptide
- Mary Varughese (Sun Sep 09 2012 - 07:09:27 PDT)
- FyD (Sat Sep 08 2012 - 00:10:45 PDT)
- Mary Varughese (Fri Sep 07 2012 - 09:59:02 PDT)
- FyD (Tue Sep 04 2012 - 02:55:40 PDT)
- Mary Varughese (Tue Sep 04 2012 - 01:40:04 PDT)
[AMBER] Fwd: MTK++ Error: no active site found
- Francesco Pietra (Mon Sep 24 2012 - 02:40:44 PDT)
[AMBER] Fwd: patching AmberTools 12 failed
- Francesco Pietra (Fri Sep 28 2012 - 02:53:18 PDT)
[AMBER] Fwd: problem in inter molecular RDF
- francesco oteri (Wed Sep 05 2012 - 00:18:31 PDT)
- Subrata Paul (Tue Sep 04 2012 - 23:26:13 PDT)
[AMBER] GAFFLipid Parameters
- Gould, Ian R (Fri Sep 14 2012 - 06:43:26 PDT)
- Albert (Wed Sep 19 2012 - 04:43:44 PDT)
- Ross Walker (Fri Sep 14 2012 - 09:01:05 PDT)
- Albert (Fri Sep 14 2012 - 07:13:21 PDT)
- Adrian Roitberg (Fri Sep 14 2012 - 06:48:51 PDT)
- Dickson, Callum (Fri Sep 14 2012 - 06:44:57 PDT)
- Adrian Roitberg (Fri Sep 14 2012 - 06:39:11 PDT)
- Dickson, Callum (Fri Sep 14 2012 - 06:36:35 PDT)
- Albert (Fri Sep 14 2012 - 06:29:37 PDT)
- Dickson, Callum (Fri Sep 14 2012 - 06:10:54 PDT)
- Albert (Fri Sep 14 2012 - 05:39:25 PDT)
- Gould, Ian R (Fri Sep 14 2012 - 04:21:36 PDT)
[AMBER] GAMESS
- FyD (Sun Sep 16 2012 - 01:17:25 PDT)
- Daniel Sindhikara (Sat Sep 15 2012 - 17:39:08 PDT)
- Shomesankar Bhunia (Sat Sep 15 2012 - 05:23:27 PDT)
[AMBER] GAMESS_RESP
- Shomesankar Bhunia (Sun Sep 16 2012 - 21:27:07 PDT)
- FyD (Sun Sep 16 2012 - 00:54:08 PDT)
- Shomesankar Bhunia (Sat Sep 15 2012 - 10:08:21 PDT)
- FyD (Sat Sep 15 2012 - 06:00:23 PDT)
- Shomesankar Bhunia (Sat Sep 15 2012 - 05:15:25 PDT)
[AMBER] General question about AmberTools with older Amber
- Ross Walker (Tue Sep 18 2012 - 19:23:50 PDT)
- Zalikha Ibrahim (Tue Sep 18 2012 - 19:07:07 PDT)
[AMBER] GPU related update to Amber12
- case (Mon Sep 03 2012 - 05:40:39 PDT)
[AMBER] hello.
- 이상민 (Sun Sep 16 2012 - 21:02:17 PDT)
[AMBER] help about rdf
- Daniel Roe (Wed Sep 12 2012 - 08:18:54 PDT)
- Yanyan ZHU (Tue Sep 11 2012 - 18:36:12 PDT)
[AMBER] help amber rdf
- Daniel Roe (Sat Sep 08 2012 - 21:09:26 PDT)
- Yanyan ZHU (Sat Sep 08 2012 - 18:44:10 PDT)
[AMBER] help for analysising my pictures
- Yanyan ZHU (Tue Sep 18 2012 - 00:43:51 PDT)
[AMBER] help for rdf
- Daniel Roe (Mon Sep 17 2012 - 19:39:18 PDT)
- Yanyan ZHU (Mon Sep 17 2012 - 18:49:25 PDT)
- Daniel Roe (Fri Sep 14 2012 - 15:36:04 PDT)
- Yanyan ZHU (Thu Sep 13 2012 - 20:23:19 PDT)
- Yanyan ZHU (Mon Sep 10 2012 - 19:48:05 PDT)
[AMBER] help for sending figures
- Daniel Roe (Mon Sep 17 2012 - 05:31:15 PDT)
- Yanyan ZHU (Mon Sep 17 2012 - 01:18:30 PDT)
[AMBER] help for TMD
- Yanyan ZHU (Mon Sep 24 2012 - 18:56:00 PDT)
- Jason Swails (Wed Sep 12 2012 - 05:25:56 PDT)
- Yanyan ZHU (Tue Sep 11 2012 - 20:41:03 PDT)
[AMBER] How can I get restart file for every step.
- David A Case (Tue Sep 04 2012 - 08:00:41 PDT)
- Sanjib Paul (Tue Sep 04 2012 - 07:40:14 PDT)
- case (Mon Sep 03 2012 - 17:44:09 PDT)
- Jason Swails (Mon Sep 03 2012 - 14:53:57 PDT)
- Sanjib Paul (Mon Sep 03 2012 - 11:13:58 PDT)
[AMBER] How can I use mixing SCEE values in NAB?
- Jason Swails (Thu Sep 20 2012 - 07:06:04 PDT)
- 양지현 (Thu Sep 20 2012 - 04:58:45 PDT)
[AMBER] How to equilibrate only protons, and only side chain
- Carlos Simmerling (Fri Sep 28 2012 - 06:05:22 PDT)
- Sindrila Dutta banik (Fri Sep 28 2012 - 05:54:32 PDT)
[AMBER] IDECOMP does not work with NTB>0 and IMIN=5 ?
- kurisaki (Wed Sep 19 2012 - 19:00:06 PDT)
- kurisaki (Wed Sep 19 2012 - 00:50:14 PDT)
[AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB
- Hai Nguyen (Thu Sep 20 2012 - 14:25:46 PDT)
- Hai Nguyen (Thu Sep 20 2012 - 14:20:53 PDT)
- Vlad Cojocaru (Tue Sep 11 2012 - 07:15:29 PDT)
- Jason Swails (Tue Sep 11 2012 - 06:50:12 PDT)
- Vlad Cojocaru (Tue Sep 11 2012 - 06:14:32 PDT)
- Carlos Simmerling (Mon Sep 10 2012 - 06:25:54 PDT)
- Vlad Cojocaru (Mon Sep 10 2012 - 06:20:48 PDT)
- Carlos Simmerling (Mon Sep 10 2012 - 05:57:52 PDT)
- Vlad Cojocaru (Mon Sep 10 2012 - 01:49:28 PDT)
[AMBER] IMIN=5 does not work with IDECOMP>0 under NTB=1?
- Jason Swails (Wed Sep 19 2012 - 20:27:03 PDT)
- kurisaki (Wed Sep 19 2012 - 19:49:00 PDT)
[AMBER] Installation of Parallel version of Amber
- David A Case (Sat Sep 29 2012 - 14:46:48 PDT)
- Sindrila Dutta banik (Sat Sep 29 2012 - 03:47:09 PDT)
[AMBER] Installation problem of AMBER12
- Jan-Philip Gehrcke (Sat Sep 29 2012 - 08:49:45 PDT)
- Catein Catherine (Sat Sep 29 2012 - 07:09:13 PDT)
[AMBER] Installation problem of AmberTools of AMBER11
- Sanjib Paul (Mon Sep 03 2012 - 03:16:16 PDT)
- Jason Swails (Sat Sep 01 2012 - 12:55:51 PDT)
- Sanjib Paul (Sat Sep 01 2012 - 05:25:29 PDT)
[AMBER] installing RESP
- shomesankar bhunia (Fri Sep 07 2012 - 05:45:29 PDT)
- FyD (Fri Sep 07 2012 - 04:49:30 PDT)
- shomesankar bhunia (Fri Sep 07 2012 - 04:27:23 PDT)
[AMBER] ions concenration
- Carlos Romero (Mon Sep 03 2012 - 13:24:20 PDT)
- Marek Maly (Mon Sep 03 2012 - 05:07:56 PDT)
[AMBER] ips=4 and pmemd.cuda
- David A Case (Wed Sep 05 2012 - 05:37:57 PDT)
- Martin Andersson (Wed Sep 05 2012 - 01:23:47 PDT)
[AMBER] Large trajectory for cluster analysis in ptraj
- Kira Armacost (Sat Sep 29 2012 - 14:42:36 PDT)
- Daniel Roe (Thu Sep 27 2012 - 20:34:20 PDT)
- Daniel Roe (Thu Sep 27 2012 - 20:29:03 PDT)
- Ganesh Kamath (Thu Sep 27 2012 - 20:24:56 PDT)
- Kira Armacost (Thu Sep 27 2012 - 20:08:32 PDT)
- Daniel Roe (Thu Sep 27 2012 - 13:39:47 PDT)
- Kira Armacost (Thu Sep 27 2012 - 13:33:38 PDT)
- Daniel Roe (Thu Sep 27 2012 - 13:25:30 PDT)
- Kira Armacost (Thu Sep 27 2012 - 11:29:56 PDT)
[AMBER] Lipid bilayer coarse-grained simulations
- Benjamin D Madej (Wed Sep 05 2012 - 08:42:33 PDT)
- jojartb.jgypk.u-szeged.hu (Sun Sep 02 2012 - 11:10:43 PDT)
- Jason Swails (Sun Sep 02 2012 - 08:06:27 PDT)
- Bharath K. Srikanth (Sat Sep 01 2012 - 23:20:33 PDT)
[AMBER] lipid params and paper
- Gould, Ian R (Tue Sep 11 2012 - 07:36:02 PDT)
- FyD (Mon Sep 10 2012 - 23:16:17 PDT)
- Igor Marques (Mon Sep 10 2012 - 02:26:09 PDT)
[AMBER] Loading across GPUs
- Duke, Robert E Jr (Wed Sep 19 2012 - 15:30:20 PDT)
- Scott Le Grand (Wed Sep 19 2012 - 14:38:55 PDT)
- Duke, Robert E Jr (Wed Sep 19 2012 - 12:03:41 PDT)
- Duke, Robert E Jr (Wed Sep 19 2012 - 12:01:29 PDT)
- Scott Le Grand (Wed Sep 19 2012 - 11:18:16 PDT)
- Jason Swails (Wed Sep 19 2012 - 05:50:22 PDT)
- Adam Jion (Wed Sep 19 2012 - 02:57:38 PDT)
[AMBER] meaning of columns in hbond output
- Daniel Roe (Wed Sep 12 2012 - 17:05:31 PDT)
- Yubo Fan (Wed Sep 12 2012 - 14:44:05 PDT)
[AMBER] meaning of various columns of closest output in cpptraj
- Daniel Roe (Sat Sep 15 2012 - 14:42:14 PDT)
- Asmita Gupta (Sat Sep 15 2012 - 10:07:25 PDT)
[AMBER] mechanical unfolding of nucleic acids
- Asmita Gupta (Thu Sep 06 2012 - 23:17:13 PDT)
[AMBER] Minimization problem on Amber 12.1 GPU version
- Scott Le Grand (Wed Sep 05 2012 - 10:31:29 PDT)
- Tim Travers (Wed Sep 05 2012 - 09:20:43 PDT)
[AMBER] Minimizations and Equilibrations for TI
- Vivek Shankar Bharadwaj (Thu Sep 27 2012 - 09:22:13 PDT)
- Brian Radak (Thu Sep 27 2012 - 08:49:16 PDT)
- Vivek Shankar Bharadwaj (Thu Sep 27 2012 - 08:20:31 PDT)
[AMBER] MMPBSA energy decomposition
- Jason Swails (Sun Sep 02 2012 - 09:33:09 PDT)
- George Tzotzos (Sun Sep 02 2012 - 08:16:07 PDT)
[AMBER] MMPBSA error
- Jason Swails (Thu Sep 27 2012 - 04:30:22 PDT)
- DEBOSTUTI GHOSHDASTIDAR (Thu Sep 27 2012 - 03:32:07 PDT)
[AMBER] MMPBSA per-residue
- Åge Skjevik (Thu Sep 20 2012 - 08:08:27 PDT)
- Soumya Lipsa Rath (Mon Sep 17 2012 - 06:58:37 PDT)
- Bill Miller III (Mon Sep 17 2012 - 06:13:16 PDT)
- Soumya Lipsa Rath (Mon Sep 17 2012 - 01:43:03 PDT)
[AMBER] MMPBSA.pl masks
- Jason Swails (Thu Sep 13 2012 - 08:43:45 PDT)
- Chiara Pallara (Thu Sep 13 2012 - 08:30:09 PDT)
- Jason Swails (Thu Sep 13 2012 - 08:17:48 PDT)
- Chiara Pallara (Thu Sep 13 2012 - 08:00:49 PDT)
- Jason Swails (Thu Sep 13 2012 - 07:56:52 PDT)
- Chiara Pallara (Thu Sep 13 2012 - 05:24:39 PDT)
[AMBER] MMPBSA.py on single snapshot
- Kasam, Vinod (Wed Sep 19 2012 - 15:25:13 PDT)
- Jason Swails (Wed Sep 19 2012 - 14:20:59 PDT)
- Kasam, Vinod (Wed Sep 19 2012 - 13:44:14 PDT)
[AMBER] MMPBSA.py per-residue decomposition
- Chiara Pallara (Fri Sep 21 2012 - 02:06:00 PDT)
- Jason Swails (Thu Sep 20 2012 - 04:38:56 PDT)
- Chiara Pallara (Thu Sep 20 2012 - 01:19:35 PDT)
[AMBER] MMPBSA: standard deviation
- Jason Swails (Fri Sep 14 2012 - 04:43:39 PDT)
- Hannes Loeffler (Fri Sep 14 2012 - 01:58:43 PDT)
- George Tzotzos (Fri Sep 14 2012 - 01:28:07 PDT)
[AMBER] modified nucleotide
- FyD (Thu Sep 20 2012 - 13:04:21 PDT)
- Krisztina Feher (Thu Sep 20 2012 - 12:32:16 PDT)
- Krisztina Feher (Thu Sep 20 2012 - 12:22:55 PDT)
- Carlos Simmerling (Thu Sep 20 2012 - 08:59:39 PDT)
- FyD (Thu Sep 20 2012 - 08:53:53 PDT)
- Krisztina Feher (Thu Sep 20 2012 - 04:28:34 PDT)
[AMBER] Molcular dynamics
- shomesankar bhunia (Sat Sep 08 2012 - 08:46:23 PDT)
- David A. Case (Sat Sep 08 2012 - 06:38:41 PDT)
- shomesankar bhunia (Sat Sep 08 2012 - 02:08:55 PDT)
[AMBER] Molecular Dynamic production
- David A Case (Sat Sep 29 2012 - 14:40:45 PDT)
- Anogna (Sat Sep 29 2012 - 01:53:35 PDT)
- Jason Swails (Fri Sep 28 2012 - 05:32:01 PDT)
- Anogna (Thu Sep 27 2012 - 23:29:42 PDT)
[AMBER] Monitoring Torsion Angles during MD Simulations
- Giorgos Lamprinidis (Tue Sep 18 2012 - 06:05:57 PDT)
- Daniel Sindhikara (Tue Sep 18 2012 - 05:58:03 PDT)
- Dickson, Callum (Tue Sep 18 2012 - 05:48:05 PDT)
- Γιώργος Λαμπρινίδης (Tue Sep 18 2012 - 04:40:28 PDT)
[AMBER] MTK++ Error: no active site found
- Ben Roberts (Wed Sep 26 2012 - 14:10:03 PDT)
- Francesco Pietra (Tue Sep 25 2012 - 22:16:23 PDT)
- Ben Roberts (Tue Sep 25 2012 - 17:02:50 PDT)
- Francesco Pietra (Sun Sep 23 2012 - 23:47:04 PDT)
- Ben Roberts (Sun Sep 23 2012 - 21:43:47 PDT)
- Francesco Pietra (Sun Sep 23 2012 - 15:19:37 PDT)
- Ben Roberts (Sun Sep 23 2012 - 14:24:53 PDT)
- Francesco Pietra (Sun Sep 23 2012 - 03:08:31 PDT)
[AMBER] My input file
- Ross Walker (Mon Sep 10 2012 - 13:49:23 PDT)
- Chris Chris (Mon Sep 10 2012 - 15:31:54 PDT)
[AMBER] need help to generate parameter file for a small molecule which is covalently bound to the main chain of the protein
- FyD (Wed Sep 19 2012 - 12:42:17 PDT)
- ARP ARP (Wed Sep 19 2012 - 05:21:52 PDT)
[AMBER] newbie question: simulating miRNA
- Michiel de Hoon (Fri Aug 31 2012 - 20:10:04 PDT)
[AMBER] nividia GTX 690 and pmed.cuda
- Scott Le Grand (Thu Sep 06 2012 - 09:03:22 PDT)
- Jonathan Gough (Thu Sep 06 2012 - 08:58:30 PDT)
[AMBER] NMODE calculation using mmpbsa.py
- Dilraj LAMA (Sat Sep 15 2012 - 02:13:38 PDT)
- Bill Miller III (Fri Sep 14 2012 - 04:15:28 PDT)
- Dilraj LAMA (Fri Sep 14 2012 - 01:54:37 PDT)
[AMBER] NMR pmemd.cuda input error
- Jason Swails (Wed Sep 19 2012 - 14:18:01 PDT)
- Larry Olson (Wed Sep 19 2012 - 13:57:37 PDT)
[AMBER] notes on mountain lion istall and a question
- Ross Walker (Tue Sep 18 2012 - 19:32:14 PDT)
- Jonathan Gough (Tue Sep 18 2012 - 19:15:40 PDT)
[AMBER] NTB does not work for trajectory analysis with IMIN=5
- Daniel Roe (Wed Sep 12 2012 - 07:35:01 PDT)
- kurisaki (Tue Sep 11 2012 - 18:32:40 PDT)
- Daniel Roe (Tue Sep 11 2012 - 07:01:01 PDT)
- Jason Swails (Tue Sep 11 2012 - 06:53:18 PDT)
- kurisaki (Tue Sep 11 2012 - 06:08:08 PDT)
- Jason Swails (Tue Sep 11 2012 - 05:45:38 PDT)
- kurisaki (Tue Sep 11 2012 - 05:20:27 PDT)
[AMBER] ntt 2 vs 3 on GPU using latest Amber 12 updates
- Scott Le Grand (Wed Sep 05 2012 - 10:32:19 PDT)
- Tim Travers (Wed Sep 05 2012 - 10:06:55 PDT)
[AMBER] nvidia settings cuda jobs with pbs?
- Jonathan Gough (Wed Sep 19 2012 - 13:06:00 PDT)
- Robert Crovella (Wed Sep 19 2012 - 12:20:38 PDT)
- Jonathan Gough (Tue Sep 18 2012 - 14:44:38 PDT)
[AMBER] output error
- Subrata Paul (Tue Sep 04 2012 - 21:52:54 PDT)
- Jason Swails (Tue Sep 04 2012 - 13:40:39 PDT)
- Subrata Paul (Mon Sep 03 2012 - 21:55:45 PDT)
- Bill Ross (Mon Sep 03 2012 - 21:27:08 PDT)
- Subrata Paul (Mon Sep 03 2012 - 20:40:09 PDT)
[AMBER] parallel error
- najmul arfin (Sun Sep 02 2012 - 01:39:50 PDT)
[AMBER] parallel error with NVT file
- najmul arfin (Sun Sep 02 2012 - 01:51:21 PDT)
[AMBER] patching AmberTools 12 failed
- Francesco Pietra (Fri Sep 28 2012 - 13:30:43 PDT)
- Jason Swails (Fri Sep 28 2012 - 11:38:29 PDT)
- Francesco Pietra (Fri Sep 28 2012 - 10:54:37 PDT)
- Jason Swails (Fri Sep 28 2012 - 05:29:26 PDT)
- Francesco Pietra (Fri Sep 28 2012 - 02:36:34 PDT)
[AMBER] pbsa: how to increase the sampling volume (grid dimensions)?
- Jan-Philip Gehrcke (Wed Sep 12 2012 - 10:43:11 PDT)
- Ray Luo, Ph.D. (Wed Sep 12 2012 - 10:39:02 PDT)
- Jan-Philip Gehrcke (Wed Sep 12 2012 - 10:32:18 PDT)
- Jan-Philip Gehrcke (Wed Sep 12 2012 - 10:23:18 PDT)
- Ray Luo, Ph.D. (Wed Sep 12 2012 - 10:10:37 PDT)
- Jan-Philip Gehrcke (Wed Sep 12 2012 - 09:41:59 PDT)
[AMBER] PCA analysis
- Daniel Roe (Fri Sep 07 2012 - 14:23:21 PDT)
- Sangita Kachhap (Thu Sep 06 2012 - 21:09:19 PDT)
- Daniel Roe (Thu Sep 06 2012 - 09:09:16 PDT)
- Sangita Kachhap (Thu Sep 06 2012 - 08:53:14 PDT)
[AMBER] performance
- marawan hussain (Sat Sep 22 2012 - 20:32:56 PDT)
- Jason Swails (Sat Sep 22 2012 - 20:15:13 PDT)
- marawan hussain (Sat Sep 22 2012 - 19:53:45 PDT)
- Jason Swails (Fri Sep 21 2012 - 05:28:29 PDT)
- marawan hussain (Thu Sep 20 2012 - 22:51:22 PDT)
- Jason Swails (Thu Sep 20 2012 - 20:49:54 PDT)
- marawan hussain (Thu Sep 20 2012 - 18:14:56 PDT)
- marawan hussain (Thu Sep 20 2012 - 18:14:17 PDT)
- Ross Walker (Thu Sep 20 2012 - 09:58:34 PDT)
- Jason Swails (Thu Sep 20 2012 - 04:33:44 PDT)
- marawan hussain (Wed Sep 19 2012 - 22:50:50 PDT)
- Jason Swails (Wed Sep 19 2012 - 20:59:39 PDT)
- marawan hussain (Wed Sep 19 2012 - 20:43:40 PDT)
[AMBER] performance of pmed.cuda.MPI
- Tru Huynh (Sun Sep 23 2012 - 13:18:57 PDT)
- Jonathan Gough (Fri Sep 21 2012 - 11:19:03 PDT)
- Ross Walker (Fri Sep 21 2012 - 11:15:12 PDT)
- Jonathan Gough (Fri Sep 21 2012 - 11:09:46 PDT)
- Ross Walker (Fri Sep 21 2012 - 10:51:01 PDT)
- Jonathan Gough (Fri Sep 21 2012 - 10:44:13 PDT)
- Ross Walker (Fri Sep 21 2012 - 10:22:28 PDT)
- Gould, Ian R (Fri Sep 21 2012 - 10:18:05 PDT)
- Jonathan Gough (Fri Sep 21 2012 - 10:09:11 PDT)
- Ross Walker (Fri Sep 21 2012 - 09:56:27 PDT)
- Gould, Ian R (Fri Sep 21 2012 - 01:04:58 PDT)
- Tru Huynh (Thu Sep 20 2012 - 23:54:54 PDT)
- Jonathan Gough (Fri Sep 14 2012 - 11:50:07 PDT)
- Scott Le Grand (Fri Sep 14 2012 - 11:46:28 PDT)
- Jonathan Gough (Fri Sep 14 2012 - 11:40:33 PDT)
[AMBER] Periodicity error in parmtop file
- Jason Swails (Tue Sep 18 2012 - 06:05:20 PDT)
- Shomesankar Bhunia (Tue Sep 18 2012 - 01:12:49 PDT)
- Shomesankar Bhunia (Tue Sep 18 2012 - 00:44:45 PDT)
- Shomesankar Bhunia (Tue Sep 18 2012 - 00:33:06 PDT)
- Jason Swails (Mon Sep 17 2012 - 09:00:59 PDT)
- David A Case (Mon Sep 17 2012 - 08:40:57 PDT)
- Shomesankar Bhunia (Mon Sep 17 2012 - 04:01:20 PDT)
- Carlos Simmerling (Mon Sep 17 2012 - 03:39:08 PDT)
- Shomesankar Bhunia (Mon Sep 17 2012 - 03:27:44 PDT)
[AMBER] PM3 instead of AM1 in ANTECHAMBER?
- David A Case (Thu Sep 20 2012 - 13:20:01 PDT)
- Shahoei, Seyyedehrezvan (Thu Sep 20 2012 - 10:21:58 PDT)
[AMBER] PMEMD and Steered MD
- Ali M. Naserian-Nik (Mon Sep 17 2012 - 02:42:51 PDT)
[AMBER] PMEMD and Steered MD with an Additional Restraint
- Jason Swails (Thu Sep 20 2012 - 10:25:20 PDT)
- Ali M. Naserian-Nik (Thu Sep 20 2012 - 09:45:12 PDT)
[AMBER] point mutation - residue swap
- Rupesh K. Nanjunda (Wed Sep 12 2012 - 10:25:09 PDT)
- Carlos Simmerling (Wed Sep 12 2012 - 10:20:15 PDT)
- Carlos Simmerling (Wed Sep 12 2012 - 10:18:07 PDT)
- FyD (Tue Sep 11 2012 - 05:49:12 PDT)
- vaibhav dixit (Tue Sep 11 2012 - 03:06:11 PDT)
- Carlos Simmerling (Tue Sep 11 2012 - 02:50:52 PDT)
- vaibhav dixit (Tue Sep 11 2012 - 01:29:29 PDT)
- FyD (Tue Sep 11 2012 - 00:24:53 PDT)
- Bill Ross (Mon Sep 10 2012 - 20:41:34 PDT)
- Aron Broom (Mon Sep 10 2012 - 20:35:06 PDT)
- vaibhav dixit (Mon Sep 10 2012 - 19:52:42 PDT)
- Aron Broom (Mon Sep 10 2012 - 17:32:45 PDT)
- Carlos Simmerling (Mon Sep 10 2012 - 15:24:42 PDT)
- Aron Broom (Mon Sep 10 2012 - 14:53:45 PDT)
- Jonathan Gough (Mon Sep 10 2012 - 13:30:36 PDT)
- Carmenza Martinez (Mon Sep 10 2012 - 12:43:27 PDT)
- Carmenza Martinez (Mon Sep 10 2012 - 12:39:51 PDT)
- Carlos Simmerling (Mon Sep 10 2012 - 12:17:16 PDT)
- Carlos Simmerling (Mon Sep 10 2012 - 12:01:01 PDT)
- FyD (Mon Sep 10 2012 - 11:48:04 PDT)
- Carlos Simmerling (Mon Sep 10 2012 - 10:30:47 PDT)
- Jonathan Gough (Mon Sep 10 2012 - 10:24:55 PDT)
[AMBER] POL3 water model run error...
- David A Case (Fri Sep 14 2012 - 07:05:00 PDT)
- 旭东肖 (Tue Sep 11 2012 - 03:34:32 PDT)
[AMBER] presumed problem with SHAKEH: disappears on passing from CUDA version to normal Sander
- Jason Swails (Wed Sep 12 2012 - 08:36:56 PDT)
- Scott Le Grand (Wed Sep 12 2012 - 07:21:29 PDT)
- Jason Swails (Wed Sep 12 2012 - 03:24:59 PDT)
- Emanuele Monza (Wed Sep 12 2012 - 02:19:19 PDT)
- Jason Swails (Fri Sep 07 2012 - 07:57:03 PDT)
- Emanuele Monza (Fri Sep 07 2012 - 06:02:16 PDT)
- Scott Le Grand (Thu Sep 06 2012 - 09:07:27 PDT)
- Emanuele Monza (Thu Sep 06 2012 - 02:08:13 PDT)
[AMBER] prmtop_inpcrd_ error
- Shomesankar Bhunia (Sun Sep 16 2012 - 21:28:51 PDT)
- David A Case (Sun Sep 16 2012 - 09:35:07 PDT)
- Shomesankar Bhunia (Sat Sep 15 2012 - 12:51:16 PDT)
[AMBER] Probably simple but, I'm stuck.
- Jason Swails (Wed Sep 12 2012 - 05:31:43 PDT)
- Jonathan Gough (Wed Sep 12 2012 - 05:08:15 PDT)
- case (Tue Sep 11 2012 - 17:24:27 PDT)
- Bill Ross (Tue Sep 11 2012 - 14:03:17 PDT)
- Jason Swails (Tue Sep 11 2012 - 11:31:20 PDT)
- Jonathan Gough (Tue Sep 11 2012 - 11:10:06 PDT)
- Sasha Buzko (Tue Sep 11 2012 - 11:07:39 PDT)
- Jonathan Gough (Tue Sep 11 2012 - 11:06:40 PDT)
- Carmenza Martinez (Tue Sep 11 2012 - 11:03:55 PDT)
- Jonathan Gough (Tue Sep 11 2012 - 10:43:14 PDT)
[AMBER] Problem (perhaps) with new precision model
- Scott Le Grand (Tue Sep 11 2012 - 16:47:43 PDT)
- Fabrício Bracht (Tue Sep 11 2012 - 16:23:17 PDT)
[AMBER] Problem in inpcrd file while running minimization
- Jitesh Doshi (Sat Sep 15 2012 - 05:11:48 PDT)
- Jason Swails (Sat Sep 15 2012 - 04:46:23 PDT)
- Jitesh Doshi (Sat Sep 15 2012 - 03:14:07 PDT)
[AMBER] problem in inter molecular RDF
- Subrata Paul (Wed Sep 05 2012 - 11:53:33 PDT)
- Thomas Cheatham III (Wed Sep 05 2012 - 09:51:52 PDT)
- Subrata Paul (Mon Sep 03 2012 - 03:57:37 PDT)
[AMBER] Problem in nmode analysis by NAB
- Sanjib Paul (Thu Sep 06 2012 - 05:39:53 PDT)
- Bill Miller III (Thu Sep 06 2012 - 05:18:28 PDT)
- Sanjib Paul (Thu Sep 06 2012 - 03:59:54 PDT)
- Jason Swails (Wed Sep 05 2012 - 06:17:12 PDT)
- Sanjib Paul (Wed Sep 05 2012 - 05:59:53 PDT)
[AMBER] Problem in nmode analysis of single water molecule by MMPBSA.py
- David A Case (Mon Sep 24 2012 - 06:05:12 PDT)
- Jason Swails (Mon Sep 24 2012 - 04:33:44 PDT)
- Sanjib Paul (Mon Sep 24 2012 - 04:20:11 PDT)
[AMBER] problem install Amber in MacOS
- Daniel Roe (Wed Sep 26 2012 - 06:52:36 PDT)
- Albert (Wed Sep 26 2012 - 06:00:07 PDT)
[AMBER] Problem related to the parallel installation og Amber11
- David A Case (Sun Sep 30 2012 - 19:02:43 PDT)
[AMBER] Problem related to the RED Tools
- Sindrila Dutta banik (Wed Sep 26 2012 - 02:46:20 PDT)
[AMBER] Problem with installation amber 9/tleap
- Ross Walker (Tue Sep 25 2012 - 12:28:34 PDT)
- Deepak Ojha (Tue Sep 25 2012 - 12:13:30 PDT)
[AMBER] Problem with PM6 in sqm
- Andreas Goetz (Fri Sep 28 2012 - 15:10:35 PDT)
- Brian Radak (Fri Sep 28 2012 - 10:54:09 PDT)
- Wei Lin (Fri Sep 28 2012 - 10:00:08 PDT)
- Matthew Zwier (Fri Sep 28 2012 - 08:50:40 PDT)
- Gerald Monard (Fri Sep 28 2012 - 07:09:26 PDT)
- Gerald Monard (Fri Sep 28 2012 - 01:58:06 PDT)
- Wei Lin (Thu Sep 27 2012 - 16:45:24 PDT)
[AMBER] problem with SCNB & SCEE
- Jason Swails (Wed Sep 05 2012 - 12:55:23 PDT)
- Subrata Paul (Wed Sep 05 2012 - 06:36:56 PDT)
[AMBER] ptraj: msd with diffusion command
- Bala subramanian (Sat Sep 01 2012 - 09:40:07 PDT)
[AMBER] puzzles about TMD
- Yanyan ZHU (Tue Sep 25 2012 - 01:50:43 PDT)
[AMBER] pyroglutamic acid parameters
- houcemeddine othman (Mon Sep 17 2012 - 03:44:38 PDT)
[AMBER] query antechamber-reg
- David A Case (Sat Sep 22 2012 - 05:51:58 PDT)
- Revthi Sanker (Fri Sep 14 2012 - 23:59:22 PDT)
- David A Case (Fri Sep 14 2012 - 06:58:15 PDT)
- Revthi Sanker (Fri Sep 14 2012 - 06:05:46 PDT)
[AMBER] query- antechamber
- Revthi Sanker (Fri Sep 14 2012 - 23:55:28 PDT)
[AMBER] question about nmode
- David A Case (Thu Sep 20 2012 - 05:52:05 PDT)
- 이상민 (Mon Sep 17 2012 - 23:00:47 PDT)
[AMBER] Question with mass weighted covariance matrix in ptraj
- Ganesh Kamath (Mon Sep 17 2012 - 17:12:22 PDT)
- Daniel Roe (Mon Sep 17 2012 - 15:53:34 PDT)
- Ganesh Kamath (Mon Sep 17 2012 - 12:55:07 PDT)
[AMBER] questions about Accelerated MD
- Romelia Salomon (Wed Sep 26 2012 - 15:27:03 PDT)
- Thomas Evangelidis (Wed Sep 26 2012 - 11:17:59 PDT)
[AMBER] Questions regarding MMPBSA.py
- Jason Swails (Wed Sep 19 2012 - 06:48:16 PDT)
- Bill Miller III (Wed Sep 19 2012 - 06:04:17 PDT)
- Dilraj LAMA (Wed Sep 19 2012 - 05:27:12 PDT)
[AMBER] random number generator in pmemd.CUDA ?
- Marek Maly (Thu Sep 13 2012 - 04:27:44 PDT)
- Jason Swails (Thu Sep 13 2012 - 04:27:13 PDT)
- Marek Maly (Thu Sep 13 2012 - 01:10:52 PDT)
[AMBER] RDF
- Daniel Roe (Thu Sep 20 2012 - 08:50:26 PDT)
- Yanyan MENG (Thu Sep 20 2012 - 00:01:06 PDT)
[AMBER] rdf1.gif
- Yanyan ZHU (Tue Sep 18 2012 - 19:57:03 PDT)
[AMBER] RE : point mutation - residue swap
- ABEL Stephane 175950 (Mon Sep 10 2012 - 12:38:25 PDT)
- Jonathan Gough (Mon Sep 10 2012 - 10:39:23 PDT)
- ABEL Stephane 175950 (Mon Sep 10 2012 - 10:34:42 PDT)
[AMBER] Read scee and scnb from topology file in NAB
- Jason Swails (Thu Sep 27 2012 - 07:01:23 PDT)
- Sangmin Lee (Tue Sep 25 2012 - 05:14:14 PDT)
[AMBER] REMD simulation
- Carlos Simmerling (Thu Sep 27 2012 - 03:09:19 PDT)
- gargi borgohai (Wed Sep 26 2012 - 22:46:08 PDT)
[AMBER] RESP
- FyD (Thu Sep 06 2012 - 23:40:58 PDT)
- shomesankar bhunia (Thu Sep 06 2012 - 23:07:32 PDT)
[AMBER] RESP charge derivation
- FyD (Tue Sep 04 2012 - 02:51:58 PDT)
- FyD (Mon Sep 03 2012 - 22:56:20 PDT)
- FyD (Fri Aug 31 2012 - 22:16:16 PDT)
- shomesankar bhunia (Fri Aug 31 2012 - 13:16:15 PDT)
[AMBER] RESP charges for HHCC motif with Zn2+ ion
- FyD (Mon Sep 03 2012 - 11:42:18 PDT)
- Sangeetha B (Sun Sep 02 2012 - 06:23:20 PDT)
[AMBER] RESP-charge fitting.
- shomesankar bhunia (Fri Sep 07 2012 - 00:12:45 PDT)
- FyD (Thu Sep 06 2012 - 23:49:38 PDT)
- shomesankar bhunia (Thu Sep 06 2012 - 23:42:50 PDT)
- FyD (Thu Sep 06 2012 - 23:20:10 PDT)
- shomesankar bhunia (Thu Sep 06 2012 - 19:00:42 PDT)
- shomesankar bhunia (Thu Sep 06 2012 - 12:10:47 PDT)
- FyD (Thu Sep 06 2012 - 11:48:23 PDT)
- shomesankar bhunia (Thu Sep 06 2012 - 06:17:23 PDT)
- shomesankar bhunia (Thu Sep 06 2012 - 06:14:01 PDT)
- Marc van der Kamp (Thu Sep 06 2012 - 06:00:18 PDT)
- shomesankar bhunia (Thu Sep 06 2012 - 05:57:46 PDT)
[AMBER] RESP_charge _derivation
- Shomesankar Bhunia (Tue Sep 11 2012 - 03:37:04 PDT)
- FyD (Mon Sep 10 2012 - 22:21:46 PDT)
- Shomesankar Bhunia (Mon Sep 10 2012 - 12:49:39 PDT)
- FyD (Sat Sep 08 2012 - 23:02:55 PDT)
- shomesankar bhunia (Sat Sep 08 2012 - 03:35:04 PDT)
[AMBER] Running Free Energy calculations for Substrate Binding
- Vivek Shankar Bharadwaj (Tue Sep 25 2012 - 11:59:04 PDT)
[AMBER] Running TI calculations on sander.MPI
- Vivek Shankar Bharadwaj (Wed Sep 26 2012 - 11:56:59 PDT)
- David A Case (Wed Sep 26 2012 - 11:04:56 PDT)
- Vivek Shankar Bharadwaj (Wed Sep 26 2012 - 10:03:31 PDT)
[AMBER] SASA and temperature
- Aron Broom (Fri Sep 07 2012 - 10:05:10 PDT)
[AMBER] simulation
- h a (Tue Sep 25 2012 - 10:02:10 PDT)
[AMBER] single residue energy contribution
- kurisaki (Sat Sep 29 2012 - 02:29:33 PDT)
- André C. Stiel (Sat Sep 29 2012 - 01:09:56 PDT)
[AMBER] Small differences in cuda calculations
- Jonathan Gough (Fri Sep 07 2012 - 10:23:22 PDT)
- Scott Le Grand (Fri Sep 07 2012 - 10:18:30 PDT)
- Jonathan Gough (Fri Sep 07 2012 - 10:13:23 PDT)
[AMBER] Softcore potentials in TI calculations
- Vivek Shankar Bharadwaj (Fri Sep 28 2012 - 09:15:04 PDT)
[AMBER] Surface Energy
- John S (Sat Sep 01 2012 - 07:51:19 PDT)
[AMBER] Tesla or GTX?
- Albert (Tue Sep 18 2012 - 09:44:49 PDT)
- Ross Walker (Tue Sep 18 2012 - 09:15:29 PDT)
- Albert (Tue Sep 18 2012 - 07:36:00 PDT)
[AMBER] test errors in cuda-enabled amber12
- Ross Walker (Fri Sep 28 2012 - 08:57:59 PDT)
- 崔幼恬 (Fri Sep 28 2012 - 08:49:19 PDT)
[AMBER] the origin of ELEC DV/DL in the case of softcore TI calculation of the solute with no charge by crgmask
- hironori.kokubo.takeda.com (Fri Sep 28 2012 - 03:49:33 PDT)
[AMBER] thioester-containing proteins (backbone with side chain )
- FyD (Tue Sep 25 2012 - 06:02:25 PDT)
- 甄云梅 (Tue Sep 25 2012 - 04:42:26 PDT)
[AMBER] TI and number of solvent molecules
- Niel Henriksen (Thu Sep 27 2012 - 10:55:09 PDT)
- Jason Swails (Thu Sep 27 2012 - 10:48:37 PDT)
- Fabrício Bracht (Thu Sep 27 2012 - 10:34:55 PDT)
[AMBER] TI input files: tleap adds unwanted hydrogen to a residue
- Jason Swails (Tue Sep 18 2012 - 12:41:01 PDT)
- Kepa K. Burusco (Tue Sep 18 2012 - 11:51:30 PDT)
[AMBER] TI on Crambin, lacking bond in backbone
- David A Case (Tue Sep 11 2012 - 05:24:44 PDT)
- Anna Bauß (Tue Sep 11 2012 - 02:18:24 PDT)
[AMBER] TI Softcore potentials and SHAKE
- David A Case (Sun Sep 30 2012 - 18:49:36 PDT)
- Brian Radak (Fri Sep 28 2012 - 11:04:02 PDT)
- Kepa K. Burusco (Fri Sep 28 2012 - 10:27:36 PDT)
[AMBER] to buy amber package
- Jason Swails (Thu Sep 13 2012 - 04:45:55 PDT)
- KUMAR K M (10PHD0309) (Wed Sep 12 2012 - 21:51:27 PDT)
[AMBER] transition metal system works on pmemd crashes on pmemd.cuda
- Scott Le Grand (Wed Sep 12 2012 - 09:15:24 PDT)
- Scott Le Grand (Tue Sep 11 2012 - 10:19:45 PDT)
- Patrick von Glehn (Mon Sep 10 2012 - 08:18:16 PDT)
- Scott Le Grand (Wed Sep 05 2012 - 05:50:16 PDT)
- Marc van der Kamp (Wed Sep 05 2012 - 04:18:58 PDT)
- Scott Le Grand (Tue Sep 04 2012 - 14:34:26 PDT)
- Marc van der Kamp (Tue Sep 04 2012 - 13:31:42 PDT)
- Marc van der Kamp (Tue Sep 04 2012 - 13:21:02 PDT)
- Scott Le Grand (Tue Sep 04 2012 - 13:15:26 PDT)
- Marc van der Kamp (Tue Sep 04 2012 - 13:08:38 PDT)
- Scott Le Grand (Tue Sep 04 2012 - 11:44:21 PDT)
- Patrick von Glehn (Tue Sep 04 2012 - 10:27:04 PDT)
[AMBER] Unable to correctly identify element N1
- Hakansson P. (Thu Sep 06 2012 - 15:57:06 PDT)
[AMBER] using antechamber to parapetrize non standard amino acid
- FyD (Wed Sep 26 2012 - 06:49:28 PDT)
- houcemeddine othman (Wed Sep 26 2012 - 02:35:40 PDT)
[AMBER] Using ff12SB force field in amber10
- David A. Case (Sun Sep 09 2012 - 14:36:43 PDT)
- H. Chen (Sun Sep 09 2012 - 01:05:43 PDT)
[AMBER] Using ff12SB force field in amber10 (David A. Case)
- H. Chen (Tue Sep 11 2012 - 18:04:33 PDT)
[AMBER] using igb=7
- Hai Nguyen (Wed Sep 05 2012 - 15:00:18 PDT)
- jit mukherjee (Wed Sep 05 2012 - 10:28:56 PDT)
- Hai Nguyen (Wed Sep 05 2012 - 09:58:19 PDT)
- David A Case (Wed Sep 05 2012 - 05:34:34 PDT)
- Thomas Gaillard (Wed Sep 05 2012 - 03:35:55 PDT)
- Carlos Simmerling (Tue Sep 04 2012 - 12:43:23 PDT)
- jit mukherjee (Tue Sep 04 2012 - 10:01:10 PDT)
- Carlos Simmerling (Tue Sep 04 2012 - 08:44:45 PDT)
- jit mukherjee (Tue Sep 04 2012 - 08:41:35 PDT)
- jit mukherjee (Tue Sep 04 2012 - 01:48:36 PDT)
[AMBER] Using mopac in antechamber with Amber11/AmberTools 1.5
- Baptiste Legrand (Fri Sep 07 2012 - 09:11:45 PDT)
- David Case (Fri Sep 07 2012 - 08:46:43 PDT)
- Baptiste Legrand (Fri Sep 07 2012 - 08:30:18 PDT)
- David A. Case (Fri Sep 07 2012 - 07:20:42 PDT)
- Baptiste Legrand (Fri Sep 07 2012 - 02:42:55 PDT)
[AMBER] visualizing normal mode
- jit mukherjee (Wed Sep 05 2012 - 09:57:20 PDT)
[AMBER] visualizing normal modes
- case (Mon Sep 10 2012 - 06:03:54 PDT)
- jit mukherjee (Mon Sep 10 2012 - 02:31:10 PDT)
[AMBER] vlimit exceeded for step 0
- Daniel Roe (Wed Sep 19 2012 - 04:58:17 PDT)
- rosy stone (Tue Sep 18 2012 - 22:32:36 PDT)
[AMBER] vlimit exceeded for step 0; vmax**********
- Jason Swails (Sun Sep 23 2012 - 00:13:56 PDT)
- rosy stone (Sat Sep 22 2012 - 23:32:19 PDT)
[AMBER] water radial distribution function experimental data
- 旭东肖 (Thu Sep 06 2012 - 07:07:23 PDT)
[AMBER] why in TI softcore potential part, 0.01 < clamda < 0.99 ?
- psu4.uic.edu (Mon Sep 24 2012 - 11:08:25 PDT)
- Brian Radak (Tue Sep 18 2012 - 06:11:34 PDT)
- Jason Swails (Mon Sep 17 2012 - 20:28:48 PDT)
- psu4.uic.edu (Mon Sep 17 2012 - 16:25:22 PDT)
[AMBER] will ACEMD accelerate Amber?
- Ross Walker (Sun Sep 16 2012 - 10:51:26 PDT)
- Albert (Sun Sep 16 2012 - 01:22:54 PDT)
[AMBER] xleap and tleap do not recognize Na+ they themselves added
- David A. Case (Wed Sep 05 2012 - 18:29:26 PDT)
- Chris Chris (Wed Sep 05 2012 - 17:47:55 PDT)

Amber Archive Sep 2012 by subject