Amber Archive Aug 2014: by subject

[AMBER] 10 Error on OPEN: ANTECHAMBER.ESP
- David A Case (Tue Aug 19 2014 - 04:55:08 PDT)
- Jason Swails (Tue Aug 19 2014 - 04:56:51 PDT)
- FyD (Tue Aug 19 2014 - 04:43:04 PDT)
- 전선희 (Mon Aug 18 2014 - 23:17:38 PDT)
[AMBER] [Private q4md] R.E.D. Server: Private assistance
- FyD (Fri Aug 22 2014 - 12:27:23 PDT)
[AMBER] Adding new Bondi radii for mmpbsa
- Sergey Samsonov (Wed Aug 06 2014 - 23:46:43 PDT)
- Jason Swails (Wed Aug 06 2014 - 09:35:12 PDT)
- Sergey Samsonov (Wed Aug 06 2014 - 07:18:39 PDT)
[AMBER] amber 14 tests errors
- Jason Swails (Thu Aug 28 2014 - 12:15:47 PDT)
- Jordi Bujons (Thu Aug 28 2014 - 11:23:27 PDT)
[AMBER] AMBER Digest, Vol 956, Issue 1
- Bajarang Kumbhar (Sun Aug 24 2014 - 23:32:02 PDT)
[AMBER] amber/gaussian find the transition state
- Jason Swails (Wed Aug 13 2014 - 05:07:08 PDT)
- 王珍 (Wed Aug 13 2014 - 02:03:19 PDT)
[AMBER] AMBER14 Tutorial: Lipid14 Edition
- Daniel Roe (Sat Aug 02 2014 - 09:46:22 PDT)
- Shekter, Lee R (Fri Aug 01 2014 - 11:03:58 PDT)
[AMBER] ambpdb error
- David A Case (Tue Aug 19 2014 - 05:01:16 PDT)
- Jason Swails (Tue Aug 19 2014 - 05:04:03 PDT)
- Urszula Uciechowska (Tue Aug 19 2014 - 04:12:58 PDT)
- Jason Swails (Tue Aug 19 2014 - 04:13:56 PDT)
- Urszula Uciechowska (Tue Aug 19 2014 - 04:01:13 PDT)
[AMBER] antechamber
- David A Case (Thu Aug 21 2014 - 07:42:54 PDT)
- Jason Swails (Thu Aug 21 2014 - 07:18:02 PDT)
- 闫玉娜 (Thu Aug 21 2014 - 06:52:51 PDT)
- 闫玉娜 (Wed Aug 20 2014 - 05:21:26 PDT)
- Mark Williamson (Wed Aug 20 2014 - 05:04:48 PDT)
- Jason Swails (Wed Aug 20 2014 - 04:41:36 PDT)
- Ying-Chieh Sun (Tue Aug 19 2014 - 21:06:29 PDT)
- 闫玉娜 (Tue Aug 19 2014 - 19:31:10 PDT)
[AMBER] Antechamber error
- David A Case (Thu Aug 14 2014 - 08:47:09 PDT)
- Valentina Romano (Thu Aug 14 2014 - 02:38:24 PDT)
[AMBER] antechamber error message
- Daniel Roe (Wed Aug 27 2014 - 22:16:25 PDT)
- 전선희 (Wed Aug 27 2014 - 20:02:13 PDT)
[AMBER] Antechamber Error: Cannot open file CORR_NAME_TYPE.DAT, exit
- David A Case (Mon Aug 11 2014 - 17:43:19 PDT)
- Andy Tsai (Mon Aug 11 2014 - 16:41:42 PDT)
[AMBER] antechamber parametrization of desoxycorticosterone
- Jason Swails (Fri Aug 22 2014 - 04:20:00 PDT)
- David A Case (Thu Aug 21 2014 - 06:30:08 PDT)
- Jason Swails (Thu Aug 21 2014 - 06:26:58 PDT)
- Jason Swails (Thu Aug 21 2014 - 06:26:13 PDT)
- BATUHAN KAV (Thu Aug 21 2014 - 06:14:41 PDT)
- BATUHAN KAV (Thu Aug 21 2014 - 05:59:39 PDT)
[AMBER] ATP and MG2+prep and frcmod files
- Jason Swails (Thu Aug 14 2014 - 05:15:31 PDT)
- Valentina Romano (Thu Aug 14 2014 - 00:59:39 PDT)
- Jason Swails (Wed Aug 13 2014 - 09:21:34 PDT)
- Valentina Romano (Wed Aug 13 2014 - 08:28:27 PDT)
[AMBER] ATTN NEED REVISION error - reg
- Jason Swails (Wed Aug 20 2014 - 11:07:35 PDT)
- Radhika Swathi (Wed Aug 20 2014 - 10:49:45 PDT)
[AMBER] bad atom type o
- Jason Swails (Wed Aug 20 2014 - 15:34:43 PDT)
- Hallel Freedman (Wed Aug 20 2014 - 14:36:51 PDT)
- Jason Swails (Wed Aug 20 2014 - 14:26:42 PDT)
- Hallel Freedman (Wed Aug 20 2014 - 14:11:11 PDT)
- Jason Swails (Wed Aug 20 2014 - 14:08:56 PDT)
- Hallel Freedman (Wed Aug 20 2014 - 12:17:40 PDT)
- Hallel Freedman (Wed Aug 20 2014 - 10:56:47 PDT)
- Jason Swails (Wed Aug 20 2014 - 10:41:31 PDT)
- Hallel Freedman (Wed Aug 20 2014 - 10:37:57 PDT)
- Jason Swails (Wed Aug 20 2014 - 10:31:53 PDT)
- Hallel Freedman (Wed Aug 20 2014 - 10:24:05 PDT)
- Jason Swails (Wed Aug 20 2014 - 09:56:15 PDT)
- Hallel Freedman (Wed Aug 20 2014 - 09:44:45 PDT)
- Hallel Freedman (Mon Aug 18 2014 - 09:58:58 PDT)
- Jason Swails (Mon Aug 18 2014 - 04:14:45 PDT)
- Hallel Freedman (Sun Aug 17 2014 - 15:42:38 PDT)
[AMBER] build branched polymer in leap?
- Jason Swails (Tue Aug 12 2014 - 19:51:35 PDT)
- Sally Pias (Tue Aug 12 2014 - 16:32:59 PDT)
[AMBER] Calculating electrostatic potential in cpptraj
- Jason Swails (Sat Aug 16 2014 - 18:05:24 PDT)
- Covington, Cody Lance (Sat Aug 16 2014 - 13:20:42 PDT)
- Covington, Cody Lance (Sat Aug 16 2014 - 13:11:24 PDT)
- Jason Swails (Fri Aug 15 2014 - 17:00:46 PDT)
- Covington, Cody Lance (Fri Aug 15 2014 - 13:21:41 PDT)
[AMBER] Calculating lipid diffusion
- Daniel Roe (Wed Aug 20 2014 - 07:57:14 PDT)
- Vijyan Achari (Tue Aug 19 2014 - 19:07:36 PDT)
[AMBER] Calculating lipid diffusion using mass weighted feature
- Vijay Manickam Achari (Tue Aug 19 2014 - 00:02:09 PDT)
[AMBER] chamber prmtop with changed LJ parameters not accepted by pmemd.cuda?
- Ross Walker (Fri Aug 08 2014 - 08:49:31 PDT)
- Jason Swails (Fri Aug 08 2014 - 06:25:48 PDT)
- Marc van der Kamp (Fri Aug 08 2014 - 04:12:44 PDT)
[AMBER] Cluster results
- Daniel Roe (Fri Aug 15 2014 - 13:06:39 PDT)
- Valentina Romano (Wed Aug 13 2014 - 07:25:31 PDT)
- Marc van der Kamp (Wed Aug 13 2014 - 06:22:03 PDT)
- Valentina Romano (Wed Aug 13 2014 - 05:59:34 PDT)
- Daniel Roe (Mon Aug 11 2014 - 09:02:22 PDT)
- Valentina Romano (Mon Aug 11 2014 - 03:13:24 PDT)
- Daniel Roe (Fri Aug 08 2014 - 08:00:52 PDT)
- Jason Swails (Fri Aug 08 2014 - 07:40:15 PDT)
- Daniel Roe (Fri Aug 08 2014 - 07:35:53 PDT)
- Valentina Romano (Fri Aug 08 2014 - 07:30:39 PDT)
- Daniel Roe (Fri Aug 08 2014 - 07:25:36 PDT)
- Valentina Romano (Fri Aug 08 2014 - 07:10:02 PDT)
- Daniel Roe (Fri Aug 08 2014 - 06:56:34 PDT)
- Valentina Romano (Fri Aug 08 2014 - 04:42:49 PDT)
- Daniel Roe (Thu Aug 07 2014 - 07:18:09 PDT)
- Valentina Romano (Thu Aug 07 2014 - 01:34:00 PDT)
- Thomas Cheatham (Wed Aug 06 2014 - 11:28:34 PDT)
- Daniel Roe (Wed Aug 06 2014 - 08:09:23 PDT)
- Valentina Romano (Wed Aug 06 2014 - 07:27:40 PDT)
- Brian Radak (Wed Aug 06 2014 - 06:37:44 PDT)
- Valentina Romano (Wed Aug 06 2014 - 05:22:41 PDT)
[AMBER] clustering
- David A Case (Thu Aug 21 2014 - 11:14:47 PDT)
- Lara rajam (Thu Aug 21 2014 - 10:27:07 PDT)
[AMBER] Contacts
- Sourav Purohit (Wed Aug 20 2014 - 09:56:12 PDT)
- Daniel Roe (Wed Aug 20 2014 - 08:23:06 PDT)
- Sourav Purohit (Wed Aug 20 2014 - 07:26:04 PDT)
- Jason Swails (Wed Aug 20 2014 - 06:58:32 PDT)
- Sourav Purohit (Wed Aug 20 2014 - 06:14:30 PDT)
- Jason Swails (Wed Aug 20 2014 - 05:34:54 PDT)
- Sourav Purohit (Wed Aug 20 2014 - 05:22:07 PDT)
[AMBER] Converting (rst) file to PDB using ambpdb
- Soumendranath Bhakat (Wed Aug 06 2014 - 01:48:25 PDT)
- menwer momo (Tue Aug 05 2014 - 15:24:44 PDT)
- menwer momo (Tue Aug 05 2014 - 15:23:33 PDT)
- Bill Ross (Tue Aug 05 2014 - 15:18:52 PDT)
- Jason Swails (Tue Aug 05 2014 - 14:57:48 PDT)
- menwer momo (Tue Aug 05 2014 - 13:40:11 PDT)
[AMBER] cpptraj.MPI running in 'ensemble' mode.
- Daniel Roe (Sat Aug 09 2014 - 15:54:26 PDT)
- Jonathan Gough (Sat Aug 09 2014 - 12:53:24 PDT)
- Jason Swails (Sat Aug 09 2014 - 11:55:14 PDT)
- Jonathan Gough (Sat Aug 09 2014 - 11:31:47 PDT)
- Jonathan Gough (Sat Aug 09 2014 - 11:28:41 PDT)
[AMBER] Distance command
- zahra khatti (Tue Aug 26 2014 - 12:10:15 PDT)
- zahra khatti (Tue Aug 26 2014 - 05:30:38 PDT)
[AMBER] Do the Charmm FF parameters apply to Amber?
- David A Case (Sun Aug 31 2014 - 10:56:24 PDT)
- 张冬冬 (Sun Aug 31 2014 - 08:09:42 PDT)
[AMBER] Dynamic selection of donor and acceptor mask for hbond analysis
- Daniel Roe (Fri Aug 15 2014 - 12:52:50 PDT)
- DEBOSTUTI GHOSHDASTIDAR (Fri Aug 15 2014 - 03:11:22 PDT)
[AMBER] error ambpdb - Old style inpcrd file read
- Jason Swails (Wed Aug 20 2014 - 07:48:21 PDT)
- Urszula Uciechowska (Wed Aug 20 2014 - 07:20:42 PDT)
- Jason Swails (Wed Aug 20 2014 - 05:33:22 PDT)
- Urszula Uciechowska (Wed Aug 20 2014 - 05:15:08 PDT)
- Jason Swails (Wed Aug 20 2014 - 05:09:52 PDT)
- Urszula Uciechowska (Wed Aug 20 2014 - 04:38:46 PDT)
- Jason Swails (Wed Aug 20 2014 - 04:34:24 PDT)
- Jason Swails (Wed Aug 20 2014 - 04:30:55 PDT)
- Urszula Uciechowska (Wed Aug 20 2014 - 04:22:51 PDT)
- Valentina Romano (Wed Aug 20 2014 - 04:09:25 PDT)
- Urszula Uciechowska (Wed Aug 20 2014 - 03:55:11 PDT)
- Urszula Uciechowska (Wed Aug 20 2014 - 01:20:23 PDT)
[AMBER] Error in making and running xleap
- Jason Swails (Thu Aug 28 2014 - 04:34:59 PDT)
- ammarah.ghaffar.comsats.edu.pk (Thu Aug 28 2014 - 02:52:23 PDT)
- Jason Swails (Tue Aug 26 2014 - 04:30:45 PDT)
- ammarah.ghaffar.comsats.edu.pk (Tue Aug 26 2014 - 01:16:09 PDT)
- David A Case (Mon Aug 25 2014 - 05:01:04 PDT)
- ammarah.ghaffar.comsats.edu.pk (Mon Aug 25 2014 - 02:25:46 PDT)
[AMBER] error: "STOP PMEMD terminated abnormally"
- Hirdesh Kumar (Wed Aug 13 2014 - 13:18:26 PDT)
- Hirdesh Kumar (Wed Aug 13 2014 - 13:15:40 PDT)
- Jason Swails (Wed Aug 13 2014 - 09:15:50 PDT)
- Hirdesh Kumar (Wed Aug 13 2014 - 08:57:00 PDT)
- David A Case (Wed Aug 13 2014 - 07:51:32 PDT)
- Chinh Su Tran To (Wed Aug 13 2014 - 00:06:48 PDT)
[AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
- Pablo Ródenas (Wed Aug 13 2014 - 06:31:58 PDT)
- Jason Swails (Wed Aug 13 2014 - 04:56:51 PDT)
- Pablo Ródenas (Wed Aug 13 2014 - 04:11:39 PDT)
- Pablo Ródenas (Tue Aug 12 2014 - 23:59:17 PDT)
- Daniel Roe (Tue Aug 12 2014 - 10:34:34 PDT)
- Pablo Ródenas (Mon Aug 11 2014 - 23:00:26 PDT)
- Pablo Ródenas (Thu Aug 07 2014 - 07:54:05 PDT)
[AMBER] errors for surf command in cpptraj
- Daniel Roe (Fri Aug 15 2014 - 13:15:32 PDT)
- Wei Chen (Fri Aug 15 2014 - 12:58:49 PDT)
- Daniel Roe (Fri Aug 15 2014 - 10:47:39 PDT)
- Wei Chen (Fri Aug 15 2014 - 09:50:07 PDT)
[AMBER] Fwd: problem with chamber & vmd generated psf (line 2349 of file psfprm.F90)
- Jason Swails (Thu Aug 14 2014 - 09:48:09 PDT)
- Sarah Witzke (Thu Aug 14 2014 - 09:31:16 PDT)
- Sarah Witzke (Thu Aug 07 2014 - 09:11:48 PDT)
[AMBER] Fwd: Unable to generate RESP charges for a charged ligand
- Manikanthan Bhavaraju (Wed Aug 06 2014 - 07:36:44 PDT)
[AMBER] glycated residue parameter
- Sangita Kachhap (Mon Aug 04 2014 - 02:49:16 PDT)
- mmaestre.gate.sinica.edu.tw (Mon Aug 04 2014 - 02:45:56 PDT)
- Sangita Kachhap (Mon Aug 04 2014 - 02:24:51 PDT)
- mmaestre.gate.sinica.edu.tw (Mon Aug 04 2014 - 00:35:39 PDT)
- Sangita Kachhap (Sun Aug 03 2014 - 23:57:47 PDT)
- mmaestre.gate.sinica.edu.tw (Sun Aug 03 2014 - 23:45:49 PDT)
- Sangita Kachhap (Sun Aug 03 2014 - 22:10:39 PDT)
[AMBER] harmonic restraint
- Nadia Li (Wed Aug 27 2014 - 21:09:15 PDT)
- David A Case (Wed Aug 27 2014 - 19:10:19 PDT)
- Nadia Li (Wed Aug 27 2014 - 17:00:42 PDT)
[AMBER] help in analysis
- Daniel Roe (Wed Aug 06 2014 - 07:55:05 PDT)
- Robin Jain (Wed Aug 06 2014 - 02:44:16 PDT)
- Robin Jain (Wed Aug 06 2014 - 02:44:16 PDT)
[AMBER] HELP Needed: AMBER12 cuda compilation ERROR
- Saikat Dutta chowdhury (Thu Jul 31 2014 - 23:03:38 PDT)
[AMBER] Help on Normal Mode Analysis
- Jason Swails (Thu Aug 14 2014 - 08:19:10 PDT)
- xy21hb (Thu Aug 14 2014 - 07:55:12 PDT)
[AMBER] How to visualize PCA
- Daniel Roe (Mon Aug 18 2014 - 20:11:24 PDT)
- Tamara Meirelles (Mon Aug 18 2014 - 18:08:39 PDT)
[AMBER] Hydrogen bond analysis
- David A Case (Tue Aug 05 2014 - 08:50:30 PDT)
- menwer momo (Tue Aug 05 2014 - 04:45:35 PDT)
[AMBER] Implicit solvation method: problem with the rst file
- Jason Swails (Mon Aug 25 2014 - 05:10:17 PDT)
- M.Venkata Satish Kumar (Mon Aug 25 2014 - 04:54:52 PDT)
- Jason Swails (Mon Aug 25 2014 - 04:33:41 PDT)
- M.Venkata Satish Kumar (Mon Aug 25 2014 - 04:08:51 PDT)
[AMBER] Implicit solvent simulation study
- Carlos Simmerling (Sun Aug 24 2014 - 08:06:47 PDT)
- Jason Swails (Sun Aug 24 2014 - 07:12:27 PDT)
- Bajarang Kumbhar (Sat Aug 23 2014 - 22:42:54 PDT)
[AMBER] Kinase and ATP MD simulation
- Jason Swails (Thu Aug 14 2014 - 09:18:49 PDT)
- Valentina Romano (Thu Aug 14 2014 - 08:49:45 PDT)
[AMBER] MCPB and sidechain.bcl problem
- Pengfei Li (Wed Aug 27 2014 - 07:47:14 PDT)
- 高彧辉 (Tue Aug 26 2014 - 22:33:23 PDT)
- Pengfei Li (Tue Aug 26 2014 - 12:05:58 PDT)
- Chris Gao (Mon Aug 25 2014 - 20:32:23 PDT)
- Pengfei Li (Mon Aug 25 2014 - 06:26:37 PDT)
- Chris Gao (Sun Aug 24 2014 - 04:21:10 PDT)
- Pengfei Li (Sat Aug 23 2014 - 05:34:24 PDT)
- 高彧辉 (Fri Aug 22 2014 - 05:55:30 PDT)
[AMBER] Memory keyword for QM/MM using ORCA
- Kshatresh Dutta Dubey (Wed Aug 06 2014 - 00:43:53 PDT)
[AMBER] Metal parametrization problem!!
- Pedro A. Baldera Aguayo (Tue Aug 05 2014 - 14:01:25 PDT)
- Pengfei Li (Tue Aug 05 2014 - 13:33:05 PDT)
- Pedro A. Baldera Aguayo (Tue Aug 05 2014 - 10:56:10 PDT)
- Pedro A. Baldera Aguayo (Mon Aug 04 2014 - 19:46:58 PDT)
- Pengfei Li (Mon Aug 04 2014 - 18:58:40 PDT)
- Pengfei Li (Mon Aug 04 2014 - 18:51:30 PDT)
- Pedro A. Baldera Aguayo (Mon Aug 04 2014 - 18:39:06 PDT)
- Pengfei Li (Fri Aug 01 2014 - 14:42:57 PDT)
- Pedro A. Baldera Aguayo (Fri Aug 01 2014 - 13:13:27 PDT)
- Jason Swails (Fri Aug 01 2014 - 12:27:07 PDT)
- Pedro A. Baldera Aguayo (Fri Aug 01 2014 - 11:38:29 PDT)
- Jason Swails (Fri Aug 01 2014 - 11:29:48 PDT)
- Pedro A. Baldera Aguayo (Fri Aug 01 2014 - 11:17:24 PDT)
[AMBER] Mg 12-6-4 potential using parmed
- Pengfei Li (Fri Aug 29 2014 - 07:51:35 PDT)
- Brian Radak (Fri Aug 29 2014 - 06:39:19 PDT)
- Brian Radak (Thu Aug 28 2014 - 16:47:35 PDT)
- Pengfei Li (Thu Aug 28 2014 - 15:23:17 PDT)
- Brian Radak (Thu Aug 28 2014 - 12:45:19 PDT)
[AMBER] Minimization and equilibration with SANDER.MPI and production with PMEMD.cuda ??
- Jason Swails (Tue Aug 12 2014 - 09:15:24 PDT)
- Hirdesh Kumar (Tue Aug 12 2014 - 07:45:57 PDT)
- Hirdesh Kumar (Tue Aug 12 2014 - 07:30:30 PDT)
- Jason Swails (Tue Aug 12 2014 - 07:17:48 PDT)
- Hirdesh Kumar (Tue Aug 12 2014 - 07:09:58 PDT)
[AMBER] MM-PBSA ALA scanning module
- Jason Swails (Fri Aug 01 2014 - 14:41:53 PDT)
- bharat lakhani (Fri Aug 01 2014 - 14:17:36 PDT)
[AMBER] mmpbsa on charged sytem
- Alessandro Contini (Tue Aug 05 2014 - 09:04:49 PDT)
- Thomas Cheatham (Tue Aug 05 2014 - 08:24:41 PDT)
- Brian Radak (Tue Aug 05 2014 - 07:42:00 PDT)
- Mary Varughese (Tue Aug 05 2014 - 00:19:26 PDT)
[AMBER] MMPBSA prmtop problem
- Jason Swails (Sat Aug 02 2014 - 15:16:00 PDT)
- Nadia Li (Sat Aug 02 2014 - 08:47:06 PDT)
- David A Case (Sat Aug 02 2014 - 05:27:38 PDT)
- Jason Swails (Sat Aug 02 2014 - 05:00:51 PDT)
- Nadia Li (Fri Aug 01 2014 - 23:40:59 PDT)
[AMBER] MMPBSA.py -make-mdins does not work with nmode
- Hiromasa WATANABE (Tue Aug 05 2014 - 17:13:48 PDT)
- Jason Swails (Tue Aug 05 2014 - 07:10:37 PDT)
- Hiromasa WATANABE (Mon Aug 04 2014 - 18:55:23 PDT)
- Jason Swails (Mon Aug 04 2014 - 04:32:09 PDT)
- Hiromasa WATANABE (Mon Aug 04 2014 - 03:57:36 PDT)
[AMBER] MMPBSA.py -nan values.
- Jason Swails (Mon Aug 25 2014 - 10:27:02 PDT)
- Dhananjay (Mon Aug 25 2014 - 09:36:58 PDT)
[AMBER] nab
- Mary Varughese (Sun Aug 31 2014 - 00:26:21 PDT)
- David A Case (Sat Aug 30 2014 - 05:28:58 PDT)
- Mary Varughese (Fri Aug 29 2014 - 22:16:26 PDT)
- svrci (Fri Aug 29 2014 - 03:37:36 PDT)
- Mary Varughese (Fri Aug 29 2014 - 01:56:39 PDT)
[AMBER] NaN and asterisks error in md.out, and mdinfo files
- Hoshin Kim (Mon Aug 11 2014 - 09:52:46 PDT)
- Scott Le Grand (Sat Aug 09 2014 - 08:23:49 PDT)
- Hoshin Kim (Fri Aug 08 2014 - 10:54:30 PDT)
- Scott Le Grand (Wed Aug 06 2014 - 12:24:15 PDT)
- Ross Walker (Wed Aug 06 2014 - 11:38:15 PDT)
- Hoshin Kim (Tue Aug 05 2014 - 11:08:27 PDT)
- Ross Walker (Tue Aug 05 2014 - 10:55:44 PDT)
- Hoshin Kim (Tue Aug 05 2014 - 10:49:39 PDT)
- Ross Walker (Mon Aug 04 2014 - 12:14:14 PDT)
- Hoshin Kim (Mon Aug 04 2014 - 12:04:34 PDT)
[AMBER] New CPPTRAJ Tutorials
- Daniel Roe (Fri Aug 08 2014 - 12:49:19 PDT)
[AMBER] nmode for chamber prmtop
- David A Case (Mon Aug 18 2014 - 07:26:57 PDT)
- Wei Chen (Mon Aug 18 2014 - 07:01:01 PDT)
[AMBER] Obtaining representative structures from clustering
- Jonathan Gough (Fri Aug 29 2014 - 09:22:39 PDT)
- Daniel Roe (Fri Aug 29 2014 - 09:21:33 PDT)
- Jonathan Gough (Fri Aug 29 2014 - 09:01:04 PDT)
- Jonathan Gough (Fri Aug 29 2014 - 08:40:10 PDT)
- Daniel Roe (Fri Aug 29 2014 - 08:22:51 PDT)
- Jonathan Gough (Fri Aug 29 2014 - 07:56:06 PDT)
[AMBER] On combining different force-fields and charge-derivation methods
- FyD (Sat Aug 30 2014 - 04:08:48 PDT)
- Mohammad Salem (Thu Aug 28 2014 - 21:13:35 PDT)
- Jason Swails (Thu Aug 28 2014 - 18:03:47 PDT)
- Mohammad Salem (Thu Aug 28 2014 - 16:27:29 PDT)
[AMBER] Parameters for ATP and MG2+
- Jason Swails (Wed Aug 13 2014 - 09:24:23 PDT)
- Valentina Romano (Wed Aug 13 2014 - 07:56:32 PDT)
[AMBER] parameters for Mutant HP35 NelNel (PDB code 2F4K)
- Subrata Paul (Fri Aug 01 2014 - 05:42:08 PDT)
[AMBER] Parametrization of glycerol and desoxycorticosterone
- David A Case (Wed Aug 20 2014 - 11:32:57 PDT)
- Jason Swails (Wed Aug 20 2014 - 11:21:51 PDT)
- BATUHAN KAV (Wed Aug 20 2014 - 10:59:16 PDT)
- BATUHAN KAV (Wed Aug 20 2014 - 10:54:56 PDT)
[AMBER] PCA projection
- Daniel Roe (Tue Aug 19 2014 - 07:32:32 PDT)
- de Manzanos Guinot, Angela (Tue Aug 19 2014 - 02:52:42 PDT)
[AMBER] Percent occupancy of a hydrogen bond
- menwer momo (Thu Aug 07 2014 - 08:40:44 PDT)
- Jason Swails (Thu Aug 07 2014 - 08:32:05 PDT)
- menwer momo (Thu Aug 07 2014 - 05:00:46 PDT)
[AMBER] Performance of RuBisCo (74, 916) atoms on NVIDIA Tesla K40 GPU
- Gerald Monard (Wed Aug 13 2014 - 12:36:08 PDT)
- David A Case (Tue Aug 12 2014 - 07:37:30 PDT)
- Amit Harode (Tue Aug 12 2014 - 00:03:04 PDT)
- Ross Walker (Mon Aug 11 2014 - 10:08:16 PDT)
- Amit Harode (Mon Aug 11 2014 - 05:34:30 PDT)
[AMBER] perl script to convert GIST output to .dx file
- DEBOSTUTI GHOSHDASTIDAR (Mon Aug 18 2014 - 21:45:29 PDT)
- Nguyen, Crystal (Mon Aug 18 2014 - 11:23:04 PDT)
- DEBOSTUTI GHOSHDASTIDAR (Mon Aug 18 2014 - 11:11:13 PDT)
[AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error)
- Ying-Chieh Sun (Tue Aug 05 2014 - 22:28:03 PDT)
- Jason Swails (Tue Aug 05 2014 - 07:03:25 PDT)
- Ying-Chieh Sun (Mon Aug 04 2014 - 19:45:27 PDT)
- Brian Radak (Mon Aug 04 2014 - 11:27:30 PDT)
- sun (Mon Aug 04 2014 - 10:06:14 PDT)
- Ross Walker (Mon Aug 04 2014 - 09:23:06 PDT)
- sun (Mon Aug 04 2014 - 08:39:02 PDT)
[AMBER] pmemdTI test failure
- David A Case (Mon Aug 25 2014 - 18:00:01 PDT)
- Huang (Mon Aug 25 2014 - 02:37:24 PDT)
- Jason Swails (Tue Aug 19 2014 - 05:41:30 PDT)
- Huang (Tue Aug 19 2014 - 05:15:46 PDT)
[AMBER] positive free energy
- Ray Luo, Ph.D. (Wed Aug 20 2014 - 17:03:02 PDT)
- Jason Swails (Wed Aug 20 2014 - 15:29:46 PDT)
- Vlad Cojocaru (Wed Aug 20 2014 - 14:45:26 PDT)
- Jason Swails (Wed Aug 20 2014 - 14:36:44 PDT)
- Vlad Cojocaru (Wed Aug 20 2014 - 13:32:03 PDT)
- Vlad Cojocaru (Wed Aug 20 2014 - 13:29:06 PDT)
- Ray Luo, Ph.D. (Wed Aug 20 2014 - 12:21:13 PDT)
- Ray Luo, Ph.D. (Wed Aug 20 2014 - 11:59:23 PDT)
- David A Case (Wed Aug 20 2014 - 11:48:37 PDT)
- Jason Swails (Wed Aug 20 2014 - 11:34:17 PDT)
- zahra khatti (Wed Aug 20 2014 - 11:11:29 PDT)
[AMBER] Potential Energy is positve for a normal ligand
- Carlos Simmerling (Mon Aug 04 2014 - 07:53:34 PDT)
- Sun (Mon Aug 04 2014 - 07:49:06 PDT)
[AMBER] Prediction of the protonation state for the ensemble of pdb structures
- Chris Gao (Wed Aug 27 2014 - 05:00:57 PDT)
- James Starlight (Wed Aug 27 2014 - 03:27:47 PDT)
- James Starlight (Wed Aug 27 2014 - 02:39:39 PDT)
- Chris Gao (Wed Aug 27 2014 - 02:33:54 PDT)
- James Starlight (Wed Aug 27 2014 - 00:40:51 PDT)
[AMBER] principal axes calculation in ptraj
- Daniel Roe (Wed Aug 20 2014 - 07:11:37 PDT)
- Asmita Gupta (Wed Aug 20 2014 - 00:45:37 PDT)
- Daniel Roe (Tue Aug 19 2014 - 07:50:28 PDT)
- Asmita Gupta (Tue Aug 19 2014 - 02:12:48 PDT)
[AMBER] Principal Component/Kullback-Leibler Analysis
- Jonathan Gough (Tue Aug 12 2014 - 12:47:50 PDT)
- Daniel Roe (Tue Aug 12 2014 - 12:33:12 PDT)
- Jonathan Gough (Tue Aug 12 2014 - 12:17:11 PDT)
- Daniel Roe (Tue Aug 12 2014 - 12:06:30 PDT)
- Jonathan Gough (Tue Aug 12 2014 - 10:47:19 PDT)
- Daniel Roe (Fri Aug 08 2014 - 09:41:55 PDT)
- Jonathan Gough (Fri Aug 08 2014 - 09:17:26 PDT)
[AMBER] problem in understanding the K+ parameter
- Indrajit Deb (Tue Aug 26 2014 - 06:28:04 PDT)
- Jason Swails (Tue Aug 26 2014 - 06:25:33 PDT)
- Indrajit Deb (Tue Aug 26 2014 - 05:34:54 PDT)
[AMBER] Problem with atommap in cpptraj
- Rajeswari A. (Fri Aug 01 2014 - 22:03:23 PDT)
[AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90)
- Jason Swails (Thu Aug 14 2014 - 10:37:46 PDT)
- Sarah Witzke (Thu Aug 14 2014 - 10:09:14 PDT)
- Jason Swails (Tue Aug 12 2014 - 13:36:59 PDT)
- Marc van der Kamp (Tue Aug 12 2014 - 09:20:13 PDT)
- Jason Swails (Tue Aug 12 2014 - 07:16:06 PDT)
- Marc van der Kamp (Tue Aug 12 2014 - 05:43:11 PDT)
- Jason Swails (Tue Aug 12 2014 - 04:52:09 PDT)
- Marc van der Kamp (Mon Aug 11 2014 - 22:50:03 PDT)
- Jason Swails (Mon Aug 11 2014 - 19:37:48 PDT)
- Marc van der Kamp (Mon Aug 11 2014 - 13:14:04 PDT)
- Jason Swails (Mon Aug 11 2014 - 10:37:48 PDT)
- Marc van der Kamp (Mon Aug 11 2014 - 06:40:53 PDT)
- Jason Swails (Sun Aug 10 2014 - 14:44:19 PDT)
- Marc van der Kamp (Sun Aug 10 2014 - 14:05:36 PDT)
- Jason Swails (Sat Aug 09 2014 - 14:16:29 PDT)
- Marc van der Kamp (Thu Aug 07 2014 - 08:58:12 PDT)
- Jason Swails (Thu Aug 07 2014 - 08:27:07 PDT)
- Marc van der Kamp (Thu Aug 07 2014 - 04:53:23 PDT)
- Sarah Witzke (Wed Aug 06 2014 - 13:56:24 PDT)
- Jason Swails (Wed Aug 06 2014 - 11:54:34 PDT)
- Sarah Witzke (Wed Aug 06 2014 - 11:30:09 PDT)
- Jason Swails (Wed Aug 06 2014 - 09:18:46 PDT)
- Jason Swails (Wed Aug 06 2014 - 09:17:47 PDT)
- Marc van der Kamp (Wed Aug 06 2014 - 09:06:34 PDT)
- Robin Betz (Wed Aug 06 2014 - 08:50:34 PDT)
- Jason Swails (Wed Aug 06 2014 - 08:44:59 PDT)
- Sarah Witzke (Wed Aug 06 2014 - 08:27:08 PDT)
- Marc van der Kamp (Wed Aug 06 2014 - 05:01:25 PDT)
- Sarah Witzke (Wed Aug 06 2014 - 04:50:14 PDT)
- Marc van der Kamp (Wed Aug 06 2014 - 00:55:07 PDT)
- Marc van der Kamp (Wed Aug 06 2014 - 00:39:39 PDT)
- Jason Swails (Tue Aug 05 2014 - 12:30:45 PDT)
- Marc van der Kamp (Tue Aug 05 2014 - 09:27:19 PDT)
[AMBER] Problem with Firefly optimisation in R.E.D server
- George Patargias (Wed Aug 20 2014 - 02:06:44 PDT)
[AMBER] Ptraj cluster error
- Thomas Cheatham (Mon Aug 04 2014 - 08:21:28 PDT)
- Valentina Romano (Mon Aug 04 2014 - 07:58:42 PDT)
[AMBER] puckering of 6 member ring
- Jason Swails (Tue Aug 19 2014 - 07:11:17 PDT)
- Lara rajam (Tue Aug 19 2014 - 06:06:31 PDT)
[AMBER] QM/MM in Amber
- Dr. Vitaly Chaban (Mon Aug 18 2014 - 12:47:46 PDT)
- Brian Radak (Mon Aug 18 2014 - 11:13:21 PDT)
- Muthukumaran R (Mon Aug 18 2014 - 10:12:00 PDT)
[AMBER] question about lipid tutorial
- Jonathan Gough (Fri Aug 01 2014 - 07:24:15 PDT)
- Dickson, Callum J (Fri Aug 01 2014 - 04:49:09 PDT)
[AMBER] Question concerning a torsion parameter
- Mohammad Salem (Thu Aug 07 2014 - 12:14:58 PDT)
- Ross Walker (Thu Aug 07 2014 - 10:23:09 PDT)
- Mohammad Salem (Wed Aug 06 2014 - 21:47:53 PDT)
- David A Case (Wed Aug 06 2014 - 20:55:52 PDT)
- Ross Walker (Wed Aug 06 2014 - 18:42:58 PDT)
- Mohammad Salem (Wed Aug 06 2014 - 17:35:47 PDT)
- Mohammad Salem (Wed Aug 06 2014 - 17:26:29 PDT)
[AMBER] Question for residues.py to parameterize a nonstandard residue for constant pH MD
- Jason Swails (Wed Aug 27 2014 - 14:26:55 PDT)
- M Olivia Kim (Wed Aug 27 2014 - 12:30:20 PDT)
[AMBER] Question on Updating AMBER
- Jason Swails (Tue Aug 19 2014 - 09:16:24 PDT)
- Gulsevin,Alican (Tue Aug 19 2014 - 08:42:34 PDT)
- Jason Swails (Tue Aug 19 2014 - 05:51:45 PDT)
- Gulsevin,Alican (Tue Aug 19 2014 - 05:18:58 PDT)
[AMBER] Questions for pH-REMD by Jason Swails
- Brian Radak (Wed Aug 06 2014 - 11:40:17 PDT)
- M Olivia Kim (Wed Aug 06 2014 - 10:43:35 PDT)
[AMBER] restraints with natural language
- Jason Swails (Fri Aug 15 2014 - 15:49:46 PDT)
- Hugo Azurmendi (Fri Aug 15 2014 - 13:06:53 PDT)
- Jason Swails (Fri Aug 15 2014 - 12:33:22 PDT)
- Hugo Azurmendi (Fri Aug 15 2014 - 12:11:21 PDT)
[AMBER] ScaledMD for proline dipeptide
- Niels Geudens (Mon Aug 04 2014 - 05:20:59 PDT)
[AMBER] SCF convergence failed during QMMM
- Brian Radak (Wed Aug 06 2014 - 06:32:58 PDT)
- Muthukumaran R (Tue Aug 05 2014 - 21:55:39 PDT)
- Brian Radak (Tue Aug 05 2014 - 11:12:00 PDT)
- Muthukumaran R (Tue Aug 05 2014 - 09:23:55 PDT)
[AMBER] Script error in Umbrella tutorial
- Kshatresh Dutta Dubey (Sun Aug 03 2014 - 13:10:15 PDT)
- Jason Swails (Sun Aug 03 2014 - 13:03:34 PDT)
- Kshatresh Dutta Dubey (Sun Aug 03 2014 - 12:42:58 PDT)
- Asaminew Haile (Sun Aug 03 2014 - 12:35:45 PDT)
- Kshatresh Dutta Dubey (Sun Aug 03 2014 - 11:56:46 PDT)
[AMBER] significance of attaching a dummy atom in smd
- Jason Swails (Thu Aug 07 2014 - 10:52:20 PDT)
- Asmita Gupta (Thu Aug 07 2014 - 10:32:12 PDT)
[AMBER] SQM error while preparing ATP with antechamber
- David A Case (Wed Aug 06 2014 - 09:04:30 PDT)
- Hirdesh Kumar (Wed Aug 06 2014 - 07:47:54 PDT)
[AMBER] system size more than 1000 residues
- Jason Swails (Thu Aug 28 2014 - 13:53:14 PDT)
- Pengzhi Zhang (Thu Aug 28 2014 - 12:36:12 PDT)
[AMBER] Testing of the convergence by means of PCA
- James Starlight (Fri Aug 22 2014 - 10:00:13 PDT)
[AMBER] the force constant in umberlla simpling
- Sun (Sun Aug 31 2014 - 01:35:42 PDT)
[AMBER] this a very green neophyte's question.
- David A Case (Sat Aug 02 2014 - 05:27:46 PDT)
- J.W. Halley (Fri Aug 01 2014 - 18:02:27 PDT)
- David A Case (Fri Aug 01 2014 - 06:40:31 PDT)
- Parker de Waal (Thu Jul 31 2014 - 20:13:57 PDT)
[AMBER] Triply bonded oxygen
- David A Case (Wed Aug 27 2014 - 05:02:51 PDT)
- Gulsevin,Alican (Tue Aug 26 2014 - 15:21:05 PDT)
[AMBER] Undocumented DSSP commands and torsional analysis
- Daniel Roe (Tue Aug 26 2014 - 10:33:01 PDT)
- Eugene Yedvabny (Tue Aug 26 2014 - 00:48:53 PDT)
[AMBER] unfolding molecule after heating
- Ross Walker (Thu Aug 07 2014 - 22:35:15 PDT)
- Ross Walker (Thu Aug 07 2014 - 22:33:47 PDT)
- Annika Wittenbecher (Thu Aug 07 2014 - 22:16:03 PDT)
- Annika Wittenbecher (Thu Aug 07 2014 - 21:14:51 PDT)
[AMBER] updates about ACPYPE
- Alan (Sat Aug 30 2014 - 03:41:24 PDT)
[AMBER] Using iwrap with a dimer
- Daniel Roe (Thu Aug 21 2014 - 06:52:02 PDT)
- Caitlin Scott (Thu Aug 21 2014 - 06:45:28 PDT)
[AMBER] Using polarized force field lead to large RMS in the second step of minimization
- Jason Swails (Fri Aug 22 2014 - 09:10:56 PDT)
- 张冬冬 (Fri Aug 22 2014 - 07:56:01 PDT)
- David A Case (Fri Aug 15 2014 - 07:17:16 PDT)
- 张冬冬 (Fri Aug 15 2014 - 02:26:33 PDT)
- David A Case (Thu Aug 14 2014 - 08:44:38 PDT)
- 张冬冬 (Thu Aug 14 2014 - 02:23:13 PDT)
[AMBER] Using setbox command to prepare files for Umbrella Sampling
- George Green (Wed Aug 27 2014 - 13:16:18 PDT)
- Jason Swails (Tue Aug 26 2014 - 12:09:24 PDT)
- Brian Radak (Tue Aug 26 2014 - 11:41:26 PDT)
- Daniel Roe (Tue Aug 26 2014 - 11:35:28 PDT)
- George Green (Tue Aug 26 2014 - 10:58:46 PDT)
- David A Case (Fri Aug 22 2014 - 10:54:32 PDT)
- George Green (Fri Aug 22 2014 - 10:25:21 PDT)
- David A Case (Thu Aug 21 2014 - 13:08:57 PDT)
- George Green (Thu Aug 21 2014 - 12:28:45 PDT)
[AMBER] Very high values of Diffusion coefficient of water
- DEBOSTUTI GHOSHDASTIDAR (Sat Aug 16 2014 - 02:52:13 PDT)
- Jason Swails (Fri Aug 15 2014 - 12:27:41 PDT)
- DEBOSTUTI GHOSHDASTIDAR (Fri Aug 15 2014 - 09:46:13 PDT)
- Daniel Roe (Fri Aug 15 2014 - 08:07:05 PDT)
- DEBOSTUTI GHOSHDASTIDAR (Wed Aug 13 2014 - 22:09:52 PDT)
[AMBER] Visualyze avg structure in VMD
- Daniel Roe (Tue Aug 05 2014 - 05:33:58 PDT)
- Marc van der Kamp (Tue Aug 05 2014 - 03:39:44 PDT)
- Valentina Romano (Tue Aug 05 2014 - 03:23:16 PDT)
[AMBER] what's the difference between imin=1 and imin=5 when performing minimizations on structures from MD trajectory
- Brian Radak (Fri Aug 01 2014 - 06:16:41 PDT)
- ye renlo (Fri Aug 01 2014 - 01:18:56 PDT)
[AMBER] Zinc parameterization
- Nadia Li (Fri Aug 01 2014 - 15:20:44 PDT)
- Jason Swails (Fri Aug 01 2014 - 15:15:03 PDT)
- Nadia Li (Fri Aug 01 2014 - 15:11:18 PDT)
- Pengfei Li (Fri Aug 01 2014 - 14:54:40 PDT)
- Nadia Li (Fri Aug 01 2014 - 10:34:41 PDT)

Amber Archive Aug 2014 by subject