Amber Archive Jan 2017: by subject

[AMBER] 'Diffusion' calculation in Ptraj - could not understand a description of Ptraj code in Amber14
- Daniel Roe (Thu Jan 05 2017 - 05:52:17 PST)
- wei (Thu Jan 05 2017 - 04:39:40 PST)
[AMBER] /dev/hfi1_0 device failed to appear after 15 seconds: Connection timed out
- jacky zhao (Thu Jan 05 2017 - 08:34:46 PST)
[AMBER] /tmp/sh24281: Permission denied.
- Thakur, Abhishek (Wed Jan 11 2017 - 08:40:13 PST)
- Hannes Loeffler (Wed Jan 11 2017 - 08:38:05 PST)
- Thakur, Abhishek (Wed Jan 11 2017 - 08:34:58 PST)
- Hannes Loeffler (Wed Jan 11 2017 - 08:26:42 PST)
- Thakur, Abhishek (Wed Jan 11 2017 - 08:07:56 PST)
- Hai Nguyen (Wed Jan 11 2017 - 08:05:12 PST)
- Thakur, Abhishek (Wed Jan 11 2017 - 07:48:18 PST)
[AMBER] 2nd eChemInfo Training and Innovation Course in Drug Design 2017 in Milano
- Thomas Exner (Mon Jan 09 2017 - 01:17:00 PST)
[AMBER] 5' Terminal Phosphate Parameters
- David Case (Fri Jan 27 2017 - 06:30:01 PST)
- FyD (Thu Jan 26 2017 - 22:47:42 PST)
- David Case (Thu Jan 26 2017 - 19:05:11 PST)
- Paul Meister (Thu Jan 26 2017 - 11:28:19 PST)
- David Case (Thu Jan 26 2017 - 09:21:00 PST)
- Paul Meister (Thu Jan 26 2017 - 07:49:19 PST)
- Qinghua Liao (Thu Jan 26 2017 - 06:57:06 PST)
- Paul Meister (Thu Jan 26 2017 - 06:54:30 PST)
[AMBER] About constraints on QM system of QM/MM simulation
- Pengfei Li (Wed Jan 18 2017 - 14:33:06 PST)
- Goetz, Andreas (Wed Jan 18 2017 - 14:14:30 PST)
- Marc van der Kamp (Wed Jan 18 2017 - 14:14:24 PST)
- Pengfei Li (Wed Jan 18 2017 - 14:04:07 PST)
[AMBER] ACPYPE ERROR
- Subashini .K (Tue Jan 10 2017 - 09:57:39 PST)
- Alan (Tue Jan 10 2017 - 09:24:55 PST)
- Subashini .K (Tue Jan 10 2017 - 01:12:55 PST)
- Subashini .K (Tue Jan 10 2017 - 01:11:22 PST)
- Alan (Tue Jan 10 2017 - 00:38:38 PST)
- Subashini .K (Tue Jan 10 2017 - 00:28:51 PST)
[AMBER] ACPYPE now works with GAFF2
- Alan (Tue Jan 17 2017 - 10:42:26 PST)
[AMBER] adqmmm with PM6 for copper complex
- M_Chikira (Fri Jan 20 2017 - 20:46:45 PST)
- Dr. Robert Molt (Fri Jan 20 2017 - 05:25:34 PST)
- M_Chikira (Fri Jan 20 2017 - 05:13:46 PST)
[AMBER] All working now, except some trajectories
- David Case (Wed Jan 11 2017 - 11:57:32 PST)
- Daniel Roe (Wed Jan 11 2017 - 08:47:00 PST)
- erik rp zuiderweg (Wed Jan 11 2017 - 07:48:22 PST)
[AMBER] alpha helical content as reaction coordinate
- David Case (Sun Jan 15 2017 - 10:52:42 PST)
- Bin Sun (Sun Jan 15 2017 - 09:28:15 PST)
[AMBER] amber installation test failure
- Hirdesh Kumar (Mon Jan 30 2017 - 08:06:38 PST)
- David Case (Fri Jan 27 2017 - 12:52:11 PST)
- Hirdesh Kumar (Fri Jan 27 2017 - 10:20:41 PST)
[AMBER] amber installation test question
- James Kress (Sun Jan 29 2017 - 12:51:48 PST)
- David Case (Sat Jan 28 2017 - 17:48:17 PST)
- James Kress (Sat Jan 28 2017 - 12:25:40 PST)
- David Case (Sat Jan 28 2017 - 07:01:15 PST)
- James Kress (Fri Jan 27 2017 - 20:11:04 PST)
[AMBER] Amber tutorial of APR(attach-pull-release) approach
- Jian Yin (Thu Jan 19 2017 - 10:58:52 PST)
[AMBER] amber14 parallel build problems
- Ada Sedova (Sun Jan 15 2017 - 11:32:04 PST)
- Ada Sedova (Sun Jan 15 2017 - 11:18:23 PST)
- David Case (Sun Jan 15 2017 - 10:42:00 PST)
- Ada Sedova (Sat Jan 14 2017 - 20:01:57 PST)
- David Case (Sat Jan 14 2017 - 12:05:59 PST)
- David Case (Sat Jan 14 2017 - 11:50:20 PST)
- Ada Sedova (Sat Jan 14 2017 - 09:33:28 PST)
- Nhai (Sat Jan 14 2017 - 09:27:25 PST)
- Ada Sedova (Sat Jan 14 2017 - 09:14:36 PST)
- Nhai (Sat Jan 14 2017 - 09:09:30 PST)
- Ada Sedova (Sat Jan 14 2017 - 09:01:04 PST)
- Nhai (Sat Jan 14 2017 - 08:59:26 PST)
- Ada Sedova (Sat Jan 14 2017 - 08:48:25 PST)
- Hai Nguyen (Sat Jan 14 2017 - 08:07:22 PST)
- Ada Sedova (Sat Jan 14 2017 - 07:22:41 PST)
- Ada Sedova (Sat Jan 14 2017 - 06:22:58 PST)
- Hai Nguyen (Fri Jan 13 2017 - 21:07:51 PST)
- Ada Sedova (Fri Jan 13 2017 - 20:22:09 PST)
- Hai Nguyen (Fri Jan 13 2017 - 12:34:31 PST)
- Ada Sedova (Fri Jan 13 2017 - 12:29:48 PST)
- Hai Nguyen (Fri Jan 13 2017 - 12:26:40 PST)
- Ada Sedova (Fri Jan 13 2017 - 12:25:11 PST)
- Hai Nguyen (Fri Jan 13 2017 - 12:23:38 PST)
- Ada Sedova (Fri Jan 13 2017 - 12:12:43 PST)
- Scott Brozell (Fri Jan 13 2017 - 11:35:07 PST)
- Ada Sedova (Fri Jan 13 2017 - 09:52:40 PST)
[AMBER] Amber16 benchmark suite error
- jacky zhao (Tue Jan 10 2017 - 07:26:19 PST)
- jacky zhao (Sun Jan 08 2017 - 22:02:11 PST)
- jacky zhao (Sun Jan 08 2017 - 06:37:50 PST)
- David Case (Sun Jan 08 2017 - 05:25:45 PST)
- Ross Walker (Sat Jan 07 2017 - 15:06:57 PST)
- jacky zhao (Fri Jan 06 2017 - 23:16:46 PST)
- Ross Walker (Fri Jan 06 2017 - 11:55:14 PST)
- jacky zhao (Thu Jan 05 2017 - 22:51:31 PST)
[AMBER] amber16 Centos 7
- Hai Nguyen (Wed Jan 18 2017 - 08:36:35 PST)
- James Kress (Wed Jan 18 2017 - 08:22:23 PST)
- Coleman, Marcus [JRDUS Non-J&J] (Tue Jan 17 2017 - 21:03:57 PST)
- Jason Swails (Tue Jan 17 2017 - 19:55:33 PST)
- Hai Nguyen (Tue Jan 17 2017 - 19:46:52 PST)
- Coleman, Marcus [JRDUS Non-J&J] (Tue Jan 17 2017 - 19:45:20 PST)
- Hai Nguyen (Tue Jan 17 2017 - 19:35:29 PST)
- Coleman, Marcus [JRDUS Non-J&J] (Tue Jan 17 2017 - 19:24:06 PST)
- Coleman, Marcus [JRDUS Non-J&J] (Tue Jan 17 2017 - 19:23:04 PST)
- Hai Nguyen (Tue Jan 17 2017 - 19:17:07 PST)
- Coleman, Marcus [JRDUS Non-J&J] (Tue Jan 17 2017 - 19:08:57 PST)
- Daniel Roe (Tue Jan 17 2017 - 16:23:45 PST)
- Coleman, Marcus [JRDUS Non-J&J] (Tue Jan 17 2017 - 16:17:13 PST)
- Nhai (Tue Jan 17 2017 - 16:05:19 PST)
- Coleman, Marcus [JRDUS Non-J&J] (Tue Jan 17 2017 - 15:50:54 PST)
[AMBER] Amber16 on K80 GPUs --poor performance on multiple GPUs
- Huang Jing (Thu Jan 05 2017 - 13:46:28 PST)
- Jason Swails (Thu Jan 05 2017 - 12:44:24 PST)
- Susan Chacko (Thu Jan 05 2017 - 11:15:30 PST)
- Susan Chacko (Thu Jan 05 2017 - 08:41:00 PST)
- Ross Walker (Wed Jan 04 2017 - 05:05:08 PST)
- Ross Walker (Wed Jan 04 2017 - 05:03:50 PST)
- Susan Chacko (Tue Jan 03 2017 - 09:36:21 PST)
- Huang Jing (Tue Jan 03 2017 - 08:32:23 PST)
- Daniel Roe (Tue Jan 03 2017 - 08:25:24 PST)
- Susan Chacko (Tue Jan 03 2017 - 08:00:09 PST)
[AMBER] amber16 on parallel GPUs
- Ross Walker (Mon Jan 30 2017 - 16:30:33 PST)
- Hirdesh Kumar (Mon Jan 30 2017 - 08:10:03 PST)
- Ross Walker (Fri Jan 27 2017 - 17:04:26 PST)
- Hirdesh Kumar (Fri Jan 27 2017 - 13:06:23 PST)
[AMBER] ambmask issue
- Aseel Bala (Thu Jan 19 2017 - 11:06:13 PST)
- Hai Nguyen (Thu Jan 19 2017 - 10:52:17 PST)
- Aseel Bala (Thu Jan 19 2017 - 10:16:48 PST)
- Daniel Roe (Thu Jan 19 2017 - 07:34:17 PST)
- Aseel Bala (Thu Jan 19 2017 - 07:20:56 PST)
- David Case (Thu Jan 19 2017 - 05:25:36 PST)
- Hai Nguyen (Wed Jan 18 2017 - 14:38:37 PST)
- Hai Nguyen (Wed Jan 18 2017 - 14:23:09 PST)
- Aseel Bala (Wed Jan 18 2017 - 14:20:15 PST)
- Hai Nguyen (Wed Jan 18 2017 - 12:59:09 PST)
- Aseel Bala (Wed Jan 18 2017 - 12:53:44 PST)
- Hai Nguyen (Tue Jan 17 2017 - 11:15:08 PST)
- Huang Jing (Mon Jan 16 2017 - 14:37:20 PST)
- Aseel Bala (Mon Jan 16 2017 - 13:50:20 PST)
[AMBER] antechamber syntax error
- David A Case (Wed Jan 18 2017 - 12:18:51 PST)
- Aseel Bala (Wed Jan 18 2017 - 07:25:52 PST)
- David A Case (Wed Jan 18 2017 - 05:27:06 PST)
- Hai Nguyen (Tue Jan 17 2017 - 19:45:05 PST)
- Aseel Bala Ahmed (Tue Jan 17 2017 - 17:38:03 PST)
[AMBER] antechamber: why the net charge does not sum up to zero?
- FyD (Mon Jan 16 2017 - 22:04:01 PST)
- FyD (Mon Jan 16 2017 - 06:51:38 PST)
- David Case (Sun Jan 08 2017 - 18:41:56 PST)
- FyD (Sun Jan 08 2017 - 10:25:07 PST)
- David Case (Sat Jan 07 2017 - 15:12:49 PST)
- Huang Jing (Sat Jan 07 2017 - 12:26:54 PST)
- FyD (Sat Jan 07 2017 - 10:33:39 PST)
- Jason Swails (Thu Jan 05 2017 - 09:55:23 PST)
- Hannes Loeffler (Thu Jan 05 2017 - 03:06:06 PST)
- Azade Yazdan Yar (Thu Jan 05 2017 - 02:52:34 PST)
[AMBER] autoimage
- Daniel Roe (Tue Jan 17 2017 - 07:35:21 PST)
- Daniel Roe (Tue Jan 17 2017 - 06:38:19 PST)
- Daniel Roe (Fri Jan 13 2017 - 10:50:01 PST)
- colvin (Thu Jan 12 2017 - 21:09:00 PST)
- Daniel Roe (Mon Jan 09 2017 - 06:40:52 PST)
- colvin (Mon Jan 09 2017 - 00:10:57 PST)
[AMBER] Center atoms (translate & rotate reference)
- Daniel Roe (Thu Jan 19 2017 - 07:00:02 PST)
- abdennour braka (Wed Jan 18 2017 - 08:40:07 PST)
[AMBER] clustering
- Bill Ross (Tue Jan 31 2017 - 10:11:20 PST)
- Daniel Roe (Tue Jan 31 2017 - 09:59:59 PST)
- Sowmya Indrakumar (Tue Jan 31 2017 - 07:03:32 PST)
[AMBER] compatibility issues
- Jason Swails (Thu Jan 05 2017 - 18:35:22 PST)
- David Case (Thu Jan 05 2017 - 17:34:31 PST)
- Hai Nguyen (Thu Jan 05 2017 - 09:45:05 PST)
- erik rp zuiderweg (Thu Jan 05 2017 - 09:33:53 PST)
- David Case (Wed Jan 04 2017 - 19:06:03 PST)
- David Case (Wed Jan 04 2017 - 18:58:33 PST)
- Huang Jing (Wed Jan 04 2017 - 11:34:31 PST)
- Hai Nguyen (Wed Jan 04 2017 - 11:06:31 PST)
- erik rp zuiderweg (Wed Jan 04 2017 - 10:50:08 PST)
- Huang Jing (Wed Jan 04 2017 - 10:43:10 PST)
- Hai Nguyen (Wed Jan 04 2017 - 10:25:14 PST)
- Huang Jing (Wed Jan 04 2017 - 10:13:30 PST)
- Hai Nguyen (Wed Jan 04 2017 - 10:00:00 PST)
- erik rp zuiderweg (Wed Jan 04 2017 - 09:54:18 PST)
[AMBER] constrain nitrate as bound and neutral
- Pengfei Li (Wed Jan 25 2017 - 13:56:42 PST)
- Liyang Zhu (Wed Jan 25 2017 - 10:54:04 PST)
- Pengfei Li (Wed Jan 25 2017 - 07:54:29 PST)
- Liyang Zhu (Sun Jan 22 2017 - 16:01:44 PST)
- Pengfei Li (Sat Jan 21 2017 - 20:11:30 PST)
- Liyang Zhu (Sat Jan 21 2017 - 19:57:45 PST)
- David Case (Sat Jan 21 2017 - 19:24:47 PST)
- Liyang Zhu (Wed Jan 18 2017 - 12:22:03 PST)
[AMBER] Continue running an incomplete MD with NMR restraints
- David Case (Sun Jan 15 2017 - 10:44:18 PST)
- Bill Ross (Sat Jan 14 2017 - 23:18:54 PST)
- Kat G (Sat Jan 14 2017 - 22:43:04 PST)
[AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds
- Eric Lang (Mon Jan 30 2017 - 04:33:37 PST)
[AMBER] CpHREMD (explicit solvent) parameter settings inquiry
- Jason Swails (Mon Jan 16 2017 - 19:46:13 PST)
- Andrew Schaub (Mon Jan 16 2017 - 17:50:57 PST)
- Jason Swails (Mon Jan 16 2017 - 17:30:19 PST)
- Andrew Schaub (Sun Jan 15 2017 - 01:39:41 PST)
[AMBER] cpptraj clustering doubt
- Daniel Roe (Mon Jan 09 2017 - 06:05:53 PST)
- Mary Varughese (Sun Jan 08 2017 - 20:55:11 PST)
- Daniel Roe (Sun Jan 08 2017 - 10:32:26 PST)
- Elvis Martis (Sat Jan 07 2017 - 06:56:27 PST)
- Mary Varughese (Sat Jan 07 2017 - 02:33:17 PST)
- Mary Varughese (Thu Jan 05 2017 - 07:23:38 PST)
- Daniel Roe (Thu Jan 05 2017 - 05:30:50 PST)
- Christina Bergonzo (Thu Jan 05 2017 - 04:48:21 PST)
- Elvis Martis (Thu Jan 05 2017 - 03:41:22 PST)
- Mary Varughese (Thu Jan 05 2017 - 02:59:52 PST)
[AMBER] cpptraj LIE on a ghost-atom
- Elisa Pieri (Tue Jan 03 2017 - 03:36:25 PST)
[AMBER] cpptraj PCA of crystal structure
- anu chandra (Thu Jan 12 2017 - 05:00:09 PST)
- Daniel Roe (Tue Jan 10 2017 - 05:03:48 PST)
- anu chandra (Tue Jan 10 2017 - 02:50:23 PST)
- Daniel Roe (Thu Jan 05 2017 - 08:30:14 PST)
- anu chandra (Thu Jan 05 2017 - 08:25:48 PST)
[AMBER] cpptraj: autoimage DCD trajectories (with Amber topology)
- vlad.cojocaru.mpi-muenster.mpg.de (Tue Jan 31 2017 - 09:59:57 PST)
- Daniel Roe (Tue Jan 31 2017 - 09:48:08 PST)
- Vlad Cojocaru (Tue Jan 31 2017 - 06:16:20 PST)
- Daniel Roe (Tue Jan 31 2017 - 05:07:59 PST)
- Vlad Cojocaru (Tue Jan 31 2017 - 04:32:37 PST)
- Vlad Cojocaru (Tue Jan 31 2017 - 04:16:23 PST)
- Daniel Roe (Tue Jan 31 2017 - 03:54:53 PST)
- Vlad Cojocaru (Tue Jan 31 2017 - 01:10:02 PST)
[AMBER] cpptraj: list command throws seqfault
- Daniel Roe (Thu Jan 19 2017 - 06:42:36 PST)
- Daniel Roe (Thu Jan 19 2017 - 05:22:20 PST)
- Thomas Fox (Thu Jan 19 2017 - 04:58:36 PST)
[AMBER] cpptraj: segfault after list command
- Thomas Fox (Fri Jan 20 2017 - 05:07:53 PST)
[AMBER] csh to bash
- Huang Jing (Thu Jan 12 2017 - 09:57:47 PST)
- Nhai (Thu Jan 12 2017 - 09:18:44 PST)
- Thakur, Abhishek (Thu Jan 12 2017 - 09:11:12 PST)
[AMBER] DFTB3 in Amber is not there, but it may be in gromacs.
- Goetz, Andreas (Tue Jan 31 2017 - 10:59:52 PST)
- Markus Kaukonen (Tue Jan 31 2017 - 08:06:54 PST)
[AMBER] Differences using leaprc.ff14SB from AmberTools15 and oldff/leaprc.ff14SB from AmberTools16
- Joao Damas (Tue Jan 31 2017 - 12:33:16 PST)
[AMBER] Distance between the center of gravities of tow molecules-CPPTRAJ
- Daniel Roe (Thu Jan 19 2017 - 11:21:24 PST)
- konda003 . (Thu Jan 19 2017 - 11:01:06 PST)
[AMBER] distance restraints failed
- Qinghua Liao (Wed Jan 25 2017 - 11:31:51 PST)
- Qinghua Liao (Wed Jan 25 2017 - 11:11:50 PST)
- David Case (Wed Jan 25 2017 - 11:06:12 PST)
- Qinghua Liao (Wed Jan 25 2017 - 10:50:13 PST)
- Adrian Roitberg (Wed Jan 25 2017 - 10:45:44 PST)
- Qinghua Liao (Wed Jan 25 2017 - 10:40:51 PST)
- Qinghua Liao (Wed Jan 25 2017 - 10:32:23 PST)
- Adrian Roitberg (Wed Jan 25 2017 - 09:52:16 PST)
- Carlos Simmerling (Wed Jan 25 2017 - 09:46:53 PST)
- Thakur, Abhishek (Wed Jan 25 2017 - 08:37:51 PST)
- Qinghua Liao (Wed Jan 25 2017 - 08:15:10 PST)
- Qinghua Liao (Wed Jan 25 2017 - 08:10:59 PST)
- Nhai (Wed Jan 25 2017 - 07:52:37 PST)
- Carlos Simmerling (Wed Jan 25 2017 - 07:49:42 PST)
- Qinghua Liao (Wed Jan 25 2017 - 07:44:55 PST)
[AMBER] error in finding vdW (or other) parameters for type
- David Case (Tue Jan 24 2017 - 05:52:20 PST)
- Fatemeh Fatemi (Tue Jan 24 2017 - 03:42:54 PST)
[AMBER] Error in leaprc.ff14SB (Amber14)
- Subashini .K (Mon Jan 09 2017 - 22:28:06 PST)
- Hai Nguyen (Mon Jan 09 2017 - 21:39:46 PST)
- Subashini .K (Mon Jan 09 2017 - 21:29:03 PST)
[AMBER] Error in reordering pH-REMD trajectories
- Elisa Pieri (Tue Jan 03 2017 - 05:22:25 PST)
- Daniel Roe (Tue Jan 03 2017 - 05:15:59 PST)
- Elisa Pieri (Tue Jan 03 2017 - 04:09:30 PST)
- Jason Swails (Mon Jan 02 2017 - 12:33:52 PST)
- Elisa Pieri (Mon Jan 02 2017 - 12:31:16 PST)
[AMBER] Error opening unit 15: File "remd.groupfile" is missing or unreadable
- Adrian Roitberg (Mon Jan 23 2017 - 15:31:05 PST)
- Thakur, Abhishek (Mon Jan 23 2017 - 15:15:31 PST)
- Nhai (Mon Jan 23 2017 - 14:58:58 PST)
- Thakur, Abhishek (Mon Jan 23 2017 - 14:25:19 PST)
[AMBER] Error while creation topology and coordinate files in tleap
- David A Case (Wed Jan 18 2017 - 12:32:50 PST)
- Elvis Martis (Wed Jan 18 2017 - 03:06:13 PST)
- Manjula Saravanan (Wed Jan 18 2017 - 02:53:24 PST)
[AMBER] failed to visualize trajectories in vmd.
- Daniel Roe (Tue Jan 03 2017 - 05:31:39 PST)
- Saman Yousuf ali (Mon Jan 02 2017 - 08:59:17 PST)
- Elvis Martis (Mon Jan 02 2017 - 08:20:07 PST)
- Nhai (Mon Jan 02 2017 - 07:56:57 PST)
- Saman Yousuf ali (Mon Jan 02 2017 - 07:46:31 PST)
- Saman Yousuf ali (Mon Jan 02 2017 - 07:32:57 PST)
- David Case (Mon Jan 02 2017 - 07:20:20 PST)
- Saman Yousuf ali (Mon Jan 02 2017 - 07:08:41 PST)
- David Case (Mon Jan 02 2017 - 06:14:03 PST)
- Saman Yousuf ali (Mon Jan 02 2017 - 02:02:25 PST)
[AMBER] Force field modifications
- David Case (Fri Jan 06 2017 - 14:38:14 PST)
- Jonathan Huihui (Fri Jan 06 2017 - 13:36:58 PST)
- Carlos Simmerling (Fri Jan 06 2017 - 13:28:42 PST)
- Jonathan Huihui (Fri Jan 06 2017 - 13:25:14 PST)
- Carlos Simmerling (Fri Jan 06 2017 - 13:22:47 PST)
- Jonathan Huihui (Fri Jan 06 2017 - 13:09:26 PST)
[AMBER] Free energy techniques for conformational changes and alchemical mutations
- Hadházi Ádám (Fri Jan 27 2017 - 02:25:20 PST)
[AMBER] From PMF to free energy of binding
- Andreas Tosstorff (Tue Jan 24 2017 - 07:42:39 PST)
- David Case (Tue Jan 24 2017 - 05:46:20 PST)
- Andreas Tosstorff (Tue Jan 24 2017 - 00:53:30 PST)
- Niel Henriksen (Mon Jan 23 2017 - 11:51:09 PST)
- Andreas Tosstorff (Mon Jan 23 2017 - 09:03:17 PST)
[AMBER] Fwd: [AMBER-Developers] non-neutral ethane from antechamber
- FyD (Mon Jan 16 2017 - 21:40:17 PST)
[AMBER] Fwd: amber14 parallel build problems
- Ada Sedova (Wed Jan 18 2017 - 12:30:21 PST)
- Hai Nguyen (Wed Jan 18 2017 - 12:23:37 PST)
- Ada Sedova (Wed Jan 18 2017 - 12:20:31 PST)
- Hai Nguyen (Wed Jan 18 2017 - 12:09:32 PST)
- Ada Sedova (Wed Jan 18 2017 - 12:05:50 PST)
- Hai Nguyen (Wed Jan 18 2017 - 12:00:09 PST)
- Ada Sedova (Wed Jan 18 2017 - 11:58:35 PST)
- Hai Nguyen (Wed Jan 18 2017 - 11:54:20 PST)
- Ada Sedova (Wed Jan 18 2017 - 11:44:38 PST)
[AMBER] Fwd: Error during installation process
- Hai Nguyen (Tue Jan 31 2017 - 20:12:26 PST)
- Hai Nguyen (Tue Jan 31 2017 - 09:58:15 PST)
- Hai Nguyen (Tue Jan 31 2017 - 06:29:46 PST)
- Danu Fajar (Tue Jan 31 2017 - 06:25:07 PST)
[AMBER] Fwd: some clues about yacc errors on OLCF rhea
- Ada Sedova (Wed Jan 18 2017 - 20:04:45 PST)
- Scott Brozell (Wed Jan 18 2017 - 13:57:55 PST)
- Ada Sedova (Wed Jan 18 2017 - 13:29:37 PST)
- David A Case (Wed Jan 18 2017 - 12:25:21 PST)
- Ada Sedova (Wed Jan 18 2017 - 11:43:37 PST)
- Ada Sedova (Wed Jan 18 2017 - 11:41:22 PST)
- Scott Brozell (Wed Jan 18 2017 - 11:06:33 PST)
- Hai Nguyen (Wed Jan 18 2017 - 10:44:51 PST)
- Scott Brozell (Wed Jan 18 2017 - 10:44:41 PST)
- Ada Sedova (Wed Jan 18 2017 - 10:19:24 PST)
[AMBER] Give the correct charge to heme using antechamber
- Elvis Martis (Thu Jan 26 2017 - 20:22:38 PST)
- David Case (Thu Jan 26 2017 - 09:11:44 PST)
- Matteo Uggeri (Thu Jan 26 2017 - 06:15:44 PST)
[AMBER] Handling modified residues
- asdda asa (Sat Jan 14 2017 - 04:50:18 PST)
- Huang Jing (Sat Jan 14 2017 - 04:26:09 PST)
- asdda asa (Sat Jan 14 2017 - 04:10:59 PST)
- Huang Jing (Sat Jan 14 2017 - 03:36:17 PST)
- asdda asa (Sat Jan 14 2017 - 01:12:46 PST)
[AMBER] hbond Backbone CPPTRAJ.
- Daniel Roe (Mon Jan 30 2017 - 08:53:15 PST)
- Saman Yousuf ali (Sun Jan 29 2017 - 08:19:38 PST)
[AMBER] How to have a certain number of water molecules?
- David Case (Fri Jan 13 2017 - 10:29:43 PST)
- Azade Yazdan Yar (Fri Jan 13 2017 - 02:57:49 PST)
[AMBER] How to make restrt file for specific step
- Daniel Roe (Fri Jan 27 2017 - 10:18:15 PST)
- Bill Ross (Fri Jan 27 2017 - 09:01:57 PST)
- Thakur, Abhishek (Fri Jan 27 2017 - 06:47:09 PST)
- Thakur, Abhishek (Thu Jan 26 2017 - 15:54:20 PST)
- Bill Ross (Thu Jan 26 2017 - 15:34:33 PST)
- Bill Ross (Thu Jan 26 2017 - 13:13:01 PST)
- Thakur, Abhishek (Thu Jan 26 2017 - 12:57:33 PST)
- Daniel Roe (Thu Jan 26 2017 - 12:30:16 PST)
- Thakur, Abhishek (Thu Jan 26 2017 - 12:16:44 PST)
- Bill Ross (Thu Jan 26 2017 - 12:13:10 PST)
- Hai Nguyen (Thu Jan 26 2017 - 12:11:14 PST)
- Thakur, Abhishek (Thu Jan 26 2017 - 12:08:26 PST)
- Hai Nguyen (Thu Jan 26 2017 - 11:56:29 PST)
- Thakur, Abhishek (Thu Jan 26 2017 - 11:52:58 PST)
[AMBER] how to Neutralize system automatically?
- Eric Lang (Fri Jan 27 2017 - 03:34:35 PST)
- Albert (Fri Jan 27 2017 - 02:00:37 PST)
[AMBER] how to use depreciated cpptraj code
- Daniel Roe (Tue Jan 03 2017 - 05:24:28 PST)
- Hai Nguyen (Mon Jan 02 2017 - 11:36:51 PST)
- Hai Nguyen (Mon Jan 02 2017 - 11:33:16 PST)
- Chris Neale (Mon Jan 02 2017 - 11:21:24 PST)
[AMBER] Implicit Solvent CpHMD
- Chase Zagorec-Marks (Fri Jan 27 2017 - 17:52:17 PST)
- Jason Swails (Thu Jan 26 2017 - 17:51:34 PST)
- Chase Zagorec-Marks (Thu Jan 26 2017 - 12:29:21 PST)
[AMBER] In REMD there is two irest=0 in amber tut
- Bill Ross (Mon Jan 23 2017 - 11:16:47 PST)
- Thakur, Abhishek (Mon Jan 23 2017 - 09:18:38 PST)
[AMBER] INCREASING BOX SIZE
- David Case (Mon Jan 23 2017 - 18:48:58 PST)
- Subashini .K (Mon Jan 23 2017 - 08:05:51 PST)
[AMBER] Installing Amber
- Karla Galdamez (Thu Jan 26 2017 - 23:08:06 PST)
- David Case (Thu Jan 26 2017 - 05:21:50 PST)
- Karla Galdamez (Wed Jan 25 2017 - 23:08:38 PST)
- David A Case (Wed Jan 25 2017 - 05:03:35 PST)
- Karla Galdamez (Tue Jan 24 2017 - 22:29:22 PST)
- Hai Nguyen (Sat Jan 21 2017 - 21:55:26 PST)
- Karla Galdamez (Sat Jan 21 2017 - 21:44:14 PST)
- Bill Ross (Sat Jan 21 2017 - 01:10:55 PST)
- Hai Nguyen (Fri Jan 20 2017 - 23:43:13 PST)
- Karla Galdamez (Fri Jan 20 2017 - 23:28:48 PST)
- Hai Nguyen (Fri Jan 20 2017 - 21:58:11 PST)
- Karla Galdamez (Fri Jan 20 2017 - 21:53:30 PST)
- Nhai (Tue Jan 17 2017 - 22:47:23 PST)
- Karla Galdamez (Tue Jan 17 2017 - 22:24:50 PST)
[AMBER] intermolecular hydrogen bonding.
- Daniel Roe (Wed Jan 25 2017 - 05:53:10 PST)
- Daniel Roe (Tue Jan 17 2017 - 06:20:05 PST)
- Saman Yousuf ali (Mon Jan 16 2017 - 02:50:55 PST)
[AMBER] Interpreting energy decomposition in Amber thermodynamic integration
- Stefan Ivanov (Mon Jan 23 2017 - 11:27:38 PST)
- David Case (Mon Jan 23 2017 - 04:45:53 PST)
- Stefan Ivanov (Sun Jan 22 2017 - 02:31:05 PST)
- David Case (Sat Jan 21 2017 - 19:05:02 PST)
- Stefan Ivanov (Fri Jan 20 2017 - 09:56:06 PST)
- David A Case (Fri Jan 20 2017 - 09:25:05 PST)
- Stefan Ivanov (Fri Jan 20 2017 - 07:28:00 PST)
[AMBER] Ion Parameters for tip4pfb
- David Case (Thu Jan 05 2017 - 17:19:14 PST)
- Huang Jing (Thu Jan 05 2017 - 13:40:51 PST)
- Samaneh Ghassabi Kondalaji (Thu Jan 05 2017 - 09:44:25 PST)
[AMBER] Is there any command in tleap by which I can change Met to Leu
- Hai Nguyen (Fri Jan 27 2017 - 13:06:53 PST)
- David Case (Fri Jan 27 2017 - 12:47:43 PST)
- Thakur, Abhishek (Fri Jan 27 2017 - 08:04:41 PST)
[AMBER] is there any way by which I can use tleap to do mutation?
- Gustavo Seabra (Mon Jan 30 2017 - 06:24:41 PST)
- Elvis Martis (Sat Jan 28 2017 - 21:12:56 PST)
- Thakur, Abhishek (Fri Jan 27 2017 - 10:00:10 PST)
[AMBER] Issue with solvateOct for a large system
- David Case (Wed Jan 25 2017 - 11:10:12 PST)
- benedikt.diewald.fau.de (Wed Jan 25 2017 - 07:03:34 PST)
[AMBER] Issues for updating AmberTools 16 - update.14
- Kihoon.Yoon.dell.com (Thu Jan 12 2017 - 11:20:35 PST)
- Daniel Roe (Thu Jan 12 2017 - 10:36:47 PST)
- Kihoon.Yoon.dell.com (Thu Jan 12 2017 - 09:03:59 PST)
[AMBER] Kmeans-clustering : AvgDist query
- Daniel Roe (Fri Jan 20 2017 - 13:54:29 PST)
- Bala subramanian (Wed Jan 18 2017 - 02:51:04 PST)
[AMBER] lipid membrane tleap problem amber16
- Dickson, Callum J (Tue Jan 17 2017 - 06:29:45 PST)
- Sofia Vasilakaki (Mon Jan 16 2017 - 12:32:21 PST)
[AMBER] LJ parameters in frcmod files
- Pengfei Li (Thu Jan 12 2017 - 12:12:59 PST)
- Jacob Monroe (Thu Jan 12 2017 - 11:53:09 PST)
- Pengfei Li (Thu Jan 12 2017 - 11:11:19 PST)
- Jacob Monroe (Thu Jan 12 2017 - 10:34:37 PST)
[AMBER] lj1264 pmemd.cuda
- Marcelo Andrade Chagas (Tue Jan 31 2017 - 06:57:01 PST)
- Christina Bergonzo (Tue Jan 31 2017 - 06:11:59 PST)
- Marcelo Andrade Chagas (Tue Jan 31 2017 - 05:36:59 PST)
- Andreas Tosstorff (Tue Jan 31 2017 - 05:18:48 PST)
- Qinghua Liao (Tue Jan 31 2017 - 05:11:50 PST)
- Ross Walker (Tue Jan 31 2017 - 05:08:08 PST)
- Marcelo Andrade Chagas (Tue Jan 31 2017 - 04:53:51 PST)
- Ross Walker (Tue Jan 31 2017 - 04:24:24 PST)
- Andreas Tosstorff (Tue Jan 31 2017 - 01:40:32 PST)
[AMBER] matching times from .out with frames from .mdcrd
- David A Case (Wed Jan 18 2017 - 12:37:06 PST)
- Daniel Roe (Tue Jan 17 2017 - 10:19:21 PST)
- Chris Neale (Tue Jan 17 2017 - 10:00:30 PST)
[AMBER] MD for covalent inhibitors
- Huang Jing (Thu Jan 12 2017 - 15:12:15 PST)
- Ren Jinhong (Thu Jan 12 2017 - 14:23:58 PST)
[AMBER] Methods to count the different species
- Liyang Zhu (Tue Jan 31 2017 - 12:32:23 PST)
[AMBER] minimum distance between two sets of atoms
- anu chandra (Thu Jan 12 2017 - 04:59:38 PST)
- Hai Nguyen (Wed Jan 11 2017 - 09:20:22 PST)
- anu chandra (Wed Jan 11 2017 - 08:55:03 PST)
[AMBER] mmCIF from amber
- Nhai (Wed Jan 04 2017 - 09:00:28 PST)
- Thomas Pochapsky (Wed Jan 04 2017 - 06:34:22 PST)
[AMBER] MMPBSA failed
- Dwight McGee (Tue Jan 31 2017 - 08:31:35 PST)
- Albert (Tue Jan 31 2017 - 07:41:15 PST)
- Vlad Cojocaru (Tue Jan 31 2017 - 07:07:23 PST)
- Albert (Tue Jan 31 2017 - 06:57:07 PST)
- Vlad Cojocaru (Tue Jan 31 2017 - 06:55:40 PST)
- Albert (Tue Jan 31 2017 - 06:42:21 PST)
- Vlad Cojocaru (Tue Jan 31 2017 - 06:28:56 PST)
- Albert (Tue Jan 31 2017 - 05:38:27 PST)
- Albert (Tue Jan 31 2017 - 05:36:24 PST)
- Vlad Cojocaru (Tue Jan 31 2017 - 01:38:32 PST)
- Albert (Tue Jan 31 2017 - 01:27:37 PST)
- Vlad Cojocaru (Tue Jan 31 2017 - 01:25:54 PST)
- Elvis Martis (Tue Jan 31 2017 - 01:12:49 PST)
- Albert (Tue Jan 31 2017 - 00:00:31 PST)
- Albert (Mon Jan 30 2017 - 23:28:55 PST)
[AMBER] Model Folding
- Nhai (Tue Jan 17 2017 - 22:43:38 PST)
- Wong Li Zhe (Tue Jan 17 2017 - 22:23:16 PST)
- Nhai (Tue Jan 17 2017 - 19:10:19 PST)
- Wong Li Zhe (Tue Jan 17 2017 - 18:49:02 PST)
[AMBER] Modified residue separated in leap module
- David Case (Tue Jan 17 2017 - 05:53:56 PST)
- asdda asa (Mon Jan 16 2017 - 17:16:10 PST)
[AMBER] Molecular Modelling Workshop: March 27-29, 2017 in Erlangen, Germany
- Dr. Anselm Horn (Tue Jan 24 2017 - 00:20:22 PST)
[AMBER] mpi error in Amber16
- Hirdesh Kumar (Mon Jan 30 2017 - 15:45:20 PST)
- Hirdesh Kumar (Mon Jan 30 2017 - 14:56:11 PST)
- case (Mon Jan 30 2017 - 14:52:46 PST)
- Hirdesh Kumar (Mon Jan 30 2017 - 12:26:34 PST)
[AMBER] Multiple ligands in MMGBSA
- Abhilash J (Tue Jan 31 2017 - 08:20:05 PST)
[AMBER] New user needs help
- imam siswanto (Wed Jan 11 2017 - 21:24:17 PST)
- Hai Nguyen (Wed Jan 11 2017 - 20:49:21 PST)
- imam siswanto (Wed Jan 11 2017 - 20:23:26 PST)
[AMBER] Ntt value for Nose-hoover chain thermostat
- Samaneh Ghassabi Kondalaji (Mon Jan 23 2017 - 08:01:33 PST)
- David Case (Sat Jan 21 2017 - 19:15:11 PST)
- Samaneh Ghassabi Kondalaji (Fri Jan 20 2017 - 12:46:39 PST)
[AMBER] Parameters
- FyD (Mon Jan 30 2017 - 01:12:16 PST)
- FyD (Mon Jan 30 2017 - 00:25:08 PST)
- David Case (Fri Jan 27 2017 - 12:49:51 PST)
- Anna Cebrian Prats (Fri Jan 27 2017 - 09:00:24 PST)
[AMBER] paramfit
- stephanie.essafi.ens.fr (Tue Jan 24 2017 - 05:23:03 PST)
[AMBER] partial replica exchange molecular dynamics
- Huang Jing (Tue Jan 03 2017 - 08:50:28 PST)
- Johannes Loeffler (Mon Jan 02 2017 - 06:09:30 PST)
[AMBER] Peptide with non-standard residues
- David Case (Fri Jan 27 2017 - 12:46:33 PST)
- Andreas Tosstorff (Fri Jan 27 2017 - 07:47:59 PST)
- David Case (Fri Jan 27 2017 - 06:39:27 PST)
- Andreas Tosstorff (Fri Jan 27 2017 - 03:03:36 PST)
[AMBER] pH-REMD explicit solvent
- Jason Swails (Sun Jan 29 2017 - 13:31:03 PST)
- Sowmya Indrakumar (Sun Jan 29 2017 - 12:59:57 PST)
[AMBER] pmemd.cuda.MPI not running well with SGE
- Chris Neale (Wed Jan 18 2017 - 10:06:59 PST)
- Scott Le Grand (Wed Jan 18 2017 - 10:00:51 PST)
- Ross Walker (Tue Jan 17 2017 - 17:51:40 PST)
- Daniel Roe (Tue Jan 17 2017 - 06:07:29 PST)
- Wang, Yin (Tue Jan 17 2017 - 03:22:54 PST)
[AMBER] potential energy
- Carlos Simmerling (Fri Jan 13 2017 - 03:35:26 PST)
- Albert (Fri Jan 13 2017 - 03:16:48 PST)
- Carlos Simmerling (Fri Jan 13 2017 - 03:14:55 PST)
- Albert (Fri Jan 13 2017 - 03:12:11 PST)
- Carlos Simmerling (Fri Jan 13 2017 - 03:11:20 PST)
- Albert (Fri Jan 13 2017 - 00:42:08 PST)
[AMBER] Problem in not defining the hybridization of a atomtype
- David Case (Mon Jan 02 2017 - 08:49:57 PST)
- A kS (Mon Jan 02 2017 - 08:33:24 PST)
[AMBER] Problems about membrane protein simulation
- Daniel Roe (Thu Jan 05 2017 - 06:14:14 PST)
- Huang Jing (Thu Jan 05 2017 - 01:31:40 PST)
- 吴萌 (Thu Jan 05 2017 - 00:14:51 PST)
- Huang Jing (Wed Jan 04 2017 - 07:13:16 PST)
- Shanghaitech University WuMeng (Wed Jan 04 2017 - 06:44:22 PST)
[AMBER] problems with input file preparation
- David Case (Sun Jan 29 2017 - 10:44:28 PST)
- sunyeping (Sat Jan 28 2017 - 21:39:27 PST)
- Elvis Martis (Sat Jan 28 2017 - 21:07:34 PST)
- sunyeping (Sat Jan 28 2017 - 12:23:56 PST)
[AMBER] Process exclusive mode and GPU peer-to-peer communication
- Matthew Harrigan (Fri Jan 27 2017 - 08:58:34 PST)
- Scott Le Grand (Fri Jan 27 2017 - 08:43:03 PST)
- Ross Walker (Fri Jan 27 2017 - 04:54:13 PST)
[AMBER] Pure POPC Membrane Tilts during MD simulation
- Rodriguez, Yoel (Tue Jan 24 2017 - 11:20:07 PST)
- Daniel Roe (Tue Jan 24 2017 - 10:53:54 PST)
- Rodriguez, Yoel (Tue Jan 24 2017 - 07:48:17 PST)
- Rodriguez, Yoel (Tue Jan 24 2017 - 07:41:26 PST)
- Daniel Roe (Tue Jan 24 2017 - 05:23:29 PST)
- Dickson, Callum J (Mon Jan 23 2017 - 14:41:28 PST)
- Rodriguez, Yoel (Sat Jan 21 2017 - 16:21:52 PST)
[AMBER] Python Programs
- Chase Zagorec-Marks (Mon Jan 09 2017 - 16:56:35 PST)
- Hai Nguyen (Mon Jan 09 2017 - 13:41:48 PST)
- Chase Zagorec-Marks (Mon Jan 09 2017 - 13:29:43 PST)
- Hai Nguyen (Mon Jan 09 2017 - 13:20:43 PST)
- Chase Zagorec-Marks (Mon Jan 09 2017 - 13:13:06 PST)
- Hai Nguyen (Mon Jan 09 2017 - 13:05:50 PST)
- Chase Zagorec-Marks (Mon Jan 09 2017 - 12:53:28 PST)
[AMBER] QM method used for force constants derivation in GAFF2 ?
- Marek Maly (Thu Jan 26 2017 - 16:02:29 PST)
- Junmei Wang (Thu Jan 26 2017 - 10:04:30 PST)
- Marek Maly (Tue Jan 24 2017 - 17:24:19 PST)
- David Case (Tue Jan 24 2017 - 10:44:34 PST)
- Marek Maly (Tue Jan 24 2017 - 09:47:19 PST)
[AMBER] QMMM with MOPAC2016
- Joan Torras (Tue Jan 10 2017 - 22:38:13 PST)
- Carlos SOTO GARZA (Tue Jan 10 2017 - 15:52:23 PST)
- Goetz, Andreas (Tue Jan 10 2017 - 15:37:30 PST)
- Adrian Roitberg (Tue Jan 10 2017 - 15:35:30 PST)
- Carlos SOTO GARZA (Tue Jan 10 2017 - 15:06:10 PST)
[AMBER] Question about Empirical Valence Bond(EVB) simulation
- David Case (Thu Jan 05 2017 - 18:17:18 PST)
- Huang Jing (Tue Jan 03 2017 - 20:48:27 PST)
- 没关系 (Tue Jan 03 2017 - 18:21:21 PST)
[AMBER] Radical Carbon
- Anna Cebrian Prats (Tue Jan 31 2017 - 06:54:58 PST)
[AMBER] Radius of gyration for the hydrophobic core
- Nhai (Thu Jan 12 2017 - 15:56:58 PST)
- Aishani Prem (Thu Jan 12 2017 - 15:51:38 PST)
[AMBER] RDF between centers of mass/geometry
- Lorenzo Gontrani (Thu Jan 12 2017 - 02:36:43 PST)
[AMBER] Reference for GAFF2?
- Albert (Wed Jan 18 2017 - 00:16:07 PST)
- Alan (Wed Jan 18 2017 - 00:04:06 PST)
- Albert (Tue Jan 17 2017 - 22:53:44 PST)
- Alan (Tue Jan 17 2017 - 14:36:34 PST)
[AMBER] REGARDING ACPYPE GENERATED TOPOLOGY FILE
- Subashini .K (Wed Jan 18 2017 - 21:24:05 PST)
[AMBER] Regarding forcefields for Z-DNA
- Debayan Chakraborty (Sat Jan 28 2017 - 12:29:24 PST)
- Yogeeshwar Ajjugal (Thu Jan 26 2017 - 05:55:02 PST)
- Yogeeshwar Ajjugal (Tue Jan 24 2017 - 04:01:44 PST)
- Jiri Sponer (Tue Jan 24 2017 - 02:12:35 PST)
- Yogeeshwar Ajjugal (Tue Jan 24 2017 - 01:53:24 PST)
[AMBER] Regarding trajectory analysis
- Daniel Roe (Thu Jan 19 2017 - 06:57:15 PST)
- Debodyuti Dutta (Wed Jan 18 2017 - 21:24:48 PST)
[AMBER] REMD_just_1.10ns/day
- Carlos Simmerling (Tue Jan 24 2017 - 16:37:40 PST)
- Hai Nguyen (Tue Jan 24 2017 - 15:21:34 PST)
- Thakur, Abhishek (Tue Jan 24 2017 - 15:11:57 PST)
- Adrian Roitberg (Tue Jan 24 2017 - 13:09:35 PST)
- Thakur, Abhishek (Tue Jan 24 2017 - 12:58:37 PST)
- Carlos Simmerling (Tue Jan 24 2017 - 12:50:28 PST)
- Hai Nguyen (Tue Jan 24 2017 - 11:33:43 PST)
- Thakur, Abhishek (Tue Jan 24 2017 - 11:15:12 PST)
- Hai Nguyen (Tue Jan 24 2017 - 11:01:44 PST)
- Thakur, Abhishek (Tue Jan 24 2017 - 10:53:26 PST)
[AMBER] REMD_Multiple_GPU
- Hai Nguyen (Thu Jan 19 2017 - 08:36:17 PST)
- Thakur, Abhishek (Thu Jan 19 2017 - 08:29:57 PST)
[AMBER] REMD_suggestion
- Thakur, Abhishek (Mon Jan 23 2017 - 09:05:23 PST)
- Adrian Roitberg (Mon Jan 23 2017 - 09:01:31 PST)
- Thakur, Abhishek (Mon Jan 23 2017 - 08:59:45 PST)
- Adrian Roitberg (Mon Jan 23 2017 - 08:50:29 PST)
- Thakur, Abhishek (Mon Jan 23 2017 - 08:46:51 PST)
- Hai Nguyen (Wed Jan 18 2017 - 08:33:45 PST)
- Thakur, Abhishek (Wed Jan 18 2017 - 07:03:26 PST)
[AMBER] Remove motion of center of mass after obtaining trajectory
- Daniel Roe (Tue Jan 03 2017 - 06:06:17 PST)
[AMBER] Reproduce tetraalanine Phi and Psi amplitudes ff99SB with Paramfit
- Robin Betz (Tue Jan 24 2017 - 14:43:43 PST)
- Carlos Simmerling (Tue Jan 24 2017 - 12:49:13 PST)
- Robin Betz (Tue Jan 24 2017 - 11:35:16 PST)
- BOSISIO Stefano (Tue Jan 24 2017 - 11:07:29 PST)
[AMBER] restrain protein with two different force constant
- Elvis Martis (Tue Jan 10 2017 - 07:11:26 PST)
- Khabiri, Morteza (Tue Jan 10 2017 - 06:58:47 PST)
[AMBER] rmsf value for 2 chains
- Daniel Roe (Fri Jan 20 2017 - 13:56:55 PST)
- Hirdesh Kumar (Tue Jan 17 2017 - 15:08:59 PST)
[AMBER] Sander input into Gaussian
- Aseel Bala (Thu Jan 12 2017 - 13:02:07 PST)
- Adrian Roitberg (Thu Jan 12 2017 - 10:23:48 PST)
- Aseel Bala (Thu Jan 12 2017 - 10:17:37 PST)
- Huang Jing (Wed Jan 11 2017 - 14:33:17 PST)
- Aseel Bala (Wed Jan 11 2017 - 13:55:58 PST)
[AMBER] script to run background job?
- Hannes Loeffler (Tue Jan 31 2017 - 00:53:32 PST)
- Hannes Loeffler (Tue Jan 31 2017 - 00:23:00 PST)
- Andrea Spitaleri (Tue Jan 31 2017 - 00:04:09 PST)
- Michael Shokhen (Mon Jan 30 2017 - 08:56:33 PST)
- Elvis Martis (Mon Jan 30 2017 - 08:35:26 PST)
- Hai Nguyen (Mon Jan 30 2017 - 08:34:10 PST)
- Michael Shokhen (Mon Jan 30 2017 - 08:31:50 PST)
[AMBER] setup_equilibrate_input.x
- Hai Nguyen (Thu Jan 19 2017 - 14:15:14 PST)
- Thakur, Abhishek (Thu Jan 19 2017 - 11:40:09 PST)
[AMBER] Simple normal mode analysis in amber
- David Case (Sat Jan 07 2017 - 15:09:10 PST)
- Huang Jing (Sat Jan 07 2017 - 12:18:53 PST)
- Ella Gale (Sat Jan 07 2017 - 09:15:45 PST)
[AMBER] Simulating lipid bilayer below phase transition temperature
- Dickson, Callum J (Tue Jan 24 2017 - 11:06:28 PST)
- Casalini Tommaso (Tue Jan 24 2017 - 07:41:32 PST)
- Dickson, Callum J (Mon Jan 23 2017 - 14:37:52 PST)
- Casalini Tommaso (Mon Jan 23 2017 - 14:12:24 PST)
[AMBER] Single-Point MM-PBSA/GBSA Energy Calculations
- Huang Jing (Sat Jan 14 2017 - 08:59:24 PST)
- Nhai (Sat Jan 14 2017 - 08:55:29 PST)
- Naiem Issa (Sat Jan 14 2017 - 08:38:43 PST)
- Hai Nguyen (Sat Jan 14 2017 - 08:31:01 PST)
- Naiem Issa (Sat Jan 14 2017 - 08:20:10 PST)
[AMBER] Some notes
- David Case (Sat Jan 14 2017 - 12:41:03 PST)
- erik rp zuiderweg (Sat Jan 14 2017 - 11:12:01 PST)
[AMBER] Split a trajectory into frames
- Elisa Pieri (Thu Jan 26 2017 - 08:12:59 PST)
- Daniel Roe (Thu Jan 26 2017 - 08:00:38 PST)
- Nhai (Thu Jan 26 2017 - 07:57:27 PST)
- Elisa Pieri (Thu Jan 26 2017 - 07:53:45 PST)
- Kenneth Huang (Thu Jan 26 2017 - 07:48:10 PST)
- Adrian Roitberg (Thu Jan 26 2017 - 07:47:47 PST)
- Casalini Tommaso (Thu Jan 26 2017 - 07:45:55 PST)
- Elisa Pieri (Thu Jan 26 2017 - 07:42:31 PST)
- Nhai (Thu Jan 26 2017 - 07:38:17 PST)
- Elisa Pieri (Thu Jan 26 2017 - 07:30:26 PST)
- Nhai (Thu Jan 26 2017 - 07:26:01 PST)
- Elisa Pieri (Thu Jan 26 2017 - 07:10:19 PST)
- Daniel Roe (Thu Jan 26 2017 - 07:09:47 PST)
- Kenneth Huang (Thu Jan 26 2017 - 06:50:51 PST)
- Elisa Pieri (Thu Jan 26 2017 - 06:35:11 PST)
[AMBER] Split trajectory by atom
- The Cromicus Productions (Tue Jan 10 2017 - 00:01:25 PST)
- Hai Nguyen (Mon Jan 09 2017 - 06:26:30 PST)
- The Cromicus Productions (Mon Jan 09 2017 - 02:22:41 PST)
[AMBER] strip inpcrd
- Daniel Roe (Tue Jan 31 2017 - 05:10:32 PST)
- Saman Yousuf ali (Tue Jan 31 2017 - 02:46:44 PST)
- Elvis Martis (Tue Jan 31 2017 - 01:33:17 PST)
- Saman Yousuf ali (Tue Jan 31 2017 - 00:58:53 PST)
[AMBER] the formatting of the CPPTRAJ-generated restart files
- Vlad Cojocaru (Fri Jan 27 2017 - 02:26:08 PST)
- Hannes Loeffler (Fri Jan 27 2017 - 02:12:46 PST)
- Vlad Cojocaru (Fri Jan 27 2017 - 01:56:54 PST)
[AMBER] Thermodynamic Integration on GPU in AMBER16?
- Daniel Mermelstein (Thu Jan 26 2017 - 18:58:21 PST)
- Hadházi Ádám (Thu Jan 26 2017 - 13:30:12 PST)
[AMBER] TI simulations blowing up with clambda = 1 with pmemd
- Stefan Ivanov (Mon Jan 30 2017 - 06:20:43 PST)
- Hannes Loeffler (Mon Jan 30 2017 - 03:11:23 PST)
- Stefan Ivanov (Mon Jan 30 2017 - 02:22:04 PST)
- Hannes Loeffler (Mon Jan 30 2017 - 01:02:58 PST)
- Stefan Ivanov (Sun Jan 29 2017 - 07:07:13 PST)
- David Case (Fri Jan 27 2017 - 12:42:19 PST)
- Stefan Ivanov (Fri Jan 27 2017 - 08:17:55 PST)
- Hannes Loeffler (Fri Jan 27 2017 - 08:13:53 PST)
- Stefan Ivanov (Fri Jan 27 2017 - 08:09:16 PST)
- Stefan Ivanov (Fri Jan 27 2017 - 08:00:21 PST)
- Hannes Loeffler (Fri Jan 27 2017 - 07:46:01 PST)
- Stefan Ivanov (Fri Jan 27 2017 - 06:54:38 PST)
- Hannes Loeffler (Fri Jan 27 2017 - 06:04:07 PST)
- Hannes Loeffler (Fri Jan 27 2017 - 03:30:46 PST)
- Stefan Ivanov (Fri Jan 27 2017 - 03:15:02 PST)
[AMBER] TIP4P-Ew vs TIP3 vs TIP5
- Saeed Izadi (Wed Jan 18 2017 - 13:17:45 PST)
- DmitrySuplatov (Wed Jan 18 2017 - 03:13:35 PST)
- Saeed Izadi (Tue Jan 17 2017 - 21:13:41 PST)
- Elvis Martis (Tue Jan 17 2017 - 21:03:57 PST)
- DmitryASuplatov (Tue Jan 17 2017 - 07:21:30 PST)
[AMBER] tLeap adding non-library hydrogens
- David Case (Sun Jan 08 2017 - 18:43:32 PST)
- David Poole (Sun Jan 08 2017 - 12:41:46 PST)
- David Case (Sat Jan 07 2017 - 14:58:10 PST)
- Huang Jing (Sat Jan 07 2017 - 04:41:52 PST)
- David Poole (Sat Jan 07 2017 - 04:07:10 PST)
- David Case (Wed Jan 04 2017 - 05:20:47 PST)
- Huang Jing (Wed Jan 04 2017 - 02:16:38 PST)
- David Poole (Wed Jan 04 2017 - 02:07:31 PST)
[AMBER] tLeap and acetonitrile/chloroform solvation
- Luka Bilić (Thu Jan 05 2017 - 00:17:51 PST)
- Luka Bilić (Thu Jan 05 2017 - 00:09:41 PST)
- David Case (Wed Jan 04 2017 - 18:51:18 PST)
- Huang Jing (Wed Jan 04 2017 - 07:33:25 PST)
- Luka Bilić (Wed Jan 04 2017 - 06:12:51 PST)
[AMBER] TLEAP error
- David Case (Thu Jan 12 2017 - 08:57:27 PST)
- Subashini .K (Thu Jan 12 2017 - 06:39:55 PST)
- David Case (Thu Jan 12 2017 - 05:17:22 PST)
- Huang Jing (Thu Jan 12 2017 - 02:28:00 PST)
- Subashini .K (Thu Jan 12 2017 - 00:15:54 PST)
[AMBER] valiine chirality inversion
- David Case (Sat Jan 21 2017 - 19:09:18 PST)
- Thomas Pochapsky (Thu Jan 19 2017 - 05:52:10 PST)
[AMBER] verification of ligand rmsd script.
- Daniel Roe (Thu Jan 12 2017 - 06:05:11 PST)
- Daniel Roe (Wed Jan 11 2017 - 06:46:41 PST)
- Elvis Martis (Wed Jan 11 2017 - 06:38:15 PST)
- Saman Yousuf ali (Wed Jan 11 2017 - 03:11:53 PST)
[AMBER] visualization problem
- Adrian Roitberg (Tue Jan 31 2017 - 09:24:42 PST)
- Daniel Roe (Tue Jan 31 2017 - 09:22:10 PST)
- Andreas Tosstorff (Tue Jan 31 2017 - 08:21:32 PST)
- Albert (Tue Jan 31 2017 - 08:18:21 PST)
- Albert (Tue Jan 31 2017 - 08:17:05 PST)
- Hai Nguyen (Tue Jan 31 2017 - 08:15:03 PST)
- Albert (Tue Jan 31 2017 - 08:13:49 PST)
- Hai Nguyen (Tue Jan 31 2017 - 08:11:19 PST)
- Albert (Tue Jan 31 2017 - 08:09:13 PST)
[AMBER] VMD not working after parmed
- Andreas Tosstorff (Mon Jan 30 2017 - 02:33:56 PST)
[AMBER] VMD/netcdf
- Adrian Roitberg (Thu Jan 05 2017 - 07:09:50 PST)
[AMBER] Water density near the protein suspiciously low
- I Lőrincz (Tue Jan 03 2017 - 15:46:04 PST)
[AMBER] xmin and QM/MM
- Goetz, Andreas (Fri Jan 06 2017 - 02:37:44 PST)
- Åsmund Kjendseth Røhr (Fri Jan 06 2017 - 01:19:33 PST)
[AMBER] Zinc +2 SMD pulling
- Fabian Glaser (Wed Jan 04 2017 - 03:39:17 PST)
- Huang Jing (Wed Jan 04 2017 - 03:34:19 PST)
- Fabian gmail (Wed Jan 04 2017 - 02:24:44 PST)
- Huang Jing (Wed Jan 04 2017 - 02:07:18 PST)
- Fabian gmail (Wed Jan 04 2017 - 01:33:29 PST)
[AMBER] ZINC PERMEATION PATHWAY
- Fabian gmail (Wed Jan 04 2017 - 06:59:02 PST)
- Daniel Roe (Wed Jan 04 2017 - 06:13:49 PST)
- Fabian gmail (Wed Jan 04 2017 - 05:09:53 PST)
[AMBER] 回复： Question about Empirical Valence Bond(EVB) simulation
- 没关系 (Tue Jan 03 2017 - 22:55:31 PST)
[AMBER] 回复：AMBER Digest, Vol 1806, Issue 1
- wei (Fri Jan 06 2017 - 21:42:38 PST)
Modified residue separated in leap module]
- asdda asa (Mon Jan 23 2017 - 17:00:27 PST)
- Bill Ross (Mon Jan 23 2017 - 15:33:24 PST)
- asdda asa (Mon Jan 23 2017 - 12:34:29 PST)
- David Case (Mon Jan 23 2017 - 04:52:52 PST)
Problems with imaging
- Daniel Roe (Mon Jan 09 2017 - 06:25:41 PST)
Process exclusive mode and GPU peer-to-peer communication
- Matthew Harrigan (Thu Jan 26 2017 - 14:12:39 PST)

Amber Archive Jan 2017 by subject