Amber Archive Nov 2016: by subject

[AMBER] 20161121141138.GE88784.scarletmail.rutgers.edu
- Taylor, Miles (Wed Nov 23 2016 - 07:56:48 PST)
- David Cerutti (Mon Nov 21 2016 - 13:20:57 PST)
- Taylor, Miles (Mon Nov 21 2016 - 12:36:36 PST)
[AMBER] [Amber] Calculating Normal Modes with Restrictions
- The Cromicus Productions (Tue Nov 22 2016 - 06:49:26 PST)
- The Cromicus Productions (Tue Nov 22 2016 - 06:30:50 PST)
- David A Case (Tue Nov 22 2016 - 05:11:35 PST)
- The Cromicus Productions (Mon Nov 21 2016 - 17:00:26 PST)
[AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb)
- The Cromicus Productions (Fri Nov 18 2016 - 17:12:39 PST)
- Hai Nguyen (Fri Nov 18 2016 - 17:09:35 PST)
- The Cromicus Productions (Fri Nov 18 2016 - 16:29:10 PST)
- Hai Nguyen (Fri Nov 18 2016 - 13:06:33 PST)
- The Cromicus Productions (Fri Nov 18 2016 - 13:02:11 PST)
- Hai Nguyen (Fri Nov 18 2016 - 10:30:01 PST)
- The Cromicus Productions (Fri Nov 18 2016 - 10:26:21 PST)
[AMBER] [mdout_analyzer.py] Problem with OS X El Capitan
- Jason Swails (Tue Nov 01 2016 - 06:13:49 PDT)
- Eiros Zamora, Juan (Tue Nov 01 2016 - 06:11:45 PDT)
- Eiros Zamora, Juan (Tue Nov 01 2016 - 05:59:46 PDT)
[AMBER] About multiconformations RESP fitting
- Marion, Antoine (Fri Nov 25 2016 - 01:40:07 PST)
- FyD (Fri Nov 25 2016 - 00:07:34 PST)
- Marion, Antoine (Thu Nov 24 2016 - 05:38:45 PST)
- FyD (Thu Nov 24 2016 - 02:32:38 PST)
- Marion, Antoine (Thu Nov 24 2016 - 01:06:32 PST)
- David Cerutti (Wed Nov 23 2016 - 10:40:17 PST)
- Marion, Antoine (Wed Nov 23 2016 - 09:29:29 PST)
- David Cerutti (Wed Nov 23 2016 - 08:27:01 PST)
- Marion, Antoine (Wed Nov 23 2016 - 07:39:16 PST)
[AMBER] AMBER Digest, Vol 1763, Issue 1
- 冯国强 (Tue Nov 22 2016 - 00:52:41 PST)
[AMBER] AMBER FF for intrinsically disordered protein
- Neha Gandhi (Tue Nov 08 2016 - 19:56:46 PST)
- giulia palermo (Tue Nov 08 2016 - 19:53:35 PST)
[AMBER] AMBER Materials modelling- periodic image
- Pengfei Li (Mon Nov 28 2016 - 13:17:21 PST)
- Neha Gandhi (Sun Nov 27 2016 - 21:41:46 PST)
[AMBER] ambmask issue
- Aseel Bala (Thu Nov 17 2016 - 10:21:11 PST)
- Aseel Bala (Thu Nov 10 2016 - 15:22:18 PST)
- Hai Nguyen (Thu Nov 10 2016 - 15:11:29 PST)
- Aseel Bala (Thu Nov 10 2016 - 15:08:01 PST)
[AMBER] aMD with dt=0.004
- Nhai (Wed Nov 23 2016 - 07:47:16 PST)
- Thakur, Abhishek (Wed Nov 23 2016 - 06:53:34 PST)
[AMBER] Are Intel compilers free for academics?
- David A Case (Fri Nov 04 2016 - 05:08:32 PDT)
[AMBER] ATP Parameters for ff14SB
- David A Case (Wed Nov 16 2016 - 17:38:13 PST)
- David Cerutti (Wed Nov 16 2016 - 14:07:23 PST)
- Stevens, David Ryan (Wed Nov 16 2016 - 13:57:21 PST)
[AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations?
- Carlos Simmerling (Mon Nov 07 2016 - 06:10:11 PST)
- Adrian Roitberg (Mon Nov 07 2016 - 06:02:17 PST)
- Eric Lang (Mon Nov 07 2016 - 03:29:57 PST)
- Jason Swails (Fri Nov 04 2016 - 12:52:26 PDT)
- Carlos Simmerling (Fri Nov 04 2016 - 08:22:16 PDT)
- Eric Lang (Fri Nov 04 2016 - 08:08:55 PDT)
[AMBER] can not find chamber in amber16?
- Nhai (Fri Nov 04 2016 - 09:34:04 PDT)
- Neale, Christopher Andrew (Fri Nov 04 2016 - 09:25:51 PDT)
[AMBER] Can we combine amber and gaff atom types?
- David Cerutti (Thu Nov 03 2016 - 10:13:21 PDT)
- Aditya G Rao (Thu Nov 03 2016 - 09:39:58 PDT)
- David Cerutti (Wed Nov 02 2016 - 13:44:42 PDT)
- Carlos Simmerling (Wed Nov 02 2016 - 07:16:29 PDT)
- Aditya G Rao (Wed Nov 02 2016 - 06:55:12 PDT)
[AMBER] cap the 5' phosphate of a RNA
- Mohaddeseh Habibzadeh (Mon Nov 21 2016 - 11:48:23 PST)
[AMBER] compatibility
- Magno . (Wed Nov 16 2016 - 10:13:16 PST)
[AMBER] Compatibility of Amber parameters for FF99 and FF14SB forcefields
- Carlos Simmerling (Tue Nov 15 2016 - 08:25:12 PST)
- DmitryASuplatov (Tue Nov 15 2016 - 08:12:45 PST)
[AMBER] compute RESP charges
- asdda asa (Thu Nov 10 2016 - 14:14:00 PST)
- Dr. Anselm Horn (Thu Nov 10 2016 - 02:21:31 PST)
- asdda asa (Wed Nov 09 2016 - 14:16:45 PST)
[AMBER] Constant pH charge set
- Jason Swails (Thu Nov 10 2016 - 06:22:12 PST)
- Fabrício Bracht (Thu Nov 10 2016 - 06:05:42 PST)
[AMBER] Constraints
- Jason Swails (Tue Nov 15 2016 - 11:20:07 PST)
- Roitberg,Adrian E (Tue Nov 15 2016 - 06:21:01 PST)
- David A Case (Tue Nov 15 2016 - 05:19:34 PST)
- Ol Sta (Fri Nov 11 2016 - 06:34:07 PST)
[AMBER] Convert mdcrd files into pbd files
- Daniel Roe (Sun Nov 27 2016 - 11:01:15 PST)
- Nhai (Fri Nov 25 2016 - 14:52:28 PST)
- The Cromicus Productions (Fri Nov 25 2016 - 14:47:00 PST)
[AMBER] Convert prm into prmtop - from NAMD to AMBER
- The Cromicus Productions (Mon Nov 21 2016 - 11:43:44 PST)
- Amy Rice (Mon Nov 21 2016 - 11:39:05 PST)
- The Cromicus Productions (Mon Nov 21 2016 - 11:36:27 PST)
- Hai Nguyen (Mon Nov 21 2016 - 11:29:31 PST)
- The Cromicus Productions (Mon Nov 21 2016 - 11:21:43 PST)
[AMBER] Converting a PDB Collection to a NetCDF trajectory
- Christina Bergonzo (Fri Nov 18 2016 - 12:30:48 PST)
- Hai Nguyen (Fri Nov 18 2016 - 12:19:33 PST)
- Dmitry Suplatov (Fri Nov 18 2016 - 12:11:41 PST)
[AMBER] Converting coordinate file generated into pdb format for nuparm
- ABHIJEET CHOWDHURY (Thu Nov 17 2016 - 06:52:33 PST)
- Nhai (Thu Nov 17 2016 - 06:44:11 PST)
- ABHIJEET CHOWDHURY (Thu Nov 17 2016 - 06:39:02 PST)
- David A Case (Thu Nov 17 2016 - 05:45:46 PST)
- ABHIJEET CHOWDHURY (Thu Nov 17 2016 - 04:43:59 PST)
[AMBER] Coordinates for PEG4K, Folic acid and chitin
- Abdul Ajees (Tue Nov 08 2016 - 03:02:37 PST)
[AMBER] Could not find enough velocities in .rst
- Ruth Helena Tichauer (Wed Nov 23 2016 - 05:33:33 PST)
- Daniel Roe (Wed Nov 23 2016 - 05:02:42 PST)
- Ruth Helena Tichauer (Wed Nov 23 2016 - 01:52:23 PST)
- Daniel Roe (Tue Nov 22 2016 - 10:28:08 PST)
- Ruth Helena Tichauer (Tue Nov 22 2016 - 09:21:32 PST)
[AMBER] covalently bound ligand
- FyD (Mon Nov 14 2016 - 23:36:17 PST)
- David A Case (Mon Nov 14 2016 - 18:08:18 PST)
- Ahsan Mohd (Mon Nov 14 2016 - 10:20:14 PST)
[AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD
- Daniel Roe (Wed Nov 30 2016 - 11:18:17 PST)
- Daniel Roe (Tue Nov 29 2016 - 13:02:44 PST)
- Brian Radak (Tue Nov 29 2016 - 11:34:18 PST)
- Daniel Roe (Tue Nov 29 2016 - 11:26:29 PST)
- Brian Radak (Tue Nov 29 2016 - 10:56:50 PST)
- Daniel Roe (Tue Nov 29 2016 - 10:48:38 PST)
- Brian Radak (Tue Nov 29 2016 - 10:24:05 PST)
[AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped)
- Daniel Roe (Tue Nov 08 2016 - 08:17:35 PST)
- Michael Shokhen (Tue Nov 08 2016 - 07:38:40 PST)
- Daniel Roe (Tue Nov 08 2016 - 06:56:51 PST)
- Samuel Bowerman (Tue Nov 08 2016 - 06:23:31 PST)
- Michael Shokhen (Tue Nov 08 2016 - 05:28:06 PST)
[AMBER] cpptraj error: 'cluster': Command not found.
- Ruth Helena Tichauer (Fri Nov 04 2016 - 01:51:17 PDT)
- Daniel Roe (Thu Nov 03 2016 - 18:41:21 PDT)
- Ruth Helena Tichauer (Thu Nov 03 2016 - 08:59:45 PDT)
[AMBER] cpptraj RMSD calculation with mismatch residue numbers
- Daniel Roe (Wed Nov 30 2016 - 13:07:00 PST)
- anu chandra (Fri Nov 18 2016 - 05:12:32 PST)
- Nhai (Wed Nov 16 2016 - 15:26:16 PST)
- anu chandra (Wed Nov 16 2016 - 15:02:04 PST)
[AMBER] cpptraj: RMSD vs Residue Number.
- Daniel Roe (Fri Nov 11 2016 - 04:10:26 PST)
- Saman Yousuf ali (Fri Nov 11 2016 - 00:48:23 PST)
[AMBER] creating 5' phosphate groups
- Mohaddeseh Habibzadeh (Sun Nov 27 2016 - 10:05:57 PST)
- David A Case (Sun Nov 27 2016 - 05:44:06 PST)
- Mohaddeseh Habibzadeh (Sun Nov 27 2016 - 03:12:22 PST)
- David A Case (Mon Nov 21 2016 - 14:36:13 PST)
[AMBER] creating parameters for integrins
- Tsibela German Tebello Mofokeng (Thu Nov 17 2016 - 23:40:38 PST)
- Nhai (Thu Nov 17 2016 - 09:44:00 PST)
- Tsibela German Tebello Mofokeng (Thu Nov 17 2016 - 09:22:03 PST)
[AMBER] CUDA version for Amber14
- Ross Walker (Thu Nov 10 2016 - 06:57:27 PST)
- Sofia Vasilakaki (Wed Nov 09 2016 - 14:17:39 PST)
[AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered
- David A Case (Fri Nov 04 2016 - 04:58:41 PDT)
- Andreas Tosstorff (Thu Nov 03 2016 - 05:15:47 PDT)
[AMBER] cudaMemcpyToSymbol Error
- Ross Walker (Mon Nov 28 2016 - 05:46:45 PST)
- Charles Lin (Mon Nov 28 2016 - 01:28:46 PST)
- Charles Lin (Mon Nov 28 2016 - 01:27:35 PST)
- cuiyinglukitty (Mon Nov 28 2016 - 00:45:48 PST)
[AMBER] DIfferences between thermostats
- Gustavo Seabra (Thu Nov 24 2016 - 05:23:58 PST)
- Markowska (Thu Nov 24 2016 - 05:10:43 PST)
- Gustavo Seabra (Thu Nov 24 2016 - 04:58:43 PST)
- Markowska (Wed Nov 23 2016 - 14:45:17 PST)
- David Cerutti (Wed Nov 23 2016 - 14:04:48 PST)
- Markowska (Wed Nov 23 2016 - 13:26:54 PST)
- Gustavo Seabra (Wed Nov 23 2016 - 13:22:32 PST)
- Markowska (Wed Nov 23 2016 - 10:54:16 PST)
- Gustavo Seabra (Wed Nov 23 2016 - 08:45:47 PST)
- Nhai (Wed Nov 23 2016 - 07:57:59 PST)
- Marc van der Kamp (Wed Nov 23 2016 - 07:53:48 PST)
- David Cerutti (Wed Nov 23 2016 - 07:48:24 PST)
- Markowska (Wed Nov 23 2016 - 00:14:47 PST)
- David A Case (Tue Nov 22 2016 - 17:36:46 PST)
- David Cerutti (Tue Nov 22 2016 - 15:40:04 PST)
- Adrian Roitberg (Tue Nov 22 2016 - 15:28:14 PST)
- David Cerutti (Tue Nov 22 2016 - 14:42:05 PST)
- Geoffrey Gray (Tue Nov 22 2016 - 14:09:32 PST)
- Gustavo Seabra (Tue Nov 22 2016 - 12:13:11 PST)
- Markowska (Tue Nov 22 2016 - 12:06:24 PST)
- Geoffrey Gray (Tue Nov 22 2016 - 11:38:30 PST)
- Gustavo Seabra (Tue Nov 22 2016 - 11:38:06 PST)
- Markowska (Tue Nov 22 2016 - 11:31:18 PST)
[AMBER] Distorsion in water box size and shape
- Mahrukh Imtiaz (Wed Nov 23 2016 - 22:13:14 PST)
[AMBER] dlpc membrane
- David A Case (Tue Nov 15 2016 - 06:29:16 PST)
- jojartb.jgypk.u-szeged.hu (Mon Nov 14 2016 - 21:17:49 PST)
- David A Case (Mon Nov 14 2016 - 18:00:17 PST)
- jojartb.jgypk.u-szeged.hu (Mon Nov 14 2016 - 09:26:22 PST)
- Nhai (Mon Nov 14 2016 - 08:55:48 PST)
- jojartb.jgypk.u-szeged.hu (Mon Nov 14 2016 - 08:41:16 PST)
- David A Case (Mon Nov 14 2016 - 08:18:07 PST)
- jojartb.jgypk.u-szeged.hu (Mon Nov 14 2016 - 05:38:28 PST)
- David A Case (Mon Nov 14 2016 - 04:51:26 PST)
- jojartb.jgypk.u-szeged.hu (Mon Nov 14 2016 - 03:05:17 PST)
- Batuhan Kav (Mon Nov 14 2016 - 02:36:05 PST)
- jojartb.jgypk.u-szeged.hu (Mon Nov 14 2016 - 01:45:03 PST)
[AMBER] do_debugf changes energy
- Ulf Ryde (Fri Nov 04 2016 - 00:25:27 PDT)
- David Cerutti (Thu Nov 03 2016 - 23:43:37 PDT)
- Ulf Ryde (Thu Nov 03 2016 - 23:25:11 PDT)
[AMBER] Dynamic at high temperature
- Carlos Simmerling (Fri Nov 25 2016 - 10:24:13 PST)
- David A Case (Fri Nov 25 2016 - 05:44:21 PST)
- Imma Speciale (Fri Nov 25 2016 - 03:49:01 PST)
[AMBER] Energy decomposition of free energy profiles
- wjli (Tue Nov 15 2016 - 17:46:53 PST)
[AMBER] enhanced sampling conformations by AMD
- Eric Lang (Wed Nov 09 2016 - 01:50:10 PST)
- Kat G (Mon Nov 07 2016 - 09:03:29 PST)
[AMBER] Error for copper atom type
- Elvis Martis (Tue Nov 29 2016 - 21:40:10 PST)
- Shreeramesh (Tue Nov 29 2016 - 18:26:02 PST)
[AMBER] error in antechamber
- David A Case (Fri Nov 11 2016 - 17:14:55 PST)
- Nehad Elsalamouny (Fri Nov 11 2016 - 16:10:17 PST)
[AMBER] Error in running FEW calculations
- Hannes Loeffler (Wed Nov 09 2016 - 00:51:25 PST)
- Miguel Rivera (Wed Nov 09 2016 - 00:44:34 PST)
- Hannes Loeffler (Wed Nov 09 2016 - 00:39:31 PST)
- Miguel Rivera (Wed Nov 09 2016 - 00:26:49 PST)
- Hannes Loeffler (Wed Nov 09 2016 - 00:21:39 PST)
- Miguel Rivera (Tue Nov 08 2016 - 12:50:23 PST)
[AMBER] Error in the production of heat.rst file
- Hai Nguyen (Thu Nov 03 2016 - 17:55:16 PDT)
- Stacyann Nelson (Thu Nov 03 2016 - 17:20:51 PDT)
- David A Case (Thu Nov 03 2016 - 04:48:33 PDT)
- Elvis Martis (Wed Nov 02 2016 - 21:05:26 PDT)
- Stacyann Nelson (Wed Nov 02 2016 - 20:44:47 PDT)
- Elvis Martis (Wed Nov 02 2016 - 20:08:18 PDT)
- Stacyann Nelson (Wed Nov 02 2016 - 17:32:33 PDT)
[AMBER] Error, charge not integral
- Fabrício Bracht (Wed Nov 23 2016 - 03:29:12 PST)
- Lachele Foley (Wed Nov 23 2016 - 03:01:13 PST)
- Bill Ross (Wed Nov 23 2016 - 02:59:32 PST)
- Fabrício Bracht (Wed Nov 23 2016 - 02:39:39 PST)
- Fabrício Bracht (Wed Nov 23 2016 - 02:26:46 PST)
[AMBER] Etot = ************** with dtt=0.004
- Ross Walker (Mon Nov 28 2016 - 12:21:35 PST)
- Nhai (Mon Nov 28 2016 - 10:01:38 PST)
- Thakur, Abhishek (Mon Nov 28 2016 - 09:45:25 PST)
- Carlos Simmerling (Mon Nov 28 2016 - 09:22:13 PST)
- Thakur, Abhishek (Mon Nov 28 2016 - 09:15:12 PST)
- Thakur, Abhishek (Mon Nov 28 2016 - 09:06:21 PST)
- Roitberg,Adrian E (Mon Nov 28 2016 - 08:47:43 PST)
- Thakur, Abhishek (Mon Nov 28 2016 - 08:43:09 PST)
- Carlos Simmerling (Mon Nov 28 2016 - 08:39:05 PST)
- Thakur, Abhishek (Mon Nov 28 2016 - 08:29:40 PST)
[AMBER] Extract temperature of a subsytem
- Daniel Roe (Fri Nov 25 2016 - 07:55:40 PST)
- Nhai (Fri Nov 25 2016 - 07:54:46 PST)
- diego.soler.uam.es (Fri Nov 25 2016 - 06:15:53 PST)
- Gustavo Seabra (Fri Nov 25 2016 - 05:24:19 PST)
- diego.soler.uam.es (Fri Nov 25 2016 - 03:22:15 PST)
[AMBER] extracting velocities from rst7 file
- Daniel Roe (Thu Nov 17 2016 - 15:05:18 PST)
- Nhai (Thu Nov 17 2016 - 14:54:24 PST)
- giulia palermo (Thu Nov 17 2016 - 13:39:07 PST)
- Daniel Roe (Thu Nov 17 2016 - 13:00:12 PST)
- Hai Nguyen (Thu Nov 17 2016 - 12:58:09 PST)
- giulia palermo (Thu Nov 17 2016 - 10:55:59 PST)
[AMBER] Failed to install mpirun
- Charles Lin (Thu Nov 03 2016 - 11:39:02 PDT)
- Charles Lin (Thu Nov 03 2016 - 11:35:02 PDT)
- Adrian Roitberg (Thu Nov 03 2016 - 11:00:19 PDT)
- Nikolay N. Kuzmich (Thu Nov 03 2016 - 10:58:30 PDT)
[AMBER] Filename being truncated by pmemd.cuda
- David A Case (Mon Nov 14 2016 - 12:31:53 PST)
- Andreas Tosstorff (Mon Nov 14 2016 - 08:19:56 PST)
- Adrian Roitberg (Mon Nov 14 2016 - 08:16:25 PST)
- Andreas Tosstorff (Mon Nov 14 2016 - 08:14:03 PST)
[AMBER] Force field files for ff99IDPs
- Carlos Simmerling (Wed Nov 30 2016 - 05:10:12 PST)
- barsha bharadwaz (Wed Nov 30 2016 - 05:04:49 PST)
[AMBER] Fwd: Normal Mode Analysis
- Imma Speciale (Tue Nov 22 2016 - 06:33:07 PST)
- The Cromicus Productions (Tue Nov 22 2016 - 06:29:34 PST)
- David A Case (Tue Nov 22 2016 - 05:14:38 PST)
- Imma Speciale (Tue Nov 22 2016 - 02:42:02 PST)
- Nhai (Thu Nov 17 2016 - 06:54:09 PST)
- Imma Speciale (Thu Nov 17 2016 - 05:47:45 PST)
[AMBER] GaMD patches to Amber 14 and PME's gridhi parameter
- Kasprzak, Wojciech (NIH/NCI) [C] (Wed Nov 16 2016 - 07:36:06 PST)
- David A Case (Wed Nov 16 2016 - 06:56:09 PST)
- Kasprzak, Wojciech (NIH/NCI) [C] (Wed Nov 16 2016 - 06:07:03 PST)
[AMBER] generated correct inputfiles(.iprmtop and .inpcrd ) files
- David A Case (Tue Nov 22 2016 - 05:21:42 PST)
- 杨满意 (Fri Nov 18 2016 - 19:12:20 PST)
[AMBER] Generating parameters of HEME
- Elvis Martis (Wed Nov 02 2016 - 16:59:52 PDT)
- David A Case (Wed Nov 02 2016 - 12:35:55 PDT)
- Hai Nguyen (Wed Nov 02 2016 - 10:48:15 PDT)
- Ramin Ekhteiari (Wed Nov 02 2016 - 10:32:11 PDT)
[AMBER] Generation of parameter files of transmembrane protein system via xleap
- David A Case (Mon Nov 14 2016 - 04:47:21 PST)
- Bill Ross (Mon Nov 14 2016 - 01:21:21 PST)
- Mahrukh Imtiaz (Mon Nov 14 2016 - 01:05:39 PST)
[AMBER] GIST: convergence of the translational entropy term
- Tom Kurtzman (Fri Nov 11 2016 - 10:26:13 PST)
- Steven Ramsey (Fri Nov 11 2016 - 08:43:15 PST)
- Sergey Samsonov (Fri Nov 11 2016 - 06:28:26 PST)
[AMBER] GlcNAc-UDP problem with frcmod file
- Lachele Foley (Mon Nov 28 2016 - 23:40:16 PST)
- David A Case (Mon Nov 28 2016 - 11:57:23 PST)
- Hannes Loeffler (Fri Nov 25 2016 - 03:28:02 PST)
- Sonia Romero (Fri Nov 25 2016 - 02:15:41 PST)
[AMBER] Gromber failed.
- Dd H (Thu Nov 03 2016 - 05:31:14 PDT)
- Jason Swails (Thu Nov 03 2016 - 03:18:04 PDT)
- Dd H (Wed Nov 02 2016 - 19:05:40 PDT)
- Nhai (Wed Nov 02 2016 - 18:58:03 PDT)
- Dd H (Wed Nov 02 2016 - 18:13:16 PDT)
- Hai Nguyen (Wed Nov 02 2016 - 18:00:20 PDT)
- Dd H (Wed Nov 02 2016 - 17:56:48 PDT)
- Jason Swails (Wed Nov 02 2016 - 05:14:09 PDT)
- Dd H (Wed Nov 02 2016 - 01:43:51 PDT)
[AMBER] Hello! Distance restraint problems in SANDER
- David A Case (Sat Nov 05 2016 - 17:35:33 PDT)
- tanfei777.sina.cn (Sat Nov 05 2016 - 01:11:18 PDT)
[AMBER] Help Constant pH MD calculations
- Tsibela German Tebello Mofokeng (Wed Nov 16 2016 - 01:06:46 PST)
- Jason Swails (Tue Nov 15 2016 - 11:24:25 PST)
- Tsibela German Tebello Mofokeng (Tue Nov 15 2016 - 08:32:45 PST)
[AMBER] HMassRepartition
- Thakur, Abhishek (Wed Nov 16 2016 - 11:02:17 PST)
- Adrian Roitberg (Wed Nov 16 2016 - 10:38:58 PST)
- Thakur, Abhishek (Wed Nov 16 2016 - 10:31:28 PST)
- Adrian Roitberg (Wed Nov 16 2016 - 09:59:54 PST)
- Adrian Roitberg (Wed Nov 16 2016 - 09:54:34 PST)
- Thakur, Abhishek (Wed Nov 16 2016 - 08:41:02 PST)
- Hai Nguyen (Wed Nov 16 2016 - 08:11:24 PST)
- David Cerutti (Wed Nov 16 2016 - 08:04:22 PST)
- Elvis Martis (Wed Nov 16 2016 - 07:58:39 PST)
- Thakur, Abhishek (Wed Nov 16 2016 - 07:57:42 PST)
- Thakur, Abhishek (Wed Nov 16 2016 - 07:55:45 PST)
- Daniel Roe (Wed Nov 16 2016 - 07:54:11 PST)
- David Cerutti (Wed Nov 16 2016 - 07:46:06 PST)
- Elvis Martis (Wed Nov 16 2016 - 07:43:39 PST)
- Thakur, Abhishek (Wed Nov 16 2016 - 07:38:23 PST)
[AMBER] How to change the dielectric constant in the electrostatic energy term?
- David A Case (Sun Nov 20 2016 - 12:55:47 PST)
- 冯国强 (Sun Nov 20 2016 - 08:02:05 PST)
[AMBER] How to create the .off/.lib file of the equilibrated non-aqueous solvent box?
- David A Case (Sun Nov 27 2016 - 13:16:12 PST)
- Yew Mun Yip (Sat Nov 26 2016 - 22:05:12 PST)
[AMBER] How to generated correct inputfiles(.iprmtop and .inpcrd ) files
- 杨满意 (Tue Nov 22 2016 - 17:11:13 PST)
[AMBER] how to neutralize protein when using intrinsic water model
- David A Case (Mon Nov 14 2016 - 08:22:34 PST)
- Thakur, Abhishek (Mon Nov 14 2016 - 08:00:46 PST)
[AMBER] How to visualize modes obtained from NMA
- The Cromicus Productions (Wed Nov 02 2016 - 11:23:30 PDT)
[AMBER] Hydrophobic and covalent interactions bond length and stability
- muhammad tahir ayub (Wed Nov 23 2016 - 21:46:04 PST)
[AMBER] implicit water model in aMD
- Thakur, Abhishek (Mon Nov 21 2016 - 13:45:04 PST)
[AMBER] ImportError: Could not import Amber Python modules
- David A Case (Fri Nov 18 2016 - 06:14:38 PST)
- David A Case (Fri Nov 18 2016 - 06:13:46 PST)
- Niel Henriksen (Thu Nov 17 2016 - 13:28:36 PST)
- Jason Swails (Thu Nov 17 2016 - 13:23:48 PST)
- Thakur, Abhishek (Thu Nov 17 2016 - 12:52:31 PST)
- Daniel Roe (Thu Nov 17 2016 - 12:40:10 PST)
- David A Case (Thu Nov 17 2016 - 12:35:53 PST)
- Thakur, Abhishek (Thu Nov 17 2016 - 11:51:06 PST)
- Nhai (Thu Nov 17 2016 - 11:48:37 PST)
- Thakur, Abhishek (Thu Nov 17 2016 - 11:02:40 PST)
- Nhai (Thu Nov 17 2016 - 09:47:27 PST)
- Thakur, Abhishek (Thu Nov 17 2016 - 09:42:56 PST)
[AMBER] instal aamber "mpich2"
- David A Case (Fri Nov 25 2016 - 11:29:39 PST)
- Sepideh Jafari (Fri Nov 25 2016 - 09:51:54 PST)
- Nhai (Fri Nov 25 2016 - 09:37:15 PST)
- Sepideh Jafari (Fri Nov 25 2016 - 09:23:44 PST)
[AMBER] integer limit for nstlim
- David A Case (Wed Nov 09 2016 - 14:41:58 PST)
- Neale, Christopher Andrew (Wed Nov 09 2016 - 14:14:12 PST)
[AMBER] is it possible to run aMD in implicit water model?
- Thakur, Abhishek (Tue Nov 22 2016 - 17:46:36 PST)
- Pengfei Li (Tue Nov 22 2016 - 16:58:16 PST)
- Thakur, Abhishek (Tue Nov 22 2016 - 14:36:52 PST)
- Pengfei Li (Tue Nov 22 2016 - 12:54:33 PST)
- Thakur, Abhishek (Tue Nov 22 2016 - 12:51:26 PST)
[AMBER] Issue with addAtomType: Syntax Error
- Korey M Reid (Fri Nov 18 2016 - 13:57:34 PST)
- David A Case (Fri Nov 18 2016 - 06:18:05 PST)
- Bill Ross (Thu Nov 17 2016 - 13:21:45 PST)
- Korey M Reid (Thu Nov 17 2016 - 13:01:23 PST)
- Bill Ross (Thu Nov 17 2016 - 12:22:00 PST)
- Korey M Reid (Thu Nov 17 2016 - 12:14:36 PST)
[AMBER] Issue with the gaff parameters for "nh" atom type
- Hirdesh Kumar (Wed Nov 30 2016 - 11:13:35 PST)
- Prajwal Nandekar (Wed Nov 30 2016 - 05:58:45 PST)
[AMBER] length of restraintmask
- David A Case (Fri Nov 11 2016 - 17:09:29 PST)
- Ignacio J. General (Fri Nov 11 2016 - 09:51:50 PST)
[AMBER] Lifetime Analysis in cpptraj
- Daniel Roe (Tue Nov 22 2016 - 06:36:25 PST)
- MOHD HOMAIDUR RAHMAN (Mon Nov 21 2016 - 11:20:06 PST)
[AMBER] Ligand across membrane
- zoran matovic (Sun Nov 06 2016 - 23:38:25 PST)
[AMBER] log file in aMD
- Neha Gandhi (Wed Nov 09 2016 - 02:50:12 PST)
[AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories
- William Lees (Thu Nov 10 2016 - 02:00:46 PST)
- Daniel Roe (Wed Nov 09 2016 - 10:57:59 PST)
- David A Case (Wed Nov 09 2016 - 10:32:20 PST)
- Eric Lang (Wed Nov 09 2016 - 09:16:08 PST)
- Nhai (Wed Nov 09 2016 - 07:07:40 PST)
- Eric Lang (Wed Nov 09 2016 - 03:44:02 PST)
[AMBER] MCPB problems
- Pengfei Li (Wed Nov 02 2016 - 19:13:42 PDT)
- Fabrício Bracht (Tue Nov 01 2016 - 09:49:35 PDT)
- Fabrício Bracht (Tue Nov 01 2016 - 09:28:47 PDT)
- Pengfei Li (Tue Nov 01 2016 - 09:16:21 PDT)
- Fabrício Bracht (Tue Nov 01 2016 - 07:58:42 PDT)
[AMBER] MCPB.py
- Pengfei Li (Tue Nov 08 2016 - 10:53:11 PST)
- Mahmood Jasim (Thu Nov 03 2016 - 03:02:59 PDT)
[AMBER] MCPB.py and MMPBSA issue
- Jason Swails (Tue Nov 29 2016 - 09:17:33 PST)
- Pengfei Li (Mon Nov 28 2016 - 13:09:46 PST)
- 庄灿波 (Sat Nov 26 2016 - 01:32:53 PST)
[AMBER] MCPB.py error in Step 2
- Pengfei Li (Fri Nov 11 2016 - 09:52:42 PST)
- Jon Mujika (Thu Nov 10 2016 - 03:25:11 PST)
[AMBER] MD simulation by amber
- David A Case (Wed Nov 16 2016 - 06:00:38 PST)
- Hai Nguyen (Tue Nov 15 2016 - 18:40:12 PST)
[AMBER] MD simulations, DDR4 2133MHz vs 3200MHz
- David Cerutti (Thu Nov 03 2016 - 11:23:01 PDT)
- Nikolay N. Kuzmich (Thu Nov 03 2016 - 10:53:17 PDT)
[AMBER] MD under external electric field
- Charles Lin (Thu Nov 17 2016 - 12:48:12 PST)
- Hector A. Baldoni (Thu Nov 17 2016 - 05:56:13 PST)
- Charles Lin (Wed Nov 16 2016 - 14:18:46 PST)
- Hector A. Baldoni (Wed Nov 16 2016 - 13:36:05 PST)
[AMBER] mdfil: Error unknown flag: pdb_wat.prmtop
- Hai Nguyen (Wed Nov 30 2016 - 15:33:47 PST)
- Aishani Prem (Wed Nov 30 2016 - 15:32:29 PST)
[AMBER] Methylated adenine parameter
- David A Case (Tue Nov 15 2016 - 05:15:59 PST)
- Kshatresh Dutta Dubey (Tue Nov 15 2016 - 02:45:07 PST)
[AMBER] micro iterations in QM/MM optimization.
- Dr. Andreas W. Goetz (Wed Nov 02 2016 - 09:28:47 PDT)
- Yigal Lahav (Wed Nov 02 2016 - 07:28:57 PDT)
[AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB
- Ruth Helena Tichauer (Fri Nov 18 2016 - 07:16:57 PST)
- Hector A. Baldoni (Wed Nov 16 2016 - 05:06:59 PST)
- Ruth Helena Tichauer (Wed Nov 16 2016 - 04:32:01 PST)
- Gustavo Seabra (Wed Nov 16 2016 - 04:26:41 PST)
- Ruth Helena Tichauer (Tue Nov 15 2016 - 05:16:42 PST)
- David A Case (Tue Nov 15 2016 - 05:04:53 PST)
- Ruth Helena Tichauer (Tue Nov 15 2016 - 01:47:37 PST)
- Gustavo Seabra (Thu Nov 10 2016 - 09:44:45 PST)
- Ruth Helena Tichauer (Thu Nov 10 2016 - 06:07:29 PST)
[AMBER] MM-GBSA calculation in temperature other than 298 K
- Hai Nguyen (Mon Nov 28 2016 - 11:13:06 PST)
- Atila Petrosian (Mon Nov 28 2016 - 10:47:36 PST)
[AMBER] MM-GBSA calculation in temperature other than 298.15 K
- Daniel Roe (Sun Nov 20 2016 - 04:05:06 PST)
- Atila Petrosian (Sun Nov 20 2016 - 00:52:52 PST)
- Jason Swails (Thu Nov 17 2016 - 09:55:37 PST)
- Daniel Roe (Thu Nov 17 2016 - 08:11:13 PST)
- Carlos Simmerling (Thu Nov 17 2016 - 05:44:36 PST)
- Atila Petrosian (Thu Nov 17 2016 - 05:22:17 PST)
- Carlos Simmerling (Thu Nov 17 2016 - 05:18:35 PST)
- Atila Petrosian (Thu Nov 17 2016 - 05:12:09 PST)
- Carlos Simmerling (Thu Nov 17 2016 - 04:35:32 PST)
- Atila Petrosian (Wed Nov 16 2016 - 22:46:26 PST)
- Carlos Simmerling (Wed Nov 16 2016 - 03:12:43 PST)
- Atila Petrosian (Tue Nov 15 2016 - 21:42:37 PST)
[AMBER] MM-PBSA calculation for HEME-contained protein
- Elvis Martis (Sat Nov 05 2016 - 05:42:36 PDT)
- Ramin Ekhteiari (Sat Nov 05 2016 - 05:14:47 PDT)
[AMBER] mm_pbsa.pl error: Found unknown atflg DC
- Hai Nguyen (Tue Nov 15 2016 - 18:42:37 PST)
[AMBER] MMGBSA decomposition analysis
- George Tzotzos (Fri Nov 11 2016 - 13:30:46 PST)
- Carlos Simmerling (Fri Nov 11 2016 - 13:27:51 PST)
- George Tzotzos (Fri Nov 11 2016 - 13:16:41 PST)
[AMBER] MMGBSA: estimating "effective energy" convergence
- George Tzotzos (Wed Nov 02 2016 - 07:30:42 PDT)
- Casalini Tommaso (Wed Nov 02 2016 - 06:44:17 PDT)
- George Tzotzos (Wed Nov 02 2016 - 06:38:36 PDT)
[AMBER] MMPBSA Calculation
- Preeti Pandey (Mon Nov 21 2016 - 08:49:43 PST)
[AMBER] mmpbsa error
- Ray Luo (Tue Nov 01 2016 - 10:35:45 PDT)
- 东不拉 (Tue Nov 01 2016 - 01:31:34 PDT)
[AMBER] Modes associated to the principal components?
- David A Case (Tue Nov 22 2016 - 11:00:16 PST)
- The Cromicus Productions (Tue Nov 22 2016 - 10:52:36 PST)
- Jason Swails (Tue Nov 22 2016 - 09:26:31 PST)
- The Cromicus Productions (Tue Nov 22 2016 - 06:54:45 PST)
[AMBER] more on the Berendsen thermostat
- Markowska (Wed Nov 23 2016 - 11:07:59 PST)
- Adrian Roitberg (Wed Nov 23 2016 - 10:48:49 PST)
- David A Case (Wed Nov 23 2016 - 10:44:29 PST)
[AMBER] NAB input file containing first and second structure of RNA
- Mohaddeseh Habibzadeh (Mon Nov 28 2016 - 01:32:20 PST)
- David A Case (Sun Nov 27 2016 - 13:06:55 PST)
- Mohaddeseh Habibzadeh (Sun Nov 27 2016 - 09:56:59 PST)
- David A Case (Sun Nov 27 2016 - 09:40:13 PST)
- Mohaddeseh Habibzadeh (Sat Nov 26 2016 - 22:56:16 PST)
[AMBER] Negative interaction energy between Sodium ions?
- David Cerutti (Mon Nov 14 2016 - 14:46:16 PST)
- Oliver Emil Skytte Glue (Mon Nov 14 2016 - 14:29:17 PST)
[AMBER] No output_file during SMD with LCOD
- Ruth Helena Tichauer (Fri Nov 18 2016 - 07:04:06 PST)
- Feng Pan (Thu Nov 17 2016 - 09:03:08 PST)
- Ruth Helena Tichauer (Thu Nov 17 2016 - 02:45:47 PST)
[AMBER] NPT equilibration at constant pH with protonation states allowed to change
- Eric Lang (Mon Nov 14 2016 - 02:12:46 PST)
- Eric Lang (Fri Nov 11 2016 - 13:18:50 PST)
- Jason Swails (Fri Nov 11 2016 - 09:39:05 PST)
- Eric Lang (Fri Nov 11 2016 - 09:31:56 PST)
[AMBER] ntt = 6 and ibelly = 1
- Xiangyu Jia (Fri Nov 04 2016 - 01:50:03 PDT)
[AMBER] number of cpus in parallel GPU jobs
- Ross Walker (Tue Nov 08 2016 - 19:08:08 PST)
- Neha Gandhi (Tue Nov 08 2016 - 17:42:03 PST)
[AMBER] Obtaining infrared/Raman spectra
- Brent Krueger (Sat Nov 26 2016 - 13:45:07 PST)
- case (Sat Nov 26 2016 - 05:24:13 PST)
- The Cromicus Productions (Sat Nov 26 2016 - 00:36:22 PST)
[AMBER] Optimal values for harm and output_freq in SMD
- Ruth Helena Tichauer (Wed Nov 30 2016 - 01:32:31 PST)
- Feng Pan (Tue Nov 29 2016 - 17:22:30 PST)
- Ruth Helena Tichauer (Tue Nov 29 2016 - 07:59:07 PST)
- Feng Pan (Mon Nov 28 2016 - 18:16:18 PST)
- Ruth Helena Tichauer (Fri Nov 25 2016 - 03:47:37 PST)
- Feng Pan (Thu Nov 24 2016 - 10:55:04 PST)
- Ruth Helena Tichauer (Thu Nov 24 2016 - 03:34:04 PST)
[AMBER] Parameters for selenocysteine
- David A Case (Thu Nov 10 2016 - 10:14:14 PST)
- David A Case (Thu Nov 10 2016 - 07:43:51 PST)
- Paul Meister (Thu Nov 10 2016 - 06:06:54 PST)
[AMBER] Paramfit for multiple molecules
- Robin Betz (Mon Nov 28 2016 - 15:47:05 PST)
- Sven Hackbusch (Tue Nov 22 2016 - 15:59:22 PST)
[AMBER] PCA trajectories give unrealistic structures
- Daniel Roe (Wed Nov 09 2016 - 12:33:36 PST)
- Gulsevin,Alican (Wed Nov 09 2016 - 08:06:43 PST)
[AMBER] Performance drop for large systems
- Ross Walker (Tue Nov 08 2016 - 05:48:08 PST)
- Andreas Tosstorff (Tue Nov 08 2016 - 02:11:46 PST)
[AMBER] Phosphoryated amino acids
- David A Case (Thu Nov 17 2016 - 05:39:19 PST)
- Eiros Zamora, Juan (Thu Nov 17 2016 - 02:21:26 PST)
- Neha Gandhi (Thu Nov 17 2016 - 01:35:20 PST)
- Bill Ross (Thu Nov 17 2016 - 01:25:12 PST)
- Bill Ross (Thu Nov 17 2016 - 01:12:58 PST)
- Beale, John (Thu Nov 17 2016 - 01:10:30 PST)
[AMBER] Potential energy fluctuation of NVT ensemble
- Zhe Li (Sat Nov 05 2016 - 10:30:47 PDT)
- diego.soler.uam.es (Sat Nov 05 2016 - 01:29:38 PDT)
- Niel Henriksen (Fri Nov 04 2016 - 17:25:22 PDT)
- Zhe Li (Fri Nov 04 2016 - 15:15:49 PDT)
- Zhe Li (Thu Nov 03 2016 - 18:45:22 PDT)
[AMBER] Problem installing Amber 16 on mac OS El Capitan
- Ruth Helena Tichauer (Wed Nov 02 2016 - 08:13:25 PDT)
- Hai Nguyen (Wed Nov 02 2016 - 07:14:09 PDT)
- Ruth Helena Tichauer (Wed Nov 02 2016 - 06:32:15 PDT)
[AMBER] Problem to submit a pH-REMD on a GPU node
- Ross Walker (Fri Nov 25 2016 - 07:57:16 PST)
- Yong Wang (Fri Nov 25 2016 - 02:54:49 PST)
[AMBER] Problem with bonds in NAB
- David A Case (Thu Nov 24 2016 - 10:58:09 PST)
- Vladislav Sláma (Thu Nov 24 2016 - 06:58:16 PST)
- David A Case (Tue Nov 08 2016 - 12:24:35 PST)
- Vladislav Sláma (Tue Nov 08 2016 - 09:24:20 PST)
- David A Case (Thu Nov 03 2016 - 04:44:35 PDT)
- Vladislav Sláma (Wed Nov 02 2016 - 08:39:12 PDT)
[AMBER] problem with MMPBSApy in Amber 16
- Marek Maly (Tue Nov 01 2016 - 15:20:40 PDT)
- Ray Luo (Tue Nov 01 2016 - 14:34:01 PDT)
- Ray Luo (Tue Nov 01 2016 - 13:29:22 PDT)
- Marek Maly (Tue Nov 01 2016 - 12:14:55 PDT)
- Ray Luo (Tue Nov 01 2016 - 10:49:36 PDT)
- Marek Maly (Tue Nov 01 2016 - 10:36:24 PDT)
- Ray Luo (Tue Nov 01 2016 - 09:14:50 PDT)
- Marek Maly (Tue Nov 01 2016 - 08:54:04 PDT)
[AMBER] Problem with Parmed-generated chamber prmtop
- Marc van der Kamp (Thu Nov 24 2016 - 02:34:37 PST)
- Jason Swails (Wed Nov 23 2016 - 08:47:58 PST)
- Jason Swails (Fri Nov 18 2016 - 16:49:07 PST)
- Marc van der Kamp (Fri Nov 18 2016 - 14:39:40 PST)
- Jason Swails (Fri Nov 18 2016 - 11:45:19 PST)
- Hai Nguyen (Tue Nov 15 2016 - 18:50:32 PST)
- Marc van der Kamp (Thu Nov 10 2016 - 07:01:48 PST)
[AMBER] Protein path error
- Elvis Martis (Tue Nov 22 2016 - 03:30:32 PST)
- Arthi Venkat (Tue Nov 22 2016 - 02:58:02 PST)
- Elvis Martis (Tue Nov 22 2016 - 02:31:01 PST)
- Arthi Venkat (Tue Nov 22 2016 - 02:23:50 PST)
- Elvis Martis (Tue Nov 22 2016 - 02:08:26 PST)
- Arthi Venkat (Tue Nov 22 2016 - 01:52:18 PST)
[AMBER] Quenstions about pmemd.cuda.MPI
- Ross Walker (Thu Nov 10 2016 - 18:33:32 PST)
- Pengfei Li (Thu Nov 10 2016 - 17:48:11 PST)
- Ross Walker (Mon Nov 07 2016 - 06:29:29 PST)
- Pengfei Li (Sun Nov 06 2016 - 22:27:21 PST)
- Ross Walker (Thu Nov 03 2016 - 20:48:16 PDT)
- Pengfei Li (Thu Nov 03 2016 - 20:20:41 PDT)
[AMBER] Query regarding the MCPB.py workflow
- Pengfei Li (Mon Nov 21 2016 - 14:27:34 PST)
- Abhi Acharya (Sat Nov 19 2016 - 22:34:34 PST)
- Pengfei Li (Wed Nov 16 2016 - 17:07:22 PST)
- Pengfei Li (Wed Nov 16 2016 - 17:05:31 PST)
- Abhi Acharya (Wed Nov 16 2016 - 02:45:23 PST)
- Abhi Acharya (Sat Nov 12 2016 - 01:09:19 PST)
[AMBER] question about calculated density in sander output file
- David A Case (Wed Nov 30 2016 - 11:39:05 PST)
- amaury paquet (Wed Nov 30 2016 - 06:22:01 PST)
[AMBER] Questions concerning charges calculated by antechamber
- Daniel Roe (Mon Nov 28 2016 - 05:35:35 PST)
- Andreas Gavrielides (Mon Nov 28 2016 - 04:36:19 PST)
[AMBER] recipe for target "parallel" failed
- Elvis Martis (Sun Nov 27 2016 - 00:14:51 PST)
- Mohaddeseh Habibzadeh (Sun Nov 27 2016 - 00:07:24 PST)
- Elvis Martis (Sat Nov 26 2016 - 23:13:53 PST)
- Mohaddeseh Habibzadeh (Sat Nov 26 2016 - 23:03:56 PST)
- Mohaddeseh Habibzadeh (Sat Nov 26 2016 - 22:38:56 PST)
- David A Case (Sat Nov 26 2016 - 17:52:07 PST)
- Mohaddeseh Habibzadeh (Sat Nov 26 2016 - 11:03:35 PST)
- Elvis Martis (Sat Nov 26 2016 - 10:31:43 PST)
- Mohaddeseh Habibzadeh (Sat Nov 26 2016 - 10:08:58 PST)
[AMBER] recompile Sander suite
- Dr. Anselm Horn (Thu Nov 10 2016 - 03:13:48 PST)
- Ibrahim Said (Thu Nov 10 2016 - 02:56:34 PST)
[AMBER] Regarding integration of my code with CPPTRAJ
- Daniel Roe (Mon Nov 28 2016 - 05:16:03 PST)
- Hai Nguyen (Sun Nov 27 2016 - 21:47:06 PST)
- Nikhil Chowdary (Sun Nov 27 2016 - 21:35:46 PST)
[AMBER] RESP routine not found
- Hai Nguyen (Thu Nov 03 2016 - 09:52:52 PDT)
- Marcelo Depólo (Thu Nov 03 2016 - 05:09:32 PDT)
[AMBER] Restraints not working, What Am I doing Wrong?
- The Cromicus Productions (Fri Nov 18 2016 - 10:26:46 PST)
- Dr. Anselm Horn (Tue Nov 15 2016 - 00:45:07 PST)
- The Cromicus Productions (Mon Nov 14 2016 - 23:28:17 PST)
[AMBER] RMSD for two different MDs
- Daniel Roe (Tue Nov 29 2016 - 05:34:07 PST)
- David Cerutti (Mon Nov 28 2016 - 13:46:32 PST)
- Adrian Roitberg (Mon Nov 28 2016 - 13:32:23 PST)
- Thakur, Abhishek (Mon Nov 28 2016 - 13:27:53 PST)
- Haining Liu (Mon Nov 28 2016 - 12:49:02 PST)
[AMBER] rmsf problem
- Daniel Roe (Wed Nov 23 2016 - 05:06:31 PST)
- Eiros Zamora, Juan (Wed Nov 23 2016 - 04:42:39 PST)
- Elvis Martis (Wed Nov 23 2016 - 02:14:08 PST)
- Sepideh Jafari (Wed Nov 23 2016 - 02:07:27 PST)
[AMBER] RNA backbone dihedral restraints question
- Carlos Simmerling (Tue Nov 08 2016 - 03:39:27 PST)
- Kasprzak, Wojciech (NIH/NCI) [C] (Fri Nov 04 2016 - 07:41:00 PDT)
- Carlos Simmerling (Fri Nov 04 2016 - 07:10:31 PDT)
- Kasprzak, Wojciech (NIH/NCI) [C] (Fri Nov 04 2016 - 07:05:25 PDT)
[AMBER] selection of the residues when using MM-GBSA
- Jason Swails (Wed Nov 30 2016 - 13:31:39 PST)
- Hyun (Wed Nov 30 2016 - 08:38:08 PST)
[AMBER] simulating with "gbsa=1" on gpu give only 0.18ns per/day
- Thakur, Abhishek (Tue Nov 15 2016 - 09:12:37 PST)
- Hai Nguyen (Tue Nov 15 2016 - 07:13:20 PST)
- Adrian Roitberg (Tue Nov 15 2016 - 07:06:36 PST)
- Thakur, Abhishek (Tue Nov 15 2016 - 07:01:41 PST)
[AMBER] Simulation of protein in lipid blayer using GB solvation model
- Carlos Simmerling (Wed Nov 02 2016 - 04:34:49 PDT)
- Nikolay N. Kuzmich (Wed Nov 02 2016 - 03:49:34 PDT)
[AMBER] simulation running error.
- Saman Yousuf ali (Tue Nov 22 2016 - 22:02:30 PST)
- Bill Ross (Tue Nov 22 2016 - 21:55:08 PST)
- Saman Yousuf ali (Tue Nov 22 2016 - 21:49:50 PST)
- Elvis Martis (Tue Nov 22 2016 - 21:41:39 PST)
- Saman Yousuf ali (Tue Nov 22 2016 - 21:31:15 PST)
[AMBER] Software announcement: Release of PUPIL 3.1
- Joan Torras (Wed Nov 02 2016 - 13:33:54 PDT)
[AMBER] solvate box of long length and short width
- Lara rajam (Mon Nov 28 2016 - 12:22:12 PST)
- David A Case (Mon Nov 28 2016 - 11:40:47 PST)
- Lara rajam (Mon Nov 28 2016 - 06:58:31 PST)
[AMBER] strange format of .rst file
- Jason Swails (Fri Nov 18 2016 - 09:13:43 PST)
- Thakur, Abhishek (Fri Nov 18 2016 - 09:04:15 PST)
- Daniel Roe (Fri Nov 18 2016 - 08:20:42 PST)
- Thakur, Abhishek (Fri Nov 18 2016 - 07:53:41 PST)
[AMBER] Targeted molecular dynamics on GPU
- Sonia Ziada (Mon Nov 14 2016 - 07:14:34 PST)
[AMBER] The parameters for the fully protonated phosphate group
- David Cerutti (Mon Nov 21 2016 - 08:55:32 PST)
- David A Case (Mon Nov 21 2016 - 06:08:04 PST)
- Dd H (Sun Nov 20 2016 - 22:56:37 PST)
- David Cerutti (Sun Nov 20 2016 - 19:22:47 PST)
- jinfeng liu (Sun Nov 20 2016 - 18:45:31 PST)
[AMBER] The ultimate temperature is 11K instead of 100K in heating simulation
- Ross Walker (Tue Nov 01 2016 - 10:38:51 PDT)
- Nikolay N. Kuzmich (Tue Nov 01 2016 - 10:34:22 PDT)
[AMBER] Tools for calculation of interaction energy
- Nhai (Fri Nov 25 2016 - 12:57:48 PST)
- Andrew Bostick (Fri Nov 25 2016 - 09:41:26 PST)
[AMBER] TUTORIAL B5: Simulating the Green Fluorescent Protein -PREPGEN Error
- David A Case (Mon Nov 21 2016 - 06:11:38 PST)
- Brent Krueger (Sun Nov 20 2016 - 06:31:59 PST)
- Taylor, Miles (Sat Nov 19 2016 - 16:50:20 PST)
[AMBER] Umbrella simulation with an arbitrary bias potential
- diego.soler.uam.es (Tue Nov 15 2016 - 02:53:15 PST)
- Feng Pan (Mon Nov 07 2016 - 11:44:10 PST)
- Vlad Cojocaru (Mon Nov 07 2016 - 06:01:43 PST)
- David A Case (Mon Nov 07 2016 - 05:48:07 PST)
- diego.soler.uam.es (Fri Nov 04 2016 - 03:02:04 PDT)
[AMBER] Uridine diphosphate (UDP) - tleap
- FyD (Wed Nov 09 2016 - 02:58:18 PST)
- David A Case (Fri Nov 04 2016 - 10:07:21 PDT)
- Anna Cebrian Prats (Fri Nov 04 2016 - 04:58:51 PDT)
[AMBER] virtual box in gas phase simulation
- Xiangyu Jia (Fri Nov 04 2016 - 02:07:25 PDT)
[AMBER] Wierd line in amber-TI output Files
- Thomas Fox (Fri Nov 25 2016 - 04:37:22 PST)
problems for running step 2 of MCPB.py
- 杨满意 (Fri Nov 04 2016 - 00:00:56 PDT)
Problems with imaging
- Daniel Roe (Wed Nov 30 2016 - 10:24:32 PST)
- Mark Waterhouse [RPG] (Wed Nov 30 2016 - 01:08:00 PST)
- Daniel Roe (Tue Nov 29 2016 - 05:59:31 PST)
- Mark Waterhouse [RPG] (Mon Nov 28 2016 - 12:49:09 PST)

Amber Archive Nov 2016 by subject