Amber Archive Dec 2016: by subject

[AMBER] 10. QM/MM/MD g09 interface issues, now tleap
- David Case (Tue Dec 20 2016 - 18:09:50 PST)
- David Poole (Tue Dec 20 2016 - 12:11:39 PST)
- David Case (Mon Dec 19 2016 - 05:16:23 PST)
- David Poole (Sun Dec 11 2016 - 10:42:03 PST)
[AMBER] 2D distance plots
- Abhilash J (Mon Dec 26 2016 - 10:18:59 PST)
[AMBER] [Amber] Calculation of Velocity Autocorrelation Function
- Daniel Roe (Mon Dec 12 2016 - 05:15:06 PST)
- The Cromicus Productions (Sun Dec 11 2016 - 14:10:04 PST)
[AMBER] About Constant pH Molecular Dynamics
- 上海科技大学吴萌 (Wed Dec 14 2016 - 17:49:50 PST)
[AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence
- Andreas Tosstorff (Tue Dec 13 2016 - 06:43:25 PST)
- Bruno Falcone (Tue Dec 13 2016 - 06:33:25 PST)
- Andreas Tosstorff (Tue Dec 13 2016 - 06:14:12 PST)
- David A Case (Tue Dec 13 2016 - 06:07:10 PST)
- Andreas Tosstorff (Tue Dec 13 2016 - 01:01:37 PST)
- Andreas Tosstorff (Tue Dec 13 2016 - 00:40:52 PST)
- David A Case (Mon Dec 12 2016 - 08:27:10 PST)
- Andreas Tosstorff (Mon Dec 12 2016 - 05:12:11 PST)
[AMBER] addion issue
- Hirdesh Kumar (Wed Dec 21 2016 - 07:35:10 PST)
- Prajwal Nandekar (Wed Dec 21 2016 - 04:12:25 PST)
- Hirdesh Kumar (Tue Dec 20 2016 - 10:45:28 PST)
- Hai Nguyen (Tue Dec 20 2016 - 10:27:49 PST)
- Hirdesh Kumar (Tue Dec 20 2016 - 10:25:47 PST)
- Hai Nguyen (Tue Dec 20 2016 - 10:19:39 PST)
- Hirdesh Kumar (Tue Dec 20 2016 - 10:15:58 PST)
[AMBER] Amber 16: ** NFE-Error ** : Cannot read &colvar namelist!
- Ruth Helena Tichauer (Thu Dec 08 2016 - 09:40:28 PST)
- Feng Pan (Wed Dec 07 2016 - 10:26:03 PST)
- Ruth Helena Tichauer (Wed Dec 07 2016 - 10:08:26 PST)
- Daniel Roe (Wed Dec 07 2016 - 07:07:36 PST)
- Ruth Helena Tichauer (Wed Dec 07 2016 - 04:32:09 PST)
[AMBER] Amber16 on GPUs and speed differences between CUDA_VISIBLE_DEVICES=0, 1 or 0, 2
- Andreas Tosstorff (Mon Dec 19 2016 - 13:32:17 PST)
- Neale, Christopher Andrew (Mon Dec 19 2016 - 11:22:21 PST)
- Neale, Christopher Andrew (Mon Dec 19 2016 - 10:31:19 PST)
- Neale, Christopher Andrew (Mon Dec 19 2016 - 10:09:00 PST)
[AMBER] AmberTools16 installation problem
- a.jarmula.nencki.gov.pl (Mon Dec 19 2016 - 18:34:42 PST)
- David A Case (Mon Dec 12 2016 - 04:48:03 PST)
- David A Case (Mon Dec 12 2016 - 04:46:29 PST)
- a.jarmula.nencki.gov.pl (Mon Dec 12 2016 - 04:19:52 PST)
[AMBER] Atom type for middle nitrogen in dycyanamide?
- David A Case (Thu Dec 01 2016 - 10:28:09 PST)
- Mohd Farid Ismail (Thu Dec 01 2016 - 00:59:47 PST)
[AMBER] bad atom type MN2+ ions in the binding free energy decomposition (Amber14)
- 袁浩亮 (Tue Dec 20 2016 - 19:33:22 PST)
- Elvis Martis (Tue Dec 20 2016 - 07:43:58 PST)
- 袁浩亮 (Tue Dec 20 2016 - 06:25:27 PST)
[AMBER] Benign typo for a constant in barostats.F90
- Neale, Christopher Andrew (Mon Dec 19 2016 - 13:52:00 PST)
[AMBER] clustering doubt
- Daniel Roe (Thu Dec 15 2016 - 07:49:19 PST)
- Nhai (Thu Dec 15 2016 - 05:51:11 PST)
- Mary Varughese (Thu Dec 15 2016 - 01:54:37 PST)
- Daniel Roe (Wed Dec 14 2016 - 10:44:07 PST)
- Mary Varughese (Wed Dec 14 2016 - 02:34:34 PST)
- Mary Varughese (Tue Dec 06 2016 - 20:48:58 PST)
- Daniel Roe (Tue Dec 06 2016 - 12:09:21 PST)
- Achim Sandmann (Thu Dec 01 2016 - 03:29:44 PST)
- Mary Varughese (Thu Dec 01 2016 - 02:43:32 PST)
- Achim Sandmann (Thu Dec 01 2016 - 02:26:24 PST)
- Mary Varughese (Wed Nov 30 2016 - 23:26:29 PST)
[AMBER] Collective Variable not "Strictly" Enforced: Adaptively Biased MD Simulations of type "COM_ANGLE" using "FLOODING"
- Feng Pan (Fri Dec 02 2016 - 12:26:25 PST)
- Emmanuel (Wed Nov 30 2016 - 22:08:29 PST)
[AMBER] Constant pH across membrane
- Fabrício Bracht (Thu Dec 15 2016 - 06:45:14 PST)
- Adrian Roitberg (Thu Dec 15 2016 - 06:01:10 PST)
- Fabrício Bracht (Thu Dec 15 2016 - 04:58:06 PST)
- Jason Swails (Wed Dec 14 2016 - 20:22:20 PST)
- Fabrício Bracht (Wed Dec 14 2016 - 15:49:34 PST)
[AMBER] Constant pH Molecular Dynamics for membrane protein
- Jason Swails (Sun Dec 18 2016 - 20:57:07 PST)
- 上海科技大学吴萌 (Sun Dec 18 2016 - 18:01:43 PST)
[AMBER] CpHMD tutorial: how to generate the titration_curves.dat file in an automated way
- Eric Lang (Mon Dec 05 2016 - 12:25:14 PST)
- Jason Swails (Mon Dec 05 2016 - 10:48:15 PST)
- Fabrício Bracht (Mon Dec 05 2016 - 08:50:23 PST)
- Eric Lang (Mon Dec 05 2016 - 08:36:38 PST)
[AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD
- Daniel Roe (Tue Dec 06 2016 - 12:05:52 PST)
- Brian Radak (Fri Dec 02 2016 - 13:47:45 PST)
[AMBER] cpptraj cluster -representative structure
- Thomas Pochapsky (Wed Dec 14 2016 - 11:29:32 PST)
- Thomas Cheatham (Wed Dec 14 2016 - 10:38:55 PST)
- Elvis Martis (Wed Dec 14 2016 - 08:23:46 PST)
- Thomas Pochapsky (Wed Dec 14 2016 - 08:13:54 PST)
[AMBER] cpptraj LIE on a ghost-atom
- Jason Swails (Thu Dec 22 2016 - 13:34:27 PST)
- Elisa Pieri (Wed Dec 21 2016 - 06:45:22 PST)
[AMBER] cuda.h: No such file or directory
- David Case (Wed Dec 28 2016 - 18:12:01 PST)
- Elka Firmanda (Wed Dec 28 2016 - 17:16:25 PST)
[AMBER] difference between %occupied and lifetime in hydrogen bond analysis
- Daniel Roe (Thu Dec 15 2016 - 08:18:01 PST)
- Andrew Bostick (Thu Dec 15 2016 - 00:17:32 PST)
[AMBER] different frequencies for mdout/mdinfo writes?
- Lorenzo Gontrani (Mon Dec 12 2016 - 11:54:24 PST)
- Daniel Roe (Mon Dec 12 2016 - 11:46:25 PST)
- Bill Ross (Sun Dec 11 2016 - 17:13:42 PST)
[AMBER] Distance diffusion calculation in ptraj and cpptraj
- Daniel Roe (Wed Dec 28 2016 - 09:31:03 PST)
- Huang Jing (Tue Dec 27 2016 - 05:04:07 PST)
- wei (Mon Dec 26 2016 - 23:58:46 PST)
[AMBER] Editing residue in PDB file
- David A Case (Mon Dec 12 2016 - 08:17:50 PST)
- Nikolay N. Kuzmich (Mon Dec 12 2016 - 07:03:56 PST)
[AMBER] Eigenvector visualization in Nmode
- David A Case (Fri Dec 09 2016 - 18:25:40 PST)
- The Cromicus Productions (Fri Dec 09 2016 - 14:43:51 PST)
- The Cromicus Productions (Fri Dec 09 2016 - 14:41:23 PST)
- JPB (Fri Dec 09 2016 - 07:32:36 PST)
[AMBER] ensuring lack of non-equilibrium jolt on restart
- David Case (Sun Dec 18 2016 - 05:52:09 PST)
- Neale, Christopher Andrew (Fri Dec 16 2016 - 10:30:02 PST)
[AMBER] error
- David A Case (Sat Dec 10 2016 - 06:35:07 PST)
- 睿翟 (Fri Dec 09 2016 - 22:02:44 PST)
- Hai Nguyen (Fri Dec 09 2016 - 21:55:33 PST)
- 睿 ? (Fri Dec 09 2016 - 18:11:09 PST)
[AMBER] error in amber 16 mpi installation
- Michael Shokhen (Thu Dec 22 2016 - 11:31:23 PST)
- Hai Nguyen (Thu Dec 22 2016 - 11:15:49 PST)
- Daniel Roe (Thu Dec 22 2016 - 11:00:04 PST)
- Michael Shokhen (Thu Dec 22 2016 - 10:35:30 PST)
[AMBER] Error in rst file
- Mohaddeseh Habibzadeh (Tue Dec 20 2016 - 07:26:59 PST)
- David Case (Tue Dec 20 2016 - 05:27:34 PST)
- Mohaddeseh Habibzadeh (Tue Dec 20 2016 - 00:45:04 PST)
- Mohaddeseh Habibzadeh (Mon Dec 19 2016 - 09:34:05 PST)
- Nhai (Mon Dec 19 2016 - 08:41:01 PST)
- Mohaddeseh Habibzadeh (Mon Dec 19 2016 - 08:26:22 PST)
- Nhai (Mon Dec 19 2016 - 08:11:19 PST)
- Mohaddeseh Habibzadeh (Mon Dec 19 2016 - 07:54:53 PST)
[AMBER] ERROR no map function for HH12 ARG
- David Case (Tue Dec 20 2016 - 05:20:13 PST)
- srinivas penumutchu (Mon Dec 19 2016 - 13:53:11 PST)
[AMBER] Error: The system has extended beyond the extent of the virtual box.
- Nhai (Mon Dec 19 2016 - 22:11:41 PST)
- Taylor, Miles (Mon Dec 19 2016 - 19:11:00 PST)
[AMBER] Explicit solvent CpHMD calculation with Amber14
- Tsibela German Tebello Mofokeng (Wed Dec 07 2016 - 05:49:02 PST)
- Carlos Simmerling (Wed Dec 07 2016 - 05:38:30 PST)
- Jason Swails (Wed Dec 07 2016 - 05:35:57 PST)
- Tsibela German Tebello Mofokeng (Wed Dec 07 2016 - 05:23:24 PST)
[AMBER] failed testing cuda
- David A Case (Tue Dec 27 2016 - 08:55:58 PST)
- Michael Shokhen (Sun Dec 25 2016 - 10:36:48 PST)
[AMBER] Fitting of rms2d
- Carlos Simmerling (Fri Dec 09 2016 - 05:58:45 PST)
- Mike Nemec (Fri Dec 09 2016 - 05:56:23 PST)
[AMBER] Force field modifications
- David A Case (Thu Dec 22 2016 - 05:18:25 PST)
- Jonathan Huihui (Thu Dec 22 2016 - 03:18:20 PST)
- David Cerutti (Wed Dec 21 2016 - 11:57:51 PST)
- Jonathan Huihui (Wed Dec 21 2016 - 11:48:58 PST)
[AMBER] Freeze Atoms in Nab
- David A Case (Fri Dec 09 2016 - 18:17:27 PST)
- The Cromicus Productions (Fri Dec 09 2016 - 13:05:12 PST)
[AMBER] Frequencies in AMBER, obtaining the hessian
- David A Case (Wed Dec 14 2016 - 05:06:20 PST)
- Stregone (Wed Dec 14 2016 - 03:14:20 PST)
[AMBER] Fwd: AmberTools 16: IBM XL Compiler Support
- Jason Swails (Tue Dec 20 2016 - 13:36:58 PST)
- Hai Nguyen (Tue Dec 20 2016 - 13:32:43 PST)
- James Ostrander (Tue Dec 20 2016 - 11:37:58 PST)
- James Ostrander (Tue Dec 20 2016 - 11:29:34 PST)
- Jason Swails (Tue Dec 13 2016 - 22:14:38 PST)
- James Ostrander (Tue Dec 13 2016 - 12:52:02 PST)
[AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid
- Daniel Roe (Wed Dec 07 2016 - 13:07:50 PST)
- Bruno Falcone (Wed Dec 07 2016 - 11:41:36 PST)
- Bruno Falcone (Tue Dec 06 2016 - 10:44:06 PST)
- Daniel Roe (Tue Dec 06 2016 - 10:38:05 PST)
- Steven Ramsey (Tue Dec 06 2016 - 09:41:38 PST)
- Bruno Falcone (Tue Dec 06 2016 - 09:27:54 PST)
- Steven Ramsey (Tue Dec 06 2016 - 08:59:50 PST)
- Bruno Falcone (Tue Dec 06 2016 - 06:40:18 PST)
[AMBER] help in restart file
- David A Case (Fri Dec 30 2016 - 04:47:20 PST)
- Hai Nguyen (Thu Dec 29 2016 - 22:51:01 PST)
- Robin Jain (Thu Dec 29 2016 - 22:14:33 PST)
[AMBER] HMR with ParmEd for PSF/PDB inputs?
- Jason Swails (Tue Dec 13 2016 - 06:47:04 PST)
- Nhai (Mon Dec 12 2016 - 07:53:35 PST)
- Nhai (Mon Dec 12 2016 - 07:52:39 PST)
- Brian Radak (Mon Dec 12 2016 - 07:50:51 PST)
- Jason Swails (Sun Dec 11 2016 - 14:15:10 PST)
- Brian Radak (Sun Dec 11 2016 - 10:21:23 PST)
- Jason Swails (Sat Dec 10 2016 - 19:46:57 PST)
- Hai Nguyen (Fri Dec 09 2016 - 09:34:10 PST)
- Brian Radak (Fri Dec 09 2016 - 09:28:05 PST)
- Hai Nguyen (Fri Dec 09 2016 - 09:25:45 PST)
- Brian Radak (Fri Dec 09 2016 - 09:18:32 PST)
- Hai Nguyen (Fri Dec 09 2016 - 09:07:02 PST)
- Brian Radak (Fri Dec 09 2016 - 07:59:21 PST)
[AMBER] How to have a certain number of water molecules?
- David Case (Tue Dec 20 2016 - 10:15:35 PST)
- Azade Yazdan Yar (Tue Dec 20 2016 - 07:39:07 PST)
[AMBER] How to perform energy decomposition in Thermodynamic integration with Sander in Amber 14?
- Stefan Ivanov (Fri Dec 23 2016 - 08:01:45 PST)
- Dwight McGee (Thu Dec 22 2016 - 06:44:44 PST)
- Stefan Ivanov (Thu Dec 22 2016 - 02:55:49 PST)
[AMBER] How to turn off non-bonded interactions
- David A Case (Tue Dec 06 2016 - 04:48:43 PST)
- A kS (Tue Dec 06 2016 - 03:36:43 PST)
[AMBER] Hydrogen bond calculataion
- Daniel Roe (Wed Dec 14 2016 - 10:39:24 PST)
- richa anand (Tue Dec 13 2016 - 23:01:08 PST)
[AMBER] Installation of AMBER on Centos Rocks 6.2
- David A Case (Sat Dec 10 2016 - 06:44:52 PST)
- yasir.orionsolutions.co.in (Sat Dec 10 2016 - 02:36:19 PST)
- yasir.orionsolutions.co.in (Sat Dec 10 2016 - 00:57:55 PST)
- yasir.orionsolutions.co.in (Sat Dec 10 2016 - 00:53:23 PST)
- Hai Nguyen (Sat Dec 10 2016 - 00:48:08 PST)
- yasir.orionsolutions.co.in (Sat Dec 10 2016 - 00:43:21 PST)
- Hai Nguyen (Sat Dec 10 2016 - 00:39:55 PST)
- yasir.orionsolutions.co.in (Sat Dec 10 2016 - 00:36:32 PST)
- Elvis Martis (Thu Dec 08 2016 - 21:26:12 PST)
- Yasir Israr (Thu Dec 08 2016 - 20:09:02 PST)
- Elvis Martis (Thu Dec 08 2016 - 19:08:16 PST)
- Yasir Israr (Thu Dec 08 2016 - 18:23:09 PST)
[AMBER] Issue with the gaff parameters for "nh" atom type
- David Case (Mon Dec 19 2016 - 05:22:13 PST)
[AMBER] locating cpinutil.py file
- Hai Nguyen (Mon Dec 19 2016 - 11:32:52 PST)
- Tsibela German Tebello Mofokeng (Mon Dec 19 2016 - 11:29:00 PST)
[AMBER] Magnesium ion and MMPBSA/GBSA
- Brian Radak (Mon Dec 12 2016 - 09:11:11 PST)
- Ray Luo (Mon Dec 12 2016 - 08:52:48 PST)
- David A Case (Mon Dec 12 2016 - 08:34:10 PST)
- Elvis Martis (Sun Dec 11 2016 - 23:55:59 PST)
- Francesco Gentile (Sun Dec 11 2016 - 23:44:04 PST)
[AMBER] Minimum distance between imgaes
- A kS (Tue Dec 13 2016 - 06:02:21 PST)
- Daniel Roe (Tue Dec 13 2016 - 05:51:13 PST)
- A kS (Tue Dec 13 2016 - 05:48:05 PST)
- Daniel Roe (Tue Dec 13 2016 - 05:44:41 PST)
- A kS (Tue Dec 13 2016 - 05:39:07 PST)
[AMBER] MMGBSA vs MMPBSA
- Ray Luo (Wed Dec 07 2016 - 10:01:32 PST)
- Aronica, Pietro (Tue Dec 06 2016 - 18:14:13 PST)
- Ray Luo (Tue Dec 06 2016 - 09:03:46 PST)
- Hai Nguyen (Mon Dec 05 2016 - 20:15:02 PST)
- Aronica, Pietro (Mon Dec 05 2016 - 20:10:48 PST)
[AMBER] MMPBSA Quasi-Harmonic Entropy
- Sachin Natesh (Mon Dec 12 2016 - 20:16:26 PST)
[AMBER] mmpbsa snapshots
- Mary Varughese (Wed Dec 14 2016 - 02:58:47 PST)
- Elvis Martis (Wed Dec 14 2016 - 02:46:28 PST)
- Mary Varughese (Wed Dec 14 2016 - 01:51:19 PST)
- Elvis Martis (Wed Dec 14 2016 - 01:10:06 PST)
- Mary Varughese (Wed Dec 14 2016 - 00:18:31 PST)
[AMBER] multiple residues and solvatebox command
- David A Case (Fri Dec 02 2016 - 04:56:10 PST)
- Azade Yazdan Yar (Fri Dec 02 2016 - 04:24:22 PST)
[AMBER] NADH antechamber
- Andreas Tosstorff (Fri Dec 09 2016 - 00:31:37 PST)
- David A Case (Thu Dec 08 2016 - 11:37:15 PST)
- FyD (Thu Dec 08 2016 - 08:26:16 PST)
- Andreas Tosstorff (Thu Dec 08 2016 - 07:45:17 PST)
[AMBER] neutralization and Salt concentration for DNA simulations
- Rodrigo Galindo-Murillo (Thu Dec 22 2016 - 08:07:17 PST)
- Muthukumaran R (Thu Dec 22 2016 - 05:25:18 PST)
[AMBER] Parallel installation of MMPBSA.py.MPI failed
- Jason Swails (Thu Dec 08 2016 - 08:35:42 PST)
- MOHD HOMAIDUR RAHMAN (Thu Dec 08 2016 - 02:03:37 PST)
[AMBER] Paramfit for multiple molecules
- Robin Betz (Mon Dec 05 2016 - 16:56:00 PST)
[AMBER] Paramfit for multiple molecules (Robin Betz)
- Sven Hackbusch (Tue Dec 06 2016 - 13:44:35 PST)
[AMBER] Parmchk2 and dihedral parameters
- David A Case (Tue Dec 06 2016 - 07:02:26 PST)
- Andreas Gavrielides (Tue Dec 06 2016 - 05:02:49 PST)
- David A Case (Tue Dec 06 2016 - 04:45:47 PST)
- Andreas Gavrielides (Tue Dec 06 2016 - 02:28:37 PST)
[AMBER] parmchk2 multiple parameters
- Andreas Gavrielides (Mon Dec 19 2016 - 09:47:51 PST)
- David Case (Mon Dec 19 2016 - 09:39:24 PST)
- Andreas Gavrielides (Mon Dec 19 2016 - 06:53:01 PST)
[AMBER] pka of CYS
- Eric Lang (Fri Dec 16 2016 - 07:59:11 PST)
- Sowmya Indrakumar (Fri Dec 16 2016 - 07:33:28 PST)
- Carlos Simmerling (Tue Dec 13 2016 - 11:27:36 PST)
- Jason Swails (Tue Dec 13 2016 - 10:55:55 PST)
- Carlos Simmerling (Tue Dec 13 2016 - 10:22:53 PST)
- Jason Swails (Tue Dec 13 2016 - 09:42:35 PST)
- Sowmya Indrakumar (Tue Dec 13 2016 - 08:07:58 PST)
- Andreas Tosstorff (Tue Dec 13 2016 - 07:28:10 PST)
- Sowmya Indrakumar (Tue Dec 13 2016 - 07:21:59 PST)
- Adrian Roitberg (Tue Dec 13 2016 - 06:18:36 PST)
- Eric Lang (Tue Dec 13 2016 - 05:43:44 PST)
- Carlos Simmerling (Tue Dec 13 2016 - 03:09:57 PST)
- Eric Lang (Mon Dec 12 2016 - 23:33:05 PST)
- Sowmya Indrakumar (Mon Dec 12 2016 - 12:14:03 PST)
[AMBER] pmemd.cuda incomplete output file
- Niel Henriksen (Thu Dec 22 2016 - 07:58:17 PST)
- Andreas Tosstorff (Thu Dec 22 2016 - 07:39:27 PST)
- David Case (Sun Dec 18 2016 - 05:45:01 PST)
- Andreas Tosstorff (Sun Dec 18 2016 - 05:27:12 PST)
- David A Case (Fri Dec 16 2016 - 06:01:50 PST)
- Niel Henriksen (Fri Dec 16 2016 - 05:51:51 PST)
- Andreas Tosstorff (Thu Dec 15 2016 - 23:46:47 PST)
- Hai Nguyen (Thu Dec 15 2016 - 23:32:28 PST)
- Andreas Tosstorff (Thu Dec 15 2016 - 23:15:59 PST)
- Niel Henriksen (Thu Dec 15 2016 - 16:39:56 PST)
- Andreas Tosstorff (Thu Dec 15 2016 - 13:31:30 PST)
- Andreas Tosstorff (Thu Dec 15 2016 - 06:59:43 PST)
[AMBER] Possible conformations predicted by MD from NMR data (RDC, dihedral)
- David A Case (Wed Dec 21 2016 - 05:02:47 PST)
- Trang Nguyen (Tue Dec 20 2016 - 22:42:10 PST)
[AMBER] Principal Component Analysis (PCA) query.
- Abhilash J (Fri Dec 30 2016 - 10:28:05 PST)
- Daniel Roe (Fri Dec 30 2016 - 10:01:13 PST)
- Abhilash J (Fri Dec 30 2016 - 09:39:21 PST)
[AMBER] Problem about one GPU & multiple CPUs
- Daniel Roe (Wed Dec 21 2016 - 06:56:39 PST)
- 吴萌 (Wed Dec 21 2016 - 05:38:21 PST)
[AMBER] problem building Amber 16 with Intel compilers
- Hai Nguyen (Tue Dec 20 2016 - 13:27:35 PST)
- Susan Chacko (Tue Dec 20 2016 - 13:24:48 PST)
- Yeng-Tseng Wang (Tue Dec 20 2016 - 11:18:58 PST)
- Daniel Roe (Tue Dec 20 2016 - 11:04:39 PST)
- Hai Nguyen (Tue Dec 20 2016 - 10:50:57 PST)
- Susan Chacko (Tue Dec 20 2016 - 10:45:35 PST)
- Hai Nguyen (Tue Dec 20 2016 - 09:21:29 PST)
- Susan Chacko (Tue Dec 20 2016 - 09:10:20 PST)
- Susan Chacko (Tue Dec 20 2016 - 08:59:31 PST)
- Hai Nguyen (Tue Dec 20 2016 - 08:56:43 PST)
- Hai Nguyen (Tue Dec 20 2016 - 08:52:35 PST)
- Susan Chacko (Tue Dec 20 2016 - 08:42:19 PST)
[AMBER] Problem building FEW and mmpbsa.pl in Amber16
- David A Case (Fri Dec 23 2016 - 08:08:29 PST)
- Tong Zhu (Tue Dec 20 2016 - 22:57:23 PST)
- Nhai (Tue Dec 20 2016 - 19:17:21 PST)
- Tong Zhu (Tue Dec 20 2016 - 19:13:00 PST)
[AMBER] Problem in not defining the hybridization of a atomtype
- David A Case (Tue Dec 27 2016 - 09:02:14 PST)
- A kS (Mon Dec 26 2016 - 07:37:16 PST)
[AMBER] Problems during solvation of molecule from Protein Data Bank
- Sowmya Indrakumar (Tue Dec 13 2016 - 03:05:03 PST)
- David A Case (Mon Dec 12 2016 - 17:52:49 PST)
- Carlos Simmerling (Mon Dec 12 2016 - 16:14:47 PST)
- The Cromicus Productions (Mon Dec 12 2016 - 13:53:04 PST)
- The Cromicus Productions (Mon Dec 12 2016 - 13:52:15 PST)
[AMBER] Proplem about how to set substrate concentration
- Sérgio Marques (Wed Dec 28 2016 - 05:09:08 PST)
- Huang Jing (Tue Dec 27 2016 - 23:54:27 PST)
- Shanghaitech University WuMeng (Tue Dec 27 2016 - 23:38:54 PST)
[AMBER] QM/MM/MD g09 interface issues,
- Fabrício Bracht (Thu Dec 08 2016 - 08:46:25 PST)
- David Poole (Thu Dec 08 2016 - 08:01:14 PST)
[AMBER] Query regarding Ligand Binding Metalloprotein with MCPB.py
- Abhilash J (Wed Dec 07 2016 - 21:34:21 PST)
[AMBER] question about pol_h in ambertool15
- Thibaud von Erlach (Fri Dec 02 2016 - 00:24:45 PST)
- Anon (Thu Dec 01 2016 - 19:13:20 PST)
- David A Case (Thu Dec 01 2016 - 18:54:30 PST)
- Thibaud von Erlach (Thu Dec 01 2016 - 02:30:32 PST)
[AMBER] Questions regarding Installation of AMBER 16
- Daniel Roe (Mon Dec 12 2016 - 11:52:07 PST)
- Hai Nguyen (Sun Dec 11 2016 - 13:22:48 PST)
- James Kress (Sun Dec 11 2016 - 13:07:50 PST)
[AMBER] rdf_with_center_in_cpptraj_16
- Daniel Roe (Fri Dec 30 2016 - 10:02:20 PST)
- JAIME RUBIO MARTINEZ (Sun Dec 25 2016 - 09:54:26 PST)
- JAIME RUBIO MARTINEZ (Wed Dec 21 2016 - 08:20:24 PST)
- Daniel Roe (Wed Dec 21 2016 - 06:59:26 PST)
- JAIME RUBIO MARTINEZ (Wed Dec 21 2016 - 05:01:57 PST)
[AMBER] ReCpHMD Optimal values of ntcnstph, ntrelax, nstlim and numexchg
- Jason Swails (Mon Dec 05 2016 - 08:28:40 PST)
- Adrian Roitberg (Mon Dec 05 2016 - 08:12:43 PST)
- Jason Swails (Mon Dec 05 2016 - 07:56:45 PST)
- Fabrício Bracht (Mon Dec 05 2016 - 04:46:15 PST)
[AMBER] REMD with pressure coupling
- Feng Pan (Thu Dec 22 2016 - 19:25:26 PST)
- Chris Neale (Thu Dec 22 2016 - 19:10:06 PST)
- Chris Neale (Thu Dec 22 2016 - 19:02:08 PST)
- Feng Pan (Thu Dec 22 2016 - 18:47:25 PST)
- Jason Swails (Thu Dec 22 2016 - 13:26:23 PST)
- Chris Neale (Thu Dec 22 2016 - 09:43:17 PST)
- Feng Pan (Thu Dec 22 2016 - 08:35:20 PST)
- Neale, Christopher Andrew (Tue Dec 20 2016 - 09:09:43 PST)
- Neale, Christopher Andrew (Mon Dec 19 2016 - 09:12:50 PST)
- Giovanni Bussi (Fri Dec 16 2016 - 00:21:19 PST)
- Jason Swails (Thu Dec 15 2016 - 18:35:17 PST)
- Giovanni Bussi (Thu Dec 15 2016 - 00:07:17 PST)
- Neale, Christopher Andrew (Wed Dec 14 2016 - 14:48:37 PST)
- Adrian Roitberg (Tue Dec 13 2016 - 06:23:39 PST)
- Daniel Roe (Mon Dec 12 2016 - 13:06:02 PST)
- Neale, Christopher Andrew (Mon Dec 12 2016 - 12:44:24 PST)
[AMBER] Remove motion of center of mass after obtaining trajectory
- The Cromicus Productions (Fri Dec 30 2016 - 23:32:06 PST)
- The Cromicus Productions (Fri Dec 30 2016 - 18:23:20 PST)
- Hai Nguyen (Fri Dec 30 2016 - 13:21:51 PST)
- The Cromicus Productions (Fri Dec 30 2016 - 11:54:25 PST)
[AMBER] Remove water from mdvel file
- The Cromicus Productions (Thu Dec 15 2016 - 17:30:16 PST)
- Nhai (Thu Dec 15 2016 - 16:20:12 PST)
- The Cromicus Productions (Thu Dec 15 2016 - 13:25:16 PST)
[AMBER] SEP non-standard phosphoserine issue.
- Hai Nguyen (Mon Dec 26 2016 - 23:23:07 PST)
- Hai Nguyen (Mon Dec 26 2016 - 23:22:21 PST)
- Saman Yousuf ali (Mon Dec 26 2016 - 23:02:47 PST)
[AMBER] Should I image atoms when I calculate translational and rotational diffusion constants with cpptraj?
- David A Case (Fri Dec 30 2016 - 04:50:50 PST)
- wei (Thu Dec 29 2016 - 22:51:27 PST)
[AMBER] Slowly reducing restraints
- Elvis Martis (Fri Dec 02 2016 - 05:36:30 PST)
- Dd H (Fri Dec 02 2016 - 05:28:05 PST)
[AMBER] solvatebox command
- David A Case (Thu Dec 22 2016 - 05:11:12 PST)
- Mohaddeseh Habibzadeh (Thu Dec 22 2016 - 01:36:46 PST)
[AMBER] Specify Grid Origin in 3D-RISM - Is it possible?
- George Giambasu (Fri Dec 16 2016 - 07:19:50 PST)
- Lucia Fusani (Fri Dec 16 2016 - 06:45:16 PST)
[AMBER] sviol script error ?
- David A Case (Thu Dec 15 2016 - 06:13:29 PST)
- Benjamin Chagot (Wed Dec 14 2016 - 08:08:52 PST)
[AMBER] The AmberTools 16 build errors
- Nhai (Wed Dec 07 2016 - 16:51:32 PST)
- Juwen (Wed Dec 07 2016 - 16:46:48 PST)
- Nhai (Wed Dec 07 2016 - 16:40:45 PST)
- Nhai (Wed Dec 07 2016 - 16:39:13 PST)
- Juwen (Wed Dec 07 2016 - 16:35:23 PST)
[AMBER] The right character for logical AND in mask definition in MMPBSA ?
- Marek Maly (Tue Dec 13 2016 - 13:28:15 PST)
- Jason Swails (Tue Dec 13 2016 - 09:47:29 PST)
- Marek Maly (Tue Dec 13 2016 - 09:40:59 PST)
[AMBER] TI calculation problem in pmemd
- Hannes Loeffler (Sun Dec 18 2016 - 23:48:53 PST)
- cuiyinglukitty (Sun Dec 18 2016 - 22:34:12 PST)
[AMBER] trajectory analysis
- Elvis Martis (Thu Dec 01 2016 - 22:45:38 PST)
- Carlos Romero (Thu Dec 01 2016 - 22:39:53 PST)
[AMBER] Two different graphics cards in the same PC for pmemd.cuda
- Elvis Martis (Wed Dec 14 2016 - 20:23:25 PST)
- Elvis Martis (Wed Dec 14 2016 - 20:17:09 PST)
- Anton Perera (Wed Dec 14 2016 - 20:09:28 PST)
[AMBER] Umbrella sampling (US) along RMSD-based coordinates using targeted MD script
- Tarsis (Fri Dec 30 2016 - 07:49:51 PST)
[AMBER] Unknown atom type EP
- A kS (Sun Dec 18 2016 - 06:34:32 PST)
- David Case (Sat Dec 17 2016 - 07:49:16 PST)
- A kS (Sat Dec 17 2016 - 03:53:09 PST)
[AMBER] Untwisting a molecule
- Daniel Roe (Mon Dec 12 2016 - 05:04:06 PST)
- Christina Bergonzo (Mon Dec 12 2016 - 04:38:14 PST)
- Josh Berryman (Mon Dec 12 2016 - 02:41:20 PST)
- Bill Ross (Sun Dec 11 2016 - 18:31:41 PST)
- The Cromicus Productions (Sun Dec 11 2016 - 18:15:45 PST)
- Bill Ross (Sun Dec 11 2016 - 18:12:28 PST)
- David A Case (Sun Dec 11 2016 - 18:05:21 PST)
- The Cromicus Productions (Sun Dec 11 2016 - 14:50:07 PST)
[AMBER] Uridine diphosphate rhamnose (UDP-Rha)
- FyD (Thu Dec 15 2016 - 10:06:29 PST)
- David A Case (Wed Dec 14 2016 - 08:16:03 PST)
- Imma Speciale (Wed Dec 14 2016 - 07:10:13 PST)
[AMBER] van der Waals parameters GAFF UFF OPLS
- David Case (Tue Dec 20 2016 - 10:31:42 PST)
- Bruno Falcone (Tue Dec 20 2016 - 08:58:01 PST)
[AMBER] Water density near the protein suspiciously low
- I Lőrincz (Wed Dec 28 2016 - 00:45:16 PST)
- David Case (Tue Dec 27 2016 - 18:08:34 PST)
- Chris Moth (Tue Dec 27 2016 - 14:42:07 PST)
- Bill Ross (Tue Dec 27 2016 - 14:00:22 PST)
- Hai Nguyen (Tue Dec 27 2016 - 14:00:09 PST)
- I Lőrincz (Tue Dec 27 2016 - 13:54:53 PST)
[AMBER] Zinc Oxide and protein simulation with AMBER
- Pengfei Li (Thu Dec 22 2016 - 08:46:49 PST)
- vivek m (Wed Dec 21 2016 - 10:17:57 PST)
- Pengfei Li (Tue Dec 13 2016 - 11:47:10 PST)
- vivek m (Tue Dec 13 2016 - 09:50:41 PST)
- David A Case (Tue Dec 13 2016 - 07:34:53 PST)
- vivek m (Tue Dec 13 2016 - 01:35:19 PST)
Distance diffusion calculation in ptraj and cpptraj
- Daniel Roe (Wed Dec 28 2016 - 09:43:06 PST)
- wei (Tue Dec 27 2016 - 18:07:51 PST)
Editing residue in PDB file
- David A Case (Tue Dec 13 2016 - 07:30:41 PST)
- Nikolay N. Kuzmich (Tue Dec 13 2016 - 06:27:10 PST)
error: could not find mpi library for --enable-mpi
- Nhai (Thu Dec 22 2016 - 12:14:58 PST)
- Michael Shokhen (Thu Dec 22 2016 - 12:07:34 PST)
Problems with imaging
- Mark Waterhouse [RPG] (Thu Dec 01 2016 - 03:37:35 PST)

Amber Archive Dec 2016 by subject