Amber Archive Dec 2019: by subject

[AMBER] 34th Molecular Modelling Workshop (MMWS) February 17-19, 2020 in Erlangen, Germany
- Dr. Anselm Horn (Tue Dec 03 2019 - 01:56:09 PST)
[AMBER] AMBER 18 cuda installation
- Saikat Pal (Mon Dec 23 2019 - 05:33:19 PST)
[AMBER] amber 18 installation error
- Gustaf Olsson (Thu Dec 19 2019 - 22:59:18 PST)
- Saikat Pal (Thu Dec 19 2019 - 22:46:05 PST)
[AMBER] amber update issue
- David Case (Fri Dec 20 2019 - 09:18:56 PST)
- Saikat Pal (Thu Dec 19 2019 - 23:39:52 PST)
[AMBER] Amber18 download instructions
- Billiot, Eugene (Fri Dec 20 2019 - 14:16:01 PST)
- Billiot, Eugene (Fri Dec 20 2019 - 14:10:18 PST)
[AMBER] Amber18 installation problem
- David Case (Fri Dec 20 2019 - 14:05:03 PST)
- Billiot, Eugene (Fri Dec 20 2019 - 13:22:02 PST)
[AMBER] Amber18-bash: logFile: command not found...
- David Case (Tue Dec 24 2019 - 06:43:07 PST)
- 辛志宏 (Mon Dec 23 2019 - 19:03:49 PST)
[AMBER] Announcement: 34th Molecular Modelling Workshop (MMWS) Feb 17-19, 2020 in Erlangen, Germany
- Dr. Anselm Horn (Wed Dec 04 2019 - 05:13:39 PST)
[AMBER] Any idea on this error and how to troubleshoot
- Cruzeiro,Vinicius Wilian D (Mon Dec 16 2019 - 13:09:49 PST)
- Debarati DasGupta (Mon Dec 16 2019 - 10:43:46 PST)
[AMBER] Any way of making protein rigid in MD simulation?
- Brian Radak (Mon Dec 16 2019 - 07:13:30 PST)
- Gustaf Olsson (Sun Dec 15 2019 - 23:14:30 PST)
- Liao (Fri Dec 13 2019 - 20:59:40 PST)
[AMBER] Attaching Methoxy (OMe) Capping at C-terminal
- Pallab Dutta (Thu Dec 19 2019 - 06:40:47 PST)
- David Case (Thu Dec 19 2019 - 05:01:15 PST)
- Pallab Dutta (Thu Dec 19 2019 - 04:15:47 PST)
[AMBER] Charge distribution in molecule
- Aashish Bhatt (Thu Dec 05 2019 - 04:09:00 PST)
- Bill Ross (Mon Dec 02 2019 - 05:42:54 PST)
- Horn, Anselm (Sun Dec 01 2019 - 23:37:51 PST)
- Aashish Bhatt (Sun Dec 01 2019 - 23:04:21 PST)
[AMBER] Chemical education for MD articles
- Joanna Michelle E. Chua (Tue Dec 03 2019 - 05:18:00 PST)
- Daniel Roe (Tue Dec 03 2019 - 05:02:31 PST)
- Joanna Michelle E. Chua (Mon Dec 02 2019 - 18:25:19 PST)
- Lod King (Mon Dec 02 2019 - 12:21:12 PST)
[AMBER] Conference Announcement: Molecular Modeling Workshop, Feb 17-19, 2020 in Erlangen, Germany
- Dr. Anselm Horn (Fri Dec 06 2019 - 01:41:01 PST)
[AMBER] cpptraj RMS calculations appear to be incorrect
- Bellesis, Andrew G (Tue Dec 03 2019 - 08:00:41 PST)
- Carlos Simmerling (Mon Dec 02 2019 - 10:18:09 PST)
- Bellesis, Andrew G (Mon Dec 02 2019 - 09:02:50 PST)
[AMBER] cpptraj.MPI versus cpptraj
- Debarati DasGupta (Fri Dec 20 2019 - 05:26:26 PST)
- Debarati DasGupta (Fri Dec 20 2019 - 05:24:54 PST)
- Daniel Roe (Fri Dec 20 2019 - 05:23:54 PST)
- Daniel Roe (Fri Dec 20 2019 - 05:22:39 PST)
- Debarati DasGupta (Fri Dec 20 2019 - 05:18:43 PST)
- David Case (Thu Dec 19 2019 - 19:00:25 PST)
- Debarati DasGupta (Thu Dec 19 2019 - 11:51:47 PST)
[AMBER] Definition of restraints to avoid ligand aggregation
- Giulio RASTELLI (Sun Dec 22 2019 - 08:06:16 PST)
[AMBER] Equilibriation input file for TI
- Debarati DasGupta (Fri Dec 06 2019 - 07:57:28 PST)
- David A Case (Fri Dec 06 2019 - 05:28:04 PST)
- Debarati DasGupta (Thu Dec 05 2019 - 14:35:23 PST)
[AMBER] error
- Daniel Roe (Sun Dec 15 2019 - 12:10:09 PST)
- Bill Ross (Thu Dec 12 2019 - 11:26:17 PST)
- MYRIAN TORRES RICO (Thu Dec 12 2019 - 01:13:39 PST)
- Bill Ross (Wed Dec 11 2019 - 14:54:52 PST)
- Carlos Simmerling (Wed Dec 11 2019 - 11:28:32 PST)
- James Kress (Wed Dec 11 2019 - 09:36:15 PST)
- David A Case (Wed Dec 11 2019 - 08:40:39 PST)
- MYRIAN TORRES RICO (Wed Dec 11 2019 - 08:05:49 PST)
- Daniel Roe (Tue Dec 10 2019 - 09:01:45 PST)
- MYRIAN TORRES RICO (Tue Dec 10 2019 - 06:59:45 PST)
- David A Case (Tue Dec 10 2019 - 04:46:18 PST)
- MYRIAN TORRES RICO (Tue Dec 10 2019 - 04:27:02 PST)
[AMBER] Error during installation
- David Case (Tue Dec 24 2019 - 06:52:26 PST)
- ARITRA MITRA (Tue Dec 24 2019 - 01:23:12 PST)
[AMBER] Error when running MD
- Bill Ross (Fri Dec 13 2019 - 11:02:13 PST)
- David Case (Fri Dec 13 2019 - 10:42:10 PST)
- maya nair (Fri Dec 13 2019 - 09:51:34 PST)
[AMBER] FESetup
- Sarah Fegan - UKRI STFC (Mon Dec 16 2019 - 00:56:53 PST)
- Sushil Mishra (Sun Dec 15 2019 - 22:12:32 PST)
- Debarati DasGupta (Sun Dec 15 2019 - 14:14:34 PST)
[AMBER] ff19SB with end-caps pmemd.cuda problem
- Carlos Simmerling (Tue Dec 17 2019 - 08:21:16 PST)
- Pavlína Pokorná (Tue Dec 17 2019 - 06:21:57 PST)
- Carlos Simmerling (Tue Dec 17 2019 - 06:04:13 PST)
- Pavlína Pokorná (Mon Dec 16 2019 - 01:59:01 PST)
- Pavlína Pokorná (Wed Dec 11 2019 - 09:07:30 PST)
- Carlos Simmerling (Wed Dec 11 2019 - 08:54:39 PST)
- Pavlína Pokorná (Wed Dec 11 2019 - 08:50:41 PST)
- Carlos Simmerling (Wed Dec 11 2019 - 07:10:18 PST)
- Pavlína Pokorná (Wed Dec 11 2019 - 06:40:06 PST)
- Carlos Simmerling (Wed Dec 11 2019 - 06:02:22 PST)
- Pavlína Pokorná (Wed Dec 11 2019 - 05:34:28 PST)
- Carlos Simmerling (Wed Dec 11 2019 - 03:53:44 PST)
- Pavlína Pokorná (Wed Dec 11 2019 - 02:37:55 PST)
[AMBER] Figured Amber 16 installation on Mac
- Erik Zuiderweg (Mon Dec 30 2019 - 04:44:19 PST)
[AMBER] Fixed Minimization
- emanuele falbo (Fri Dec 06 2019 - 07:05:14 PST)
- David A Case (Fri Dec 06 2019 - 05:26:13 PST)
- emanuele falbo (Thu Dec 05 2019 - 06:15:49 PST)
[AMBER] Flexible protein!
- Debarati DasGupta (Fri Dec 13 2019 - 11:37:26 PST)
- David A Case (Fri Dec 13 2019 - 04:17:10 PST)
- Debarati DasGupta (Thu Dec 12 2019 - 10:26:20 PST)
[AMBER] Found an invalid periodicity in the prmtop file : MMPBSA
- venkat (Thu Dec 12 2019 - 03:57:16 PST)
- venkat (Thu Dec 12 2019 - 03:31:40 PST)
- David A Case (Wed Dec 11 2019 - 10:42:09 PST)
- venkat (Wed Dec 11 2019 - 08:13:02 PST)
[AMBER] Fwd: problem of compiling
- Gerald Monard (Fri Dec 13 2019 - 00:38:05 PST)
- Albert (Thu Dec 12 2019 - 23:16:59 PST)
- Gerald Monard (Thu Dec 12 2019 - 23:01:45 PST)
- Albert (Thu Dec 12 2019 - 16:44:36 PST)
- Gerald Monard (Thu Dec 12 2019 - 10:46:44 PST)
- David A Case (Thu Dec 12 2019 - 06:05:15 PST)
- Albert (Wed Dec 11 2019 - 16:21:54 PST)
[AMBER] fxyz and outxyz
- Baker, Joseph (Thu Dec 05 2019 - 19:09:11 PST)
[AMBER] GaMD problems with different computers.
- David A Case (Fri Dec 13 2019 - 04:22:32 PST)
- Seibold, Steve Allan (Thu Dec 12 2019 - 11:12:25 PST)
[AMBER] GPU installation error
- Sruthi Sudhakar (Wed Dec 11 2019 - 19:41:30 PST)
- David A Case (Wed Dec 11 2019 - 10:39:38 PST)
- Sruthi Sudhakar (Wed Dec 11 2019 - 09:47:45 PST)
[AMBER] help needed for failed installation of CUDA for GPU-accelerated versions of pmemd for AMBER 18
- Billiot, Eugene (Tue Dec 24 2019 - 10:19:16 PST)
- David Case (Mon Dec 23 2019 - 18:40:33 PST)
- Billiot, Eugene (Sun Dec 22 2019 - 14:30:26 PST)
[AMBER] help on this error
- David Case (Sat Dec 07 2019 - 06:03:43 PST)
- Debarati DasGupta (Fri Dec 06 2019 - 13:08:29 PST)
- Debarati DasGupta (Fri Dec 06 2019 - 05:24:08 PST)
- Josh Berryman (Fri Dec 06 2019 - 03:21:58 PST)
- Debarati DasGupta (Tue Dec 03 2019 - 14:06:17 PST)
[AMBER] How can I get solute-solute energy information?
- Zhonghua Xia (Fri Dec 06 2019 - 05:36:35 PST)
- Zhonghua Xia (Fri Dec 06 2019 - 04:04:38 PST)
[AMBER] How to deal with Dummy atoms of 4-coordinated Zinc in QM/MM
- Qing Lv (Fri Dec 20 2019 - 23:13:44 PST)
[AMBER] How to use AMBER on Supercomputer
- MUHAMMAD KHATTAB FATHI KHATTAB (Sat Dec 21 2019 - 09:11:32 PST)
- Liao (Sat Dec 21 2019 - 08:07:36 PST)
- MUHAMMAD KHATTAB FATHI KHATTAB (Sat Dec 21 2019 - 07:51:15 PST)
- Liao (Sat Dec 21 2019 - 07:28:20 PST)
- MUHAMMAD KHATTAB FATHI KHATTAB (Fri Dec 20 2019 - 22:49:44 PST)
[AMBER] If there is a method that can just use the soft-core potential for VDW interaction but not for electrostatic part
- David Case (Wed Dec 18 2019 - 06:44:15 PST)
- wangjianing_mail (Tue Dec 17 2019 - 22:17:07 PST)
[AMBER] imin=5 fails to produce output
- Casalini Tommaso (Fri Dec 20 2019 - 01:29:12 PST)
[AMBER] installing Amber 18 issues
- David Case (Wed Dec 18 2019 - 06:34:38 PST)
- Billiot, Eugene (Tue Dec 17 2019 - 19:17:58 PST)
- Joanna Michelle E. Chua (Tue Dec 17 2019 - 19:01:26 PST)
- Joanna Michelle E. Chua (Tue Dec 17 2019 - 18:50:24 PST)
- Billiot, Eugene (Tue Dec 17 2019 - 15:46:00 PST)
[AMBER] intel compiling failed
- David A Case (Fri Dec 13 2019 - 04:30:52 PST)
- Albert (Thu Dec 12 2019 - 19:47:28 PST)
[AMBER] Interaction entropy program （Geng Dong）
- 东庚 (Wed Dec 25 2019 - 17:52:55 PST)
[AMBER] Minimization equilibration of protein+ligand prior to TI setup
- Debarati DasGupta (Fri Dec 27 2019 - 08:07:29 PST)
- Carlos Simmerling (Wed Dec 25 2019 - 03:51:15 PST)
- Debarati DasGupta (Tue Dec 24 2019 - 06:44:24 PST)
- David Case (Mon Dec 23 2019 - 18:36:42 PST)
- Debarati DasGupta (Mon Dec 23 2019 - 12:33:03 PST)
[AMBER] MM-GBSA error
- Rui Chen (Wed Dec 18 2019 - 09:06:07 PST)
- David Case (Sat Dec 14 2019 - 06:47:27 PST)
- Rui Chen (Fri Dec 13 2019 - 19:49:26 PST)
- Rui Chen (Thu Dec 12 2019 - 18:31:57 PST)
[AMBER] mm-gbsa with more than one receptor
- Liao (Thu Dec 12 2019 - 17:42:54 PST)
- Liao (Thu Dec 12 2019 - 17:39:01 PST)
- Liao (Thu Dec 12 2019 - 17:37:41 PST)
- Liao (Thu Dec 12 2019 - 17:42:08 PST)
- Neha Gandhi (Thu Dec 12 2019 - 15:50:11 PST)
[AMBER] MMGB/PBSA parameters
- Rui Chen (Mon Dec 23 2019 - 10:57:21 PST)
- Carlos Simmerling (Mon Dec 23 2019 - 10:33:36 PST)
- Rui Chen (Mon Dec 23 2019 - 09:12:44 PST)
[AMBER] MMGBSA script file
- Rui Chen (Mon Dec 16 2019 - 19:57:47 PST)
- Rui Chen (Mon Dec 16 2019 - 16:27:40 PST)
[AMBER] MMPBSA mmpbsa_py_energy failed with prmtop
- Qing Lv (Wed Dec 04 2019 - 23:41:02 PST)
- Qing Lv (Wed Dec 04 2019 - 20:32:05 PST)
[AMBER] Molecular dynamics of tripeptide like organic molecule
- Petro (Tue Dec 10 2019 - 22:19:35 PST)
- Debasish Mandal (Tue Dec 10 2019 - 20:18:56 PST)
[AMBER] nuc.nab:no such file found error
- Sruthi Sudhakar (Tue Dec 17 2019 - 20:23:51 PST)
- David Case (Tue Dec 17 2019 - 05:30:32 PST)
- Bill Ross (Mon Dec 16 2019 - 22:52:19 PST)
- Sruthi Sudhakar (Mon Dec 16 2019 - 20:44:15 PST)
[AMBER] NVT equilibriation followed by NPT in TI
- Debarati DasGupta (Tue Dec 17 2019 - 06:54:15 PST)
- David Case (Tue Dec 17 2019 - 05:38:58 PST)
- Debarati DasGupta (Mon Dec 16 2019 - 06:30:48 PST)
[AMBER] Obtaining excess molar volumes using Molecular Dynamics
- David Case (Tue Dec 03 2019 - 05:51:28 PST)
[AMBER] On deprotonated Tyr
- David Sáez (Sun Dec 01 2019 - 20:39:54 PST)
[AMBER] Parameters to be used for protein in implicit solvent
- Carlos Simmerling (Fri Dec 27 2019 - 05:35:41 PST)
- SHAUNAK BADANI (Fri Dec 27 2019 - 03:54:08 PST)
[AMBER] PrmtopError: Complex natom != receptor natom + ligand natom
- David Case (Mon Dec 09 2019 - 05:28:18 PST)
- Bill Ross (Sun Dec 08 2019 - 18:02:59 PST)
[AMBER] problem of compiling
- Gerald Monard (Mon Dec 09 2019 - 01:48:53 PST)
- Charo del Genio (Sun Dec 08 2019 - 00:46:19 PST)
- Albert (Sat Dec 07 2019 - 20:23:04 PST)
[AMBER] Problems adding molecule on Metal-Water system
- Lucas Bandeira (Thu Dec 12 2019 - 06:19:09 PST)
- David Case (Mon Dec 09 2019 - 09:46:38 PST)
- Lucas Bandeira (Sun Dec 08 2019 - 16:59:40 PST)
- David Case (Sat Dec 07 2019 - 06:07:01 PST)
- Lucas Bandeira (Fri Dec 06 2019 - 11:22:44 PST)
[AMBER] Problems installing Amber 18
- Billiot, Eugene (Wed Dec 18 2019 - 06:46:38 PST)
- Gustaf Olsson (Tue Dec 17 2019 - 22:49:14 PST)
- Billiot, Eugene (Tue Dec 17 2019 - 13:58:14 PST)
- Billiot, Eugene (Tue Dec 17 2019 - 13:54:07 PST)
[AMBER] Problems installing mpi for AMBER 18.
- Bill Ross (Mon Dec 16 2019 - 07:45:51 PST)
- Billiot, Eugene (Mon Dec 16 2019 - 07:42:07 PST)
- Billiot, Eugene (Sun Dec 15 2019 - 18:04:35 PST)
- Bill Ross (Sun Dec 15 2019 - 17:31:03 PST)
- Billiot, Eugene (Sun Dec 15 2019 - 17:08:03 PST)
[AMBER] Problems installing mpi for AMBER 18. I was trying to install mpi I was typing in
- Billiot, Eugene (Mon Dec 16 2019 - 08:07:21 PST)
[AMBER] question about Tleap
- Rui Chen (Mon Dec 16 2019 - 10:19:27 PST)
[AMBER] reinstalling Amber 16 + Ambertools 16 on a Mac
- erik zuiderweg (Mon Dec 30 2019 - 03:38:59 PST)
[AMBER] Segmentation Fault when running constant pH Replica Exchange on GPUs
- Hofer, Florian (Fri Dec 06 2019 - 07:52:01 PST)
[AMBER] sequence command
- ankita mehta (Mon Dec 02 2019 - 02:15:44 PST)
- ankita mehta (Sun Dec 01 2019 - 22:28:03 PST)
[AMBER] Sequential equilibration versus parallel runs in TI
- David A Case (Thu Dec 05 2019 - 05:54:39 PST)
- Debarati DasGupta (Wed Dec 04 2019 - 07:45:57 PST)
- Debarati DasGupta (Wed Dec 04 2019 - 07:45:05 PST)
[AMBER] some queries
- Ayesha Fatima (Mon Dec 30 2019 - 06:24:29 PST)
- David Case (Mon Dec 30 2019 - 06:13:58 PST)
- Ayesha Fatima (Sun Dec 29 2019 - 08:41:39 PST)
[AMBER] Table 21.1 in Thermodynamic Integration section of amber18 manual
- Debarati DasGupta (Wed Dec 04 2019 - 07:17:42 PST)
[AMBER] TI calculation steps
- Debarati DasGupta (Thu Dec 05 2019 - 13:46:44 PST)
- Song, Lin (Thu Dec 05 2019 - 13:45:55 PST)
- Debarati DasGupta (Thu Dec 05 2019 - 13:39:29 PST)
- Song, Lin (Thu Dec 05 2019 - 13:25:39 PST)
- Debarati DasGupta (Thu Dec 05 2019 - 12:24:56 PST)
[AMBER] TI calculations linear scaling of atoms!
- Debarati DasGupta (Thu Dec 05 2019 - 15:01:21 PST)
[AMBER] TI on gpus
- David A Case (Thu Dec 05 2019 - 05:58:10 PST)
- Debarati DasGupta (Wed Dec 04 2019 - 10:01:14 PST)
[AMBER] Ti on pmemd.CUDA
- Carlos Simmerling (Thu Dec 12 2019 - 09:36:18 PST)
- Hosein Geraili Daronkola (Thu Dec 12 2019 - 07:22:04 PST)
[AMBER] TI support for CHARMM FF
- Jose Christian Flores Canales (Tue Dec 03 2019 - 04:58:02 PST)
[AMBER] Time shift.
- Bill Ross (Thu Dec 12 2019 - 00:17:03 PST)
- Petro (Wed Dec 11 2019 - 23:40:55 PST)
[AMBER] Timestep (dt) in TI calculations
- Debarati DasGupta (Sun Dec 08 2019 - 06:30:03 PST)
[AMBER] tip4p-d water forcefield parameters
- David Case (Wed Dec 18 2019 - 06:41:11 PST)
- Luca Codutti (Tue Dec 17 2019 - 08:06:23 PST)
- Luca Codutti (Tue Dec 17 2019 - 08:03:25 PST)
[AMBER] Tleap naming problem
- David Case (Thu Dec 26 2019 - 06:35:43 PST)
- Rui Chen (Wed Dec 25 2019 - 19:53:49 PST)
[AMBER] User-defined high precision AMBER trajectory file formats
- Daniel Roe (Sun Dec 15 2019 - 12:14:13 PST)
- Xin Bai (Thu Dec 12 2019 - 03:12:01 PST)
[AMBER] Virtual box with imin = 1 or imin = 5
- Jerome Eberhardt (Mon Dec 16 2019 - 16:38:15 PST)
- Jerome Eberhardt (Mon Dec 16 2019 - 16:38:09 PST)
- David Case (Mon Dec 16 2019 - 12:40:13 PST)
- David Case (Mon Dec 16 2019 - 12:15:34 PST)
- Jerome Eberhardt (Mon Dec 16 2019 - 10:34:52 PST)
- Carlos Simmerling (Mon Dec 16 2019 - 05:16:32 PST)
- Bill Ross (Sun Dec 15 2019 - 21:59:49 PST)
- Jerome Eberhardt (Sun Dec 15 2019 - 21:24:26 PST)
[AMBER] Warning: 2 or more molecules (3 and 4) share residue numbers (1003).
- David A Case (Fri Dec 06 2019 - 05:32:42 PST)
- Bill Ross (Thu Dec 05 2019 - 21:27:39 PST)
- David Sáez (Thu Dec 05 2019 - 21:08:38 PST)
[AMBER] Which language could tleap know?
- David Case (Thu Dec 26 2019 - 06:39:08 PST)
- mwli.mail.ustc.edu.cn (Thu Dec 26 2019 - 00:06:22 PST)

Amber Archive Dec 2019 by subject