Amber Archive Dec 2020: by subject

[AMBER] ABMD NFE queries
- Feng Pan (Fri Dec 04 2020 - 17:31:31 PST)
[AMBER] amber 20 compilation problem
- David A Case (Tue Dec 01 2020 - 17:59:57 PST)
- Jordi Bujons (Tue Dec 01 2020 - 10:14:23 PST)
[AMBER] amber 20 compilation problem (David A Case)
- Jordi Bujons (Fri Dec 04 2020 - 09:30:28 PST)
[AMBER] Amber 4/pre Amber 7 binaries?
- Bill Ross (Wed Dec 16 2020 - 15:00:29 PST)
- Bill Ross (Wed Dec 16 2020 - 14:54:17 PST)
- Ryan Novosielski (Wed Dec 16 2020 - 14:36:33 PST)
- Kenneth Huang (Wed Dec 16 2020 - 14:29:53 PST)
- Ryan Novosielski (Wed Dec 16 2020 - 13:02:18 PST)
- Kenneth Huang (Wed Dec 16 2020 - 12:49:02 PST)
- Ryan Novosielski (Wed Dec 16 2020 - 09:35:08 PST)
- Kenneth Huang (Wed Dec 16 2020 - 09:02:23 PST)
- David A Case (Wed Dec 16 2020 - 06:16:53 PST)
- Kenneth Huang (Tue Dec 15 2020 - 21:54:59 PST)
- Bill Ross (Tue Dec 15 2020 - 20:20:18 PST)
[AMBER] AMBER Digest, Vol 3215, Issue 1
- David A Case (Thu Dec 17 2020 - 05:21:27 PST)
[AMBER] Amber20 Installation Error
- David A Case (Thu Dec 31 2020 - 05:42:28 PST)
- Li,Haoxi (Wed Dec 30 2020 - 17:49:24 PST)
- David A Case (Wed Dec 30 2020 - 09:21:04 PST)
- David A Case (Tue Dec 29 2020 - 06:47:10 PST)
- Li,Haoxi (Mon Dec 28 2020 - 17:32:22 PST)
[AMBER] AMBER20 on Ubuntu 20.04 and CUDA 11.2?
- Rudy Richardson (Sat Dec 19 2020 - 10:41:52 PST)
- David A Case (Sat Dec 19 2020 - 06:36:32 PST)
- Rudy Richardson (Fri Dec 18 2020 - 15:45:57 PST)
[AMBER] ambpdb or other scipt?
- Bill Ross (Tue Dec 15 2020 - 23:38:30 PST)
- Jisha B (Tue Dec 15 2020 - 23:29:16 PST)
- Bill Ross (Tue Dec 15 2020 - 23:26:43 PST)
- Jisha B (Tue Dec 15 2020 - 23:23:23 PST)
[AMBER] An error during NPT/production (GPU run)
- David Cerutti (Mon Dec 14 2020 - 16:31:50 PST)
- David Cerutti (Fri Dec 11 2020 - 06:56:45 PST)
- Женя Елизарова (Fri Dec 11 2020 - 05:43:29 PST)
- David Cerutti (Wed Dec 09 2020 - 00:49:59 PST)
- David A Case (Fri Dec 04 2020 - 08:13:15 PST)
[AMBER] Antechamber vs R.E.D. Server
- Dr. Anselm Horn (Fri Dec 18 2020 - 01:49:33 PST)
- Sam Walsworth (Researcher) (Thu Dec 17 2020 - 11:37:28 PST)
- Dr. Anselm Horn (Thu Dec 17 2020 - 07:56:31 PST)
- Sam Walsworth (Researcher) (Wed Dec 16 2020 - 11:30:54 PST)
[AMBER] app.run_mmpbsa() and mdout files were not created
- divyabharathi korlepara (Thu Dec 03 2020 - 07:02:23 PST)
- David A Case (Thu Dec 03 2020 - 05:54:21 PST)
- divyabharathi korlepara (Wed Dec 02 2020 - 23:39:11 PST)
[AMBER] B-ob-si-c3 dihedral parametization RESP/Scan problem
- Erdem Yeler (Thu Dec 10 2020 - 02:22:30 PST)
[AMBER] Box info not found in prmtop file
- Amit Sharma (Asstt. Prof., MCARS) (Fri Dec 11 2020 - 12:18:59 PST)
- Carlos Simmerling (Fri Dec 11 2020 - 10:43:13 PST)
- Amit Sharma (Asstt. Prof., MCARS) (Fri Dec 11 2020 - 10:21:23 PST)
- Carlos Simmerling (Fri Dec 11 2020 - 09:09:36 PST)
- Amit Sharma (Asstt. Prof., MCARS) (Fri Dec 11 2020 - 08:26:43 PST)
- Carlos Simmerling (Fri Dec 11 2020 - 08:08:15 PST)
- Amit Sharma (Asstt. Prof., MCARS) (Fri Dec 11 2020 - 08:01:07 PST)
- Carlos Simmerling (Fri Dec 11 2020 - 07:28:39 PST)
- Amit Sharma (Asstt. Prof., MCARS) (Fri Dec 11 2020 - 06:52:32 PST)
- Carlos Simmerling (Fri Dec 11 2020 - 05:29:22 PST)
- Amit Sharma (Asstt. Prof., MCARS) (Fri Dec 11 2020 - 05:13:38 PST)
[AMBER] box_dims question
- Daniel Roe (Thu Dec 17 2020 - 09:10:36 PST)
- Carlos (Mon Dec 14 2020 - 13:06:02 PST)
[AMBER] Bug AmberTools20 parallel installation
- David A Case (Thu Dec 10 2020 - 05:31:07 PST)
- Arsene Marian Alain (Thu Dec 10 2020 - 04:46:00 PST)
[AMBER] C++ Programmer Position
- Lachele Foley (Tue Dec 01 2020 - 09:57:01 PST)
[AMBER] Calculation halted while running simulation
- David A Case (Fri Dec 04 2020 - 05:18:32 PST)
- Carlos Simmerling (Thu Dec 03 2020 - 12:44:27 PST)
- angad sharma (Thu Dec 03 2020 - 11:36:21 PST)
[AMBER] Cannot minimize structure with sander
- David A Case (Fri Dec 18 2020 - 11:08:30 PST)
- George Yacu (Fri Dec 18 2020 - 09:56:28 PST)
[AMBER] Cation-pi interaction characterization
- Daniel Roe (Wed Dec 30 2020 - 06:49:51 PST)
- Ramanathan Rajesh (Tue Dec 22 2020 - 11:43:58 PST)
[AMBER] cellulose crystal structure ( cellulose bundles)
- Pinky Mazumder (Thu Dec 10 2020 - 22:50:29 PST)
[AMBER] Charged species with antechamber
- David A Case (Sat Dec 12 2020 - 18:39:12 PST)
- Gustaf Olsson (Fri Dec 11 2020 - 00:15:48 PST)
- Sam Walsworth (Researcher) (Thu Dec 10 2020 - 11:18:27 PST)
- David A Case (Thu Dec 10 2020 - 10:00:45 PST)
- Dr. Anselm Horn (Thu Dec 10 2020 - 07:48:59 PST)
- Sam Walsworth (Researcher) (Thu Dec 10 2020 - 07:01:34 PST)
[AMBER] CMP-GMP
- Holly Freedman (Wed Dec 30 2020 - 11:49:15 PST)
- David A Case (Wed Dec 30 2020 - 09:26:49 PST)
- Holly Freedman (Wed Dec 30 2020 - 07:48:22 PST)
- David A Case (Tue Dec 29 2020 - 18:26:54 PST)
- Holly Freedman (Tue Dec 29 2020 - 14:31:59 PST)
[AMBER] Conversion .rst to .inpcrd
- Eduardo R. Almeida (Fri Dec 18 2020 - 05:30:37 PST)
- Daniel Roe (Thu Dec 17 2020 - 09:06:18 PST)
- Eduardo R. Almeida (Thu Dec 17 2020 - 08:19:59 PST)
[AMBER] Cpptraj (post-processing rotation)
- Daniel Roe (Wed Dec 23 2020 - 06:40:13 PST)
- Kenneth Huang (Mon Dec 21 2020 - 10:57:16 PST)
- Женя Елизарова (Mon Dec 21 2020 - 02:08:01 PST)
[AMBER] cpptraj warnings topology flags being ignored
- Daniel Roe (Thu Dec 17 2020 - 09:13:07 PST)
- David A Case (Thu Dec 17 2020 - 08:35:00 PST)
- Vaibhav Dixit (Thu Dec 17 2020 - 06:35:36 PST)
[AMBER] CPU versus GPU Divergent Minimizations
- David A Case (Thu Dec 24 2020 - 05:57:07 PST)
- Matthew Guberman-Pfeffer (Thu Dec 24 2020 - 00:22:37 PST)
[AMBER] cremer
- MYRIAN TORRES RICO (Thu Dec 31 2020 - 08:15:33 PST)
- David A Case (Thu Dec 31 2020 - 07:20:05 PST)
- MYRIAN TORRES RICO (Thu Dec 31 2020 - 06:32:28 PST)
- Daniel Roe (Thu Dec 31 2020 - 06:10:00 PST)
- MYRIAN TORRES RICO (Thu Dec 31 2020 - 02:46:25 PST)
- David A Case (Wed Dec 30 2020 - 06:10:29 PST)
- MYRIAN TORRES RICO (Wed Dec 30 2020 - 04:48:16 PST)
[AMBER] crystallographic plane
- Daniel Roe (Wed Dec 30 2020 - 06:39:58 PST)
- Bill Ross (Mon Dec 21 2020 - 21:30:10 PST)
- Pinky Mazumder (Mon Dec 21 2020 - 21:11:50 PST)
[AMBER] Disulphide bonds
- Gustaf Olsson (Mon Dec 14 2020 - 23:43:17 PST)
- David A Case (Mon Dec 14 2020 - 06:11:25 PST)
- Carlos Simmerling (Mon Dec 14 2020 - 06:02:09 PST)
- Gustaf Olsson (Mon Dec 14 2020 - 05:27:18 PST)
- Bill Ross (Mon Dec 14 2020 - 04:52:45 PST)
- Gustaf Olsson (Mon Dec 14 2020 - 00:54:19 PST)
[AMBER] doubt frames simulation
- Daniel Roe (Thu Dec 31 2020 - 06:11:53 PST)
- MYRIAN TORRES RICO (Thu Dec 31 2020 - 05:02:44 PST)
[AMBER] Effects of scalpha in softcore runs
- Sharif Nada (Sun Dec 06 2020 - 17:03:43 PST)
[AMBER] Electrostatic distance plot
- Daniel Roe (Wed Dec 30 2020 - 06:45:59 PST)
- Maria Nagan (Wed Dec 23 2020 - 07:56:57 PST)
- Adrian Roitberg (Wed Dec 23 2020 - 07:47:49 PST)
- Sruthi Sudhakar (Wed Dec 23 2020 - 07:44:33 PST)
- Carlos Simmerling (Wed Dec 23 2020 - 07:03:54 PST)
- Sruthi Sudhakar (Wed Dec 23 2020 - 06:19:34 PST)
- David A Case (Wed Dec 23 2020 - 06:07:26 PST)
- Sruthi Sudhakar (Tue Dec 22 2020 - 19:58:14 PST)
[AMBER] error after simulation
- Thomas Cheatham (Mon Dec 07 2020 - 12:40:07 PST)
- angad sharma (Mon Dec 07 2020 - 08:44:37 PST)
[AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20
- Vaibhav Dixit (Fri Dec 18 2020 - 08:50:03 PST)
- Ray Luo (Fri Dec 18 2020 - 08:36:42 PST)
- Vaibhav Dixit (Fri Dec 18 2020 - 01:33:23 PST)
- Vaibhav Dixit (Tue Dec 15 2020 - 18:13:40 PST)
- Ray Luo (Tue Dec 15 2020 - 10:23:59 PST)
- Vaibhav Dixit (Tue Dec 15 2020 - 09:04:26 PST)
[AMBER] Error in Quasi-Harmonic Entropy
- Setyanto Md (Sun Dec 20 2020 - 19:12:37 PST)
- David A Case (Mon Dec 14 2020 - 06:08:17 PST)
- Setyanto Md (Sat Dec 12 2020 - 19:09:05 PST)
[AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20
- Vaibhav Dixit (Thu Dec 10 2020 - 08:45:34 PST)
- Vaibhav Dixit (Thu Dec 10 2020 - 07:48:25 PST)
- David A Case (Thu Dec 10 2020 - 05:19:22 PST)
- Vaibhav Dixit (Thu Dec 10 2020 - 01:27:01 PST)
- Raman Preet Singh (Thu Dec 10 2020 - 04:52:57 PST)
- Vaibhav Dixit (Thu Dec 10 2020 - 01:16:57 PST)
- Raman Preet Singh (Thu Dec 10 2020 - 04:29:08 PST)
- Vaibhav Dixit (Wed Dec 09 2020 - 23:31:22 PST)
- Raman Preet Singh (Thu Dec 10 2020 - 02:58:08 PST)
- Vaibhav Dixit (Wed Dec 09 2020 - 23:26:05 PST)
[AMBER] ff15ipq-m force field for protein mimetics
- Lillian Chong (Mon Dec 21 2020 - 12:18:59 PST)
[AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card
- David A Case (Thu Dec 31 2020 - 18:41:02 PST)
- Ross Walker (Thu Dec 31 2020 - 07:14:57 PST)
- liu kai (Thu Dec 31 2020 - 05:34:05 PST)
[AMBER] G quadruplex ions minimization
- Jiri Sponer (Fri Dec 04 2020 - 11:20:49 PST)
- Bill Ross (Fri Dec 04 2020 - 09:53:49 PST)
- Juraj Dobias (Fri Dec 04 2020 - 03:48:33 PST)
- Jisha B (Thu Dec 03 2020 - 15:06:25 PST)
[AMBER] Getting error while compile AMBER20 with cuda support
- Raman Jangra (Sun Dec 20 2020 - 20:24:37 PST)
- David A Case (Wed Dec 16 2020 - 06:08:07 PST)
- Bill Ross (Tue Dec 15 2020 - 21:24:05 PST)
- Raman Jangra (Tue Dec 15 2020 - 21:16:10 PST)
[AMBER] Has anyone tried and succeeded at compiling Amber 18 with CUDA 11?
- Homeo Morphism (Fri Dec 25 2020 - 13:23:40 PST)
[AMBER] how to convert (psf) to (prmtop) and (incprd)
- David A Case (Sat Dec 12 2020 - 18:59:32 PST)
- Pinky Mazumder (Sat Dec 12 2020 - 12:55:22 PST)
- Carlos Simmerling (Sat Dec 12 2020 - 12:52:18 PST)
- Pinky Mazumder (Sat Dec 12 2020 - 12:05:44 PST)
- David A Case (Fri Dec 11 2020 - 06:08:52 PST)
- Pinky Mazumder (Thu Dec 10 2020 - 22:40:38 PST)
[AMBER] How to graph CPPTRAJ in (ns) instead of timesteps
- Daniel Roe (Wed Dec 23 2020 - 06:38:32 PST)
- Maria Nagan (Tue Dec 22 2020 - 11:09:04 PST)
- Maghsoud, Yazdan (Tue Dec 22 2020 - 10:51:03 PST)
[AMBER] how to know degrees of system
- Carlos Simmerling (Wed Dec 23 2020 - 07:35:16 PST)
- angad sharma (Wed Dec 23 2020 - 07:09:33 PST)
[AMBER] How to proceed if system charge is non-zero and non-integral
- David A Case (Thu Dec 10 2020 - 05:21:58 PST)
- Amit Sharma (Asstt. Prof., MCARS) (Thu Dec 10 2020 - 04:37:14 PST)
[AMBER] How to specify SHAKE on all bonds including hydrogen in the input file
- Bill Ross (Sat Dec 12 2020 - 10:57:32 PST)
- Carlos Simmerling (Sat Dec 12 2020 - 10:56:54 PST)
- Amit Sharma (Asstt. Prof., MCARS) (Sat Dec 12 2020 - 10:46:18 PST)
[AMBER] How to use GAFF2?
- Alexander Izvorski (Fri Dec 04 2020 - 11:24:17 PST)
- David A Case (Fri Dec 04 2020 - 05:29:33 PST)
- Alexander Izvorski (Thu Dec 03 2020 - 22:13:37 PST)
- Alexander Izvorski (Thu Dec 03 2020 - 22:11:29 PST)
- David A Case (Thu Dec 03 2020 - 05:44:42 PST)
- Gustaf Olsson (Thu Dec 03 2020 - 00:14:33 PST)
- Alexander Izvorski (Wed Dec 02 2020 - 17:41:08 PST)
[AMBER] Hydrogen bond and Dissociation constant
- David A Case (Sat Dec 12 2020 - 18:55:36 PST)
- Kehinde Idowu (Sat Dec 12 2020 - 06:32:28 PST)
[AMBER] Identifying the equilibrated production region of a MD simulation trajectory
- Thomas Cheatham (Sat Dec 05 2020 - 21:52:07 PST)
- Carlos Simmerling (Sat Dec 05 2020 - 18:51:47 PST)
- Leena Aggarwal (Fri Dec 04 2020 - 23:37:42 PST)
[AMBER] Imaging issue in DNA - cpptraj
- Daniel Roe (Fri Dec 04 2020 - 12:27:25 PST)
- Satyaseelan C (Fri Dec 04 2020 - 09:47:10 PST)
- David A Case (Wed Dec 02 2020 - 05:55:09 PST)
- lomzov (Wed Dec 02 2020 - 02:04:52 PST)
- Dr. Anselm Horn (Wed Dec 02 2020 - 01:23:56 PST)
- Gustaf Olsson (Wed Dec 02 2020 - 00:12:38 PST)
- Satyaseelan C (Tue Dec 01 2020 - 23:17:22 PST)
[AMBER] lj1264 in vacuum
- Brian Radak (Fri Dec 11 2020 - 13:07:36 PST)
- Brian Radak (Tue Dec 08 2020 - 13:29:25 PST)
[AMBER] MD run on GPU machine
- Carlos Simmerling (Tue Dec 22 2020 - 14:38:31 PST)
[AMBER] Minimization Time Limit Error with Sander
- Bill Ross (Fri Dec 18 2020 - 14:28:58 PST)
- David A Case (Fri Dec 18 2020 - 14:10:57 PST)
- Carlos Simmerling (Fri Dec 18 2020 - 13:27:29 PST)
- Aanshi Gandhi (Fri Dec 18 2020 - 13:19:01 PST)
- Carlos Simmerling (Fri Dec 18 2020 - 13:09:09 PST)
- Aanshi Gandhi (Fri Dec 18 2020 - 12:59:33 PST)
- Carlos Simmerling (Fri Dec 18 2020 - 12:46:09 PST)
- Aanshi Gandhi (Fri Dec 18 2020 - 12:39:57 PST)
[AMBER] Missing Iron (Fe) DFTB3 parameters for QM/MM simulation of Enzyme
- Hafiz Saqib Ali (Thu Dec 03 2020 - 15:04:54 PST)
[AMBER] Mixing Force Constants In DISANG Files
- Sharif Nada (Thu Dec 03 2020 - 10:43:15 PST)
- Carlos Simmerling (Thu Dec 03 2020 - 02:14:38 PST)
- Sharif Nada (Wed Dec 02 2020 - 20:01:35 PST)
[AMBER] MMBSA.py.MPI installation
- David A Case (Sat Dec 05 2020 - 06:03:00 PST)
- Jose Manuel Granadino Roldán (Fri Dec 04 2020 - 23:39:47 PST)
- David A Case (Fri Dec 04 2020 - 08:15:45 PST)
- Jose Manuel Granadino Roldán (Tue Dec 01 2020 - 07:40:03 PST)
[AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20
- Vaibhav Dixit (Tue Dec 15 2020 - 01:36:25 PST)
- Vaibhav Dixit (Mon Dec 14 2020 - 21:38:04 PST)
- Elvis Martis (Mon Dec 14 2020 - 23:33:19 PST)
- Vaibhav Dixit (Mon Dec 14 2020 - 19:56:32 PST)
- Elvis Martis (Mon Dec 14 2020 - 05:31:40 PST)
- Vaibhav Dixit (Mon Dec 14 2020 - 01:31:57 PST)
- Elvis Martis (Mon Dec 14 2020 - 04:53:25 PST)
- Vaibhav Dixit (Mon Dec 14 2020 - 01:05:21 PST)
- Elvis Martis (Mon Dec 14 2020 - 03:35:49 PST)
- Elvis Martis (Mon Dec 14 2020 - 03:35:02 PST)
- Vaibhav Dixit (Sun Dec 13 2020 - 23:52:46 PST)
- Elvis Martis (Mon Dec 14 2020 - 02:46:22 PST)
- Vaibhav Dixit (Sun Dec 13 2020 - 22:56:04 PST)
- Elvis Martis (Mon Dec 14 2020 - 02:13:45 PST)
- Vaibhav Dixit (Sun Dec 13 2020 - 22:31:52 PST)
[AMBER] MMPBSA.py bad atom type: M1 error
- Vaibhav Dixit (Thu Dec 03 2020 - 21:09:01 PST)
- Ray Luo (Thu Dec 03 2020 - 20:40:18 PST)
- Vaibhav Dixit (Thu Dec 03 2020 - 16:25:12 PST)
- Ray Luo (Thu Dec 03 2020 - 09:46:19 PST)
- Vaibhav Dixit (Thu Dec 03 2020 - 08:30:11 PST)
[AMBER] MMPBSA.py.MPI installation
- Elvis Martis (Fri Dec 18 2020 - 05:16:58 PST)
- divyabharathi korlepara (Fri Dec 18 2020 - 04:53:20 PST)
- divyabharathi korlepara (Fri Dec 18 2020 - 04:47:08 PST)
- Jaime Rubio Martinez (Thu Dec 17 2020 - 00:40:45 PST)
- Elvis Martis (Wed Dec 16 2020 - 17:32:19 PST)
- divyabharathi korlepara (Wed Dec 16 2020 - 10:10:14 PST)
[AMBER] MMPBSA.py.MPI not build in Amber20
- Setyanto Md (Sat Dec 12 2020 - 16:56:31 PST)
- Elvis Martis (Sat Dec 12 2020 - 05:39:47 PST)
- Setyanto Md (Sat Dec 12 2020 - 05:08:54 PST)
[AMBER] MMPBSA.py.MPI parallel installation using run_cmake
- David A Case (Fri Dec 04 2020 - 08:09:22 PST)
- divyabharathi korlepara (Thu Dec 03 2020 - 10:43:50 PST)
[AMBER] Molecular Dynamics Tutorial for Membrane-Bound Proteins in Amber
- ANDRES IBACACHE (Fri Dec 18 2020 - 12:22:05 PST)
[AMBER] nc files contain lesser number of atoms compared to prmtop
- Daniel Roe (Thu Dec 17 2020 - 09:03:26 PST)
- Sruthi Sudhakar (Wed Dec 16 2020 - 22:16:53 PST)
[AMBER] Negative values in RDF analyses?
- Daniel Roe (Thu Dec 10 2020 - 03:07:46 PST)
- Gustaf Olsson (Wed Dec 09 2020 - 05:44:49 PST)
[AMBER] NOE analysis with cpptraj
- Pavlína Pokorná (Wed Dec 02 2020 - 04:27:56 PST)
[AMBER] parameters for benzene, pyerene, anthracene, and coronene
- Carlos Simmerling (Mon Dec 14 2020 - 06:36:33 PST)
- Boutheïna KERKENI (Mon Dec 14 2020 - 06:34:45 PST)
- Carlos Simmerling (Mon Dec 14 2020 - 06:15:19 PST)
- David A Case (Mon Dec 14 2020 - 06:05:40 PST)
- Boutheïna KERKENI (Mon Dec 14 2020 - 02:20:11 PST)
- Boutheïna KERKENI (Sun Dec 13 2020 - 05:47:39 PST)
- Boutheïna KERKENI (Sat Dec 12 2020 - 15:26:24 PST)
[AMBER] Parmed error
- Hai Nguyen (Thu Dec 24 2020 - 09:12:05 PST)
- Elvis Martis (Wed Dec 23 2020 - 20:27:57 PST)
- Jisha B (Wed Dec 23 2020 - 09:55:50 PST)
[AMBER] pbsa calcerror
- Ray Luo (Fri Dec 18 2020 - 15:46:08 PST)
- Neha Gandhi (Thu Dec 17 2020 - 21:34:59 PST)
- Ray Luo (Thu Dec 17 2020 - 17:07:40 PST)
- Neha Gandhi (Thu Dec 17 2020 - 13:28:59 PST)
[AMBER] pmemd.cuda: error while loading shared libraries: libgfortran.so.4: cannot open shared object file: No such file or directory
- David A Case (Tue Dec 01 2020 - 06:18:40 PST)
- Sruthi Sudhakar (Tue Dec 01 2020 - 05:29:39 PST)
[AMBER] Position of the solute (center of mass) in the simulation box
- Daniel Roe (Wed Dec 30 2020 - 06:41:22 PST)
- Matias Machado (Thu Dec 24 2020 - 14:14:06 PST)
- Matias Machado (Thu Dec 24 2020 - 13:57:13 PST)
- Eduardo R. Almeida (Thu Dec 24 2020 - 05:07:04 PST)
[AMBER] positive Amber FF energies?
- Vaibhav Dixit (Wed Dec 16 2020 - 19:28:46 PST)
- Thomas Cheatham (Wed Dec 16 2020 - 20:29:17 PST)
- Jason Swails (Wed Dec 16 2020 - 19:59:35 PST)
- Vaibhav Dixit (Wed Dec 16 2020 - 08:31:55 PST)
[AMBER] Problem forming circular DNA
- Sebastian S (Mon Dec 28 2020 - 07:29:35 PST)
- David A Case (Mon Dec 28 2020 - 06:07:21 PST)
- Sebastian S (Sun Dec 27 2020 - 07:52:52 PST)
[AMBER] PROTEIN-DNA rmsd plot
- David A Case (Thu Dec 31 2020 - 18:47:41 PST)
- Dr. Anselm Horn (Thu Dec 31 2020 - 02:21:29 PST)
- Syeda Amna Arshi (Thu Dec 31 2020 - 01:54:41 PST)
- Syeda Amna Arshi (Thu Dec 31 2020 - 01:53:45 PST)
- Daniel Roe (Wed Dec 30 2020 - 06:43:05 PST)
- Syeda Amna Arshi (Wed Dec 23 2020 - 22:32:55 PST)
- David A Case (Mon Dec 21 2020 - 05:12:57 PST)
- Syeda Amna Arshi (Sun Dec 20 2020 - 23:09:01 PST)
- David A Case (Wed Dec 16 2020 - 06:11:58 PST)
- Syeda Amna Arshi (Tue Dec 15 2020 - 22:20:02 PST)
[AMBER] Query on some old sander inputs (dele, idiel, dielc)
- Kenneth Huang (Wed Dec 30 2020 - 11:55:36 PST)
- David Cerutti (Wed Dec 30 2020 - 09:17:02 PST)
- Kenneth Huang (Wed Dec 30 2020 - 08:43:49 PST)
- David A Case (Sat Dec 26 2020 - 05:58:47 PST)
- Kenneth Huang (Mon Dec 21 2020 - 08:00:37 PST)
[AMBER] Question about atomic charges
- Carlos Simmerling (Fri Dec 04 2020 - 11:45:32 PST)
- Bill Ross (Fri Dec 04 2020 - 11:19:13 PST)
- Pinky Mazumder (Fri Dec 04 2020 - 11:15:44 PST)
[AMBER] question about dihedral angles
- Gordon Richard Chalmers (Wed Dec 02 2020 - 20:09:17 PST)
- Gordon Richard Chalmers (Wed Dec 02 2020 - 19:57:56 PST)
- Bill Ross (Wed Dec 02 2020 - 19:25:14 PST)
- Bill Ross (Wed Dec 02 2020 - 19:20:38 PST)
- Bill Ross (Wed Dec 02 2020 - 19:15:51 PST)
- Gordon Richard Chalmers (Wed Dec 02 2020 - 16:01:59 PST)
- Gordon Richard Chalmers (Wed Dec 02 2020 - 15:08:32 PST)
- Gordon Richard Chalmers (Wed Dec 02 2020 - 14:58:04 PST)
- Carlos Simmerling (Wed Dec 02 2020 - 14:52:48 PST)
- Gordon Richard Chalmers (Wed Dec 02 2020 - 14:41:45 PST)
- Daniel Roe (Wed Dec 02 2020 - 08:50:58 PST)
- Gordon Richard Chalmers (Wed Dec 02 2020 - 06:10:11 PST)
- Gordon Richard Chalmers (Wed Dec 02 2020 - 06:03:54 PST)
- Gordon Richard Chalmers (Wed Dec 02 2020 - 06:03:51 PST)
- David A Case (Wed Dec 02 2020 - 05:51:08 PST)
- Karl Kirschner (Tue Dec 01 2020 - 23:53:32 PST)
- Gordon Richard Chalmers (Tue Dec 01 2020 - 20:36:39 PST)
- David A Case (Tue Dec 01 2020 - 18:07:17 PST)
- Gordon Richard Chalmers (Tue Dec 01 2020 - 15:49:46 PST)
- Gordon Richard Chalmers (Tue Dec 01 2020 - 15:43:50 PST)
[AMBER] question pmemd.cuda
- Elvis Martis (Mon Dec 21 2020 - 04:54:22 PST)
- MYRIAN TORRES RICO (Mon Dec 21 2020 - 04:45:58 PST)
[AMBER] refene2.solvent_energies refene2.dielc2_energies and refene2.dielc2.solvent_energies
- Luis Simon (Sat Dec 12 2020 - 15:03:01 PST)
[AMBER] Regarding Gaussian Accelerated MD
- Sruthi Sudhakar (Thu Dec 10 2020 - 04:29:10 PST)
- Sruthi Sudhakar (Wed Dec 09 2020 - 03:16:12 PST)
[AMBER] Regarding Ions renumbering.
- Christina Bergonzo (Wed Dec 09 2020 - 05:47:25 PST)
- Gustaf Olsson (Wed Dec 09 2020 - 01:26:15 PST)
- DHEERAJ CHITARA (Wed Dec 09 2020 - 12:12:18 PST)
[AMBER] Regarding to the parameters setup in SMD simulation
- Feng Pan (Fri Dec 04 2020 - 17:38:11 PST)
[AMBER] Renumbering
- Gustaf Olsson (Thu Dec 17 2020 - 10:07:54 PST)
- Daniel Roe (Thu Dec 17 2020 - 08:58:53 PST)
- Gustaf Olsson (Thu Dec 17 2020 - 04:52:25 PST)
- Carlos Simmerling (Thu Dec 17 2020 - 03:50:04 PST)
- Gustaf Olsson (Thu Dec 17 2020 - 02:45:01 PST)
- Gustaf Olsson (Thu Dec 17 2020 - 02:29:26 PST)
[AMBER] Reweighting error in Gaussian accelerated MD- PyReweighting-1D.py
- Athena N (Sat Dec 26 2020 - 14:17:03 PST)
[AMBER] RMSD Protein-DNA complex Plot
- Dr. Anselm Horn (Tue Dec 15 2020 - 00:38:54 PST)
- Bill Ross (Mon Dec 14 2020 - 04:15:20 PST)
- Manisha (Mon Dec 14 2020 - 01:16:06 PST)
[AMBER] S2 order parameter not being calculated in IRED analysis.
- Daniel Roe (Tue Dec 15 2020 - 07:13:59 PST)
- Gupta, Arun (Tue Dec 15 2020 - 01:11:47 PST)
- Chetna Tyagi (Fri Dec 11 2020 - 05:14:44 PST)
[AMBER] SHAKE problem
- Jonathan Church (Tue Dec 29 2020 - 08:58:48 PST)
- Bill Ross (Mon Dec 28 2020 - 00:08:04 PST)
- Jonathan Church (Sun Dec 27 2020 - 21:26:32 PST)
[AMBER] Stacking distance in CPPTRAJ
- Daniel Roe (Tue Dec 15 2020 - 07:30:32 PST)
- Carlos Simmerling (Sun Dec 13 2020 - 03:49:43 PST)
- Athena N (Sun Dec 13 2020 - 03:18:28 PST)
[AMBER] strange jump in the rmsd protein complex
- Vaibhav Dixit (Fri Dec 18 2020 - 08:47:21 PST)
- Daniel Roe (Fri Dec 18 2020 - 06:16:02 PST)
- Vaibhav Dixit (Fri Dec 18 2020 - 03:43:46 PST)
- Vaibhav Dixit (Thu Dec 17 2020 - 23:36:25 PST)
[AMBER] Terminal O5'/O3' for nucleosides in ff86?
- Kenneth Huang (Thu Dec 03 2020 - 09:02:47 PST)
- David A Case (Thu Dec 03 2020 - 05:57:40 PST)
- Kenneth Huang (Wed Dec 02 2020 - 14:27:09 PST)
[AMBER] TI electrostatic free energy
- Franz Waibl (Tue Dec 01 2020 - 04:57:37 PST)
[AMBER] TI electrostatic free energy]
- David A Case (Tue Dec 01 2020 - 11:07:04 PST)
- Franz Waibl (Tue Dec 01 2020 - 07:24:44 PST)
- David A Case (Tue Dec 01 2020 - 06:08:32 PST)
[AMBER] tleap building a peptide
- Seibold, Steve Allan (Thu Dec 10 2020 - 10:11:02 PST)
- David A Case (Thu Dec 10 2020 - 10:03:49 PST)
- Seibold, Steve Allan (Thu Dec 10 2020 - 10:03:33 PST)
- Bill Ross (Thu Dec 10 2020 - 09:30:42 PST)
- Carlos Simmerling (Thu Dec 10 2020 - 09:08:34 PST)
- Seibold, Steve Allan (Thu Dec 10 2020 - 08:48:09 PST)
[AMBER] tleap seems Si atom as S ... I don't know why
- Erdem Yeler (Thu Dec 17 2020 - 04:59:56 PST)
- David A Case (Sat Dec 12 2020 - 18:50:50 PST)
- Erdem Yeler (Fri Dec 11 2020 - 13:58:01 PST)
[AMBER] Top Mode Contribution in PCA Analysis.
- DHEERAJ CHITARA (Fri Dec 18 2020 - 09:47:02 PST)
- Daniel Roe (Thu Dec 17 2020 - 09:08:46 PST)
- DHEERAJ CHITARA (Wed Dec 16 2020 - 03:53:36 PST)
[AMBER] Tri-coordination environment in zinc
- SATYAJIT KHATUA (Thu Dec 10 2020 - 02:18:17 PST)
- SATYAJIT KHATUA (Wed Dec 09 2020 - 16:08:09 PST)
- Pengfei Li (Mon Dec 07 2020 - 12:30:21 PST)
- Pengfei Li (Mon Dec 07 2020 - 12:29:29 PST)
[AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA
- 贺俊宏 (Tue Dec 08 2020 - 22:50:17 PST)
- David A Case (Tue Dec 08 2020 - 05:59:52 PST)
- 贺俊宏 (Mon Dec 07 2020 - 18:32:44 PST)
- David A Case (Mon Dec 07 2020 - 05:45:45 PST)
- 贺俊宏 (Sun Dec 06 2020 - 17:46:20 PST)
- David A Case (Fri Dec 04 2020 - 05:24:01 PST)
- 贺俊宏 (Thu Dec 03 2020 - 19:06:29 PST)
- David A Case (Thu Dec 03 2020 - 05:47:52 PST)
- 贺俊宏 (Wed Dec 02 2020 - 19:29:29 PST)
[AMBER] Using sander.MPI in Docker
- Erdem Yeler (Thu Dec 17 2020 - 05:07:15 PST)
[AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating
- Matias Machado (Wed Dec 16 2020 - 07:18:44 PST)
- Matias Machado (Wed Dec 16 2020 - 06:45:58 PST)
- David A Case (Wed Dec 16 2020 - 06:02:54 PST)
- Bill Ross (Tue Dec 15 2020 - 19:44:36 PST)
- Chris Lee (Tue Dec 15 2020 - 15:00:32 PST)
[AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"?
- Liao (Wed Dec 16 2020 - 09:21:12 PST)
- David Cerutti (Wed Dec 09 2020 - 00:57:45 PST)

Amber Archive Dec 2020 by subject