Amber Archive Feb 2022: by subject

[AMBER] amber gaff parameters resource??
- David A Case (Sat Feb 05 2022 - 05:12:03 PST)
- Debarati DasGupta (Fri Feb 04 2022 - 08:34:45 PST)
[AMBER] Amber simulation of cyclic peptide
- saranya.cbmm.lodz.pl (Thu Feb 17 2022 - 03:57:57 PST)
- Dr. Anselm Horn (Thu Feb 17 2022 - 03:07:03 PST)
- Carlos Simmerling (Thu Feb 17 2022 - 03:00:19 PST)
- saranya.cbmm.lodz.pl (Thu Feb 17 2022 - 02:19:32 PST)
[AMBER] Amber20 Installation run_cmake problem
- Manuel Fernandez Merino (Thu Feb 03 2022 - 06:05:12 PST)
- David A Case (Wed Feb 02 2022 - 05:57:03 PST)
- Manuel Fernandez Merino (Wed Feb 02 2022 - 00:57:33 PST)
- David A Case (Tue Feb 01 2022 - 13:45:26 PST)
- Manuel Fernandez Merino (Tue Feb 01 2022 - 09:29:00 PST)
[AMBER] Ambrtool16 make install error
- spss4.iacs.res.in (Wed Feb 23 2022 - 04:00:17 PST)
- David A Case (Wed Feb 16 2022 - 13:08:53 PST)
- spss4.iacs.res.in (Wed Feb 16 2022 - 07:33:13 PST)
- David A Case (Wed Feb 16 2022 - 06:41:50 PST)
- 王世玉 (Wed Feb 16 2022 - 00:09:13 PST)
- spss4.iacs.res.in (Tue Feb 15 2022 - 23:39:40 PST)
- David A Case (Sun Feb 13 2022 - 06:08:28 PST)
- spss4.iacs.res.in (Sat Feb 12 2022 - 21:06:21 PST)
- Daniel Roe (Sat Feb 12 2022 - 12:17:58 PST)
- spss4.iacs.res.in (Sat Feb 12 2022 - 10:15:44 PST)
[AMBER] any working singularity or docker recipe? (esp for CUDA and MPI)
- Michael Coleman (Fri Feb 04 2022 - 20:54:12 PST)
- Michael Coleman (Fri Feb 04 2022 - 19:18:21 PST)
- Ross Walker (Fri Feb 04 2022 - 05:49:05 PST)
- David A Case (Fri Feb 04 2022 - 05:46:34 PST)
- Michael Coleman (Thu Feb 03 2022 - 23:58:20 PST)
- David A Case (Thu Feb 03 2022 - 03:41:20 PST)
- Michael Coleman (Wed Feb 02 2022 - 15:16:38 PST)
- David A Case (Wed Feb 02 2022 - 05:43:26 PST)
- Michael Coleman (Tue Feb 01 2022 - 17:04:04 PST)
[AMBER] boron nitride
- Erdem Yeler (Sat Feb 19 2022 - 15:02:42 PST)
- David A Case (Tue Feb 01 2022 - 05:20:25 PST)
- Victor Nazarychev (Tue Feb 01 2022 - 02:05:29 PST)
[AMBER] Bug in mmpbsa.py internal energy when idecomp is 3 or 4
- Jason Swails (Tue Feb 22 2022 - 09:23:36 PST)
- Tue Boesen (Sat Feb 19 2022 - 09:58:32 PST)
- Thomas Cheatham (Fri Feb 18 2022 - 20:47:49 PST)
- Tue Boesen (Fri Feb 18 2022 - 14:38:10 PST)
- Jason Swails (Fri Feb 18 2022 - 06:45:24 PST)
- Tue Boesen (Thu Feb 17 2022 - 09:24:17 PST)
- Jason Swails (Thu Feb 17 2022 - 07:18:37 PST)
- Tue Boesen (Sun Feb 13 2022 - 18:47:09 PST)
[AMBER] bulk properties for SPAM in mixed solvents
- David Poole (Mon Feb 21 2022 - 15:37:01 PST)
[AMBER] Cannot heat the lipid system
- David A Case (Thu Feb 17 2022 - 10:15:35 PST)
- Vic De Roo (Mon Feb 14 2022 - 01:08:53 PST)
[AMBER] Clarification in 3DRISM
- Alexis Azucena (Sat Feb 26 2022 - 18:52:32 PST)
[AMBER] coordinate and topology not generated
- Maria Nagan (Sat Feb 26 2022 - 05:22:55 PST)
- Sadaf Rani (Fri Feb 25 2022 - 17:46:18 PST)
[AMBER] Could not import Amber Python modules! Centos 7
- Suguna Sakkiah (Mon Feb 07 2022 - 15:12:30 PST)
- Suguna Sakkiah (Mon Feb 07 2022 - 09:09:24 PST)
- Daniel Roe (Mon Feb 07 2022 - 06:14:02 PST)
- David A Case (Sun Feb 06 2022 - 09:01:36 PST)
- Suguna Sakkiah (Sat Feb 05 2022 - 18:00:21 PST)
- David A Case (Sat Feb 05 2022 - 17:13:27 PST)
- Suguna Sakkiah (Sat Feb 05 2022 - 06:21:22 PST)
- David A Case (Sat Feb 05 2022 - 05:09:36 PST)
- Suguna Sakkiah (Fri Feb 04 2022 - 07:05:17 PST)
- David A Case (Fri Feb 04 2022 - 05:51:43 PST)
- Suguna Sakkiah (Thu Feb 03 2022 - 17:40:08 PST)
[AMBER] CPPTRAJ, Comparing H-bonding in two trajectories
- Daniel Roe (Wed Feb 16 2022 - 12:46:41 PST)
- Matthew Guberman-Pfeffer (Mon Feb 14 2022 - 16:30:48 PST)
- Daniel Roe (Mon Feb 14 2022 - 16:23:22 PST)
- Kenneth Huang (Mon Feb 14 2022 - 11:08:45 PST)
[AMBER] Cpptrj : How to give two hbond calculation at the same time.
- Rodrigo Galindo-Murillo (Mon Feb 14 2022 - 12:09:09 PST)
- Lara rajam (Mon Feb 14 2022 - 11:55:00 PST)
- Daniel Roe (Mon Feb 14 2022 - 10:39:05 PST)
- Lara rajam (Mon Feb 14 2022 - 09:17:36 PST)
[AMBER] Creating .lib files from prmtop/inpcrd files
- Sam Walsworth (Researcher) (Wed Feb 09 2022 - 17:05:44 PST)
- David A Case (Wed Feb 09 2022 - 16:52:01 PST)
[AMBER] CUDART lib not found during install
- Charlotta Lebedenko (Mon Feb 28 2022 - 10:04:46 PST)
[AMBER] DNA breaking down during the simulation
- Jiri Sponer (Wed Feb 16 2022 - 00:52:27 PST)
- Vlad Cojocaru (Wed Feb 16 2022 - 00:40:06 PST)
- Jiri Sponer (Wed Feb 16 2022 - 00:09:45 PST)
- Thomas Cheatham (Tue Feb 15 2022 - 17:13:01 PST)
- Carlos Simmerling (Tue Feb 15 2022 - 16:31:10 PST)
- b.ercig.nki.nl (Tue Feb 15 2022 - 15:26:29 PST)
[AMBER] Error: an illegal memory access was encountered launching kernel kClearForces
- Carlos Simmerling (Mon Feb 28 2022 - 07:33:08 PST)
- Állan Ferrari (Sun Feb 27 2022 - 17:18:11 PST)
[AMBER] Fast 3-point water residue error
- Jason Swails (Fri Feb 18 2022 - 07:02:12 PST)
- Artur Hermano (Wed Feb 16 2022 - 12:32:53 PST)
[AMBER] Finding percentage occupancy of pi-pi interactions
- Sruthi Sudhakar (Mon Feb 28 2022 - 03:39:06 PST)
[AMBER] Fortran runtime error: End of file
- Stephan Schott (Sat Feb 26 2022 - 07:26:30 PST)
[AMBER] Fwd: Ambrtool16 make install error
- spss4.iacs.res.in (Sat Feb 26 2022 - 11:53:31 PST)
- David A Case (Fri Feb 25 2022 - 04:48:04 PST)
- spss4.iacs.res.in (Fri Feb 25 2022 - 00:20:49 PST)
[AMBER] How to run 3drism.snglpnt calculations in amber20 without rst or traj files
- tluchko (Tue Feb 15 2022 - 12:02:11 PST)
- Daniel Fowles (Tue Feb 15 2022 - 04:41:43 PST)
[AMBER] In development of dihedral angle parameters; negative PK and negative PHASE values
- Barış KURT (Mon Feb 14 2022 - 10:16:07 PST)
- Cenk Andac (Mon Feb 14 2022 - 08:59:01 PST)
- Cenk Andac (Mon Feb 14 2022 - 08:51:52 PST)
- Carlos Simmerling (Mon Feb 14 2022 - 08:28:55 PST)
- Cenk Andac (Mon Feb 14 2022 - 08:23:08 PST)
- Carlos Simmerling (Mon Feb 14 2022 - 07:40:21 PST)
- Cenk Andac (Mon Feb 14 2022 - 07:09:26 PST)
- Barış KURT (Mon Feb 14 2022 - 01:22:46 PST)
- Cenk Andac (Mon Feb 14 2022 - 01:00:23 PST)
- Carlos Simmerling (Mon Feb 07 2022 - 13:54:34 PST)
- Cenk Andac (Mon Feb 07 2022 - 13:27:40 PST)
[AMBER] iron-sulphur clusters
- Ayesha Fatima (Thu Feb 03 2022 - 05:01:31 PST)
[AMBER] Issues with make test.parallel during installation of parallel version of Amber
- David A Case (Wed Feb 09 2022 - 17:00:47 PST)
- IPSITA Banerjee (Wed Feb 09 2022 - 13:49:29 PST)
[AMBER] LEaP Not Reading a Parameter in .frcmod File
- Nathan Black (Thu Feb 24 2022 - 14:36:37 PST)
- Carlos Simmerling (Thu Feb 24 2022 - 13:47:13 PST)
- Nathan Black (Thu Feb 24 2022 - 07:47:16 PST)
- Carlos Simmerling (Thu Feb 24 2022 - 07:00:02 PST)
- Nathan Black (Thu Feb 24 2022 - 06:50:33 PST)
[AMBER] Mass-weighted covariance matrix
- gmx (Wed Feb 02 2022 - 11:42:33 PST)
- Daniel Roe (Wed Feb 02 2022 - 07:56:59 PST)
- gmx (Wed Feb 02 2022 - 06:54:48 PST)
[AMBER] MCPB error for organometallic complex
- Alexej Jerschow (Fri Feb 04 2022 - 06:29:22 PST)
- Alexej Jerschow (Thu Feb 03 2022 - 06:14:12 PST)
[AMBER] MD simulations for POPC membrane
- King Wu (Tue Feb 15 2022 - 17:39:22 PST)
- Vic De Roo (Tue Feb 15 2022 - 16:16:54 PST)
- Carlos Simmerling (Tue Feb 15 2022 - 15:01:28 PST)
- King Wu (Tue Feb 15 2022 - 13:59:53 PST)
- King Wu (Tue Feb 15 2022 - 09:41:09 PST)
- Elvis Martis (Tue Feb 15 2022 - 09:32:00 PST)
- Carlos Simmerling (Tue Feb 15 2022 - 09:22:38 PST)
- King Wu (Tue Feb 15 2022 - 08:37:46 PST)
- Carlos Simmerling (Tue Feb 15 2022 - 08:25:34 PST)
- King Wu (Tue Feb 15 2022 - 08:20:33 PST)
- King Wu (Mon Feb 14 2022 - 08:22:38 PST)
[AMBER] Meaning of "Multiple 'e' in NUMBER-like thing"
- Scott Brozell (Mon Feb 21 2022 - 14:18:12 PST)
[AMBER] MMPBSA internal energy when using idecomp 4
- Tue (Thu Feb 10 2022 - 09:37:47 PST)
- Tue (Thu Feb 10 2022 - 00:44:24 PST)
[AMBER] MMPBSA.py for membrane proteins with per-residue decomposition
- Ravi Abrol (Sun Feb 20 2022 - 15:15:11 PST)
- Ray Luo (Sun Feb 20 2022 - 08:29:42 PST)
- Ravi Abrol (Fri Feb 18 2022 - 20:15:47 PST)
[AMBER] MMPBSA.py.MPI error
- Jason Swails (Fri Feb 11 2022 - 11:06:38 PST)
- Fabian Glaser (Thu Feb 03 2022 - 00:34:50 PST)
[AMBER] Modifying prmtop/inpcrd files
- David A Case (Fri Feb 04 2022 - 05:48:31 PST)
- Sam Walsworth (Researcher) (Thu Feb 03 2022 - 12:48:33 PST)
- Sam Walsworth (Researcher) (Thu Feb 03 2022 - 11:25:05 PST)
- Kenneth Huang (Thu Feb 03 2022 - 11:19:27 PST)
- Sam Walsworth (Researcher) (Thu Feb 03 2022 - 10:49:01 PST)
- David A Case (Thu Feb 03 2022 - 09:54:14 PST)
- Sam Walsworth (Researcher) (Thu Feb 03 2022 - 08:25:40 PST)
- David A Case (Thu Feb 03 2022 - 03:50:27 PST)
- Sam Walsworth (Researcher) (Wed Feb 02 2022 - 17:45:44 PST)
- Kenneth Huang (Tue Feb 01 2022 - 09:54:45 PST)
[AMBER] Move a specific residue parallel using cpptraj
- Daniel Roe (Wed Feb 16 2022 - 12:00:06 PST)
- Eugene huh (Wed Feb 16 2022 - 00:17:23 PST)
[AMBER] mpi4py Problem
- David A Case (Wed Feb 09 2022 - 05:56:18 PST)
- Ilyas Yildirim (Tue Feb 08 2022 - 14:22:50 PST)
- Jason Swails (Tue Feb 08 2022 - 12:43:42 PST)
- Jason Swails (Tue Feb 08 2022 - 12:32:02 PST)
- Ilyas Yildirim (Tue Feb 08 2022 - 08:16:28 PST)
- David A Case (Tue Feb 08 2022 - 05:58:46 PST)
- Ilyas Yildirim (Mon Feb 07 2022 - 20:31:20 PST)
- David A Case (Mon Feb 07 2022 - 10:28:02 PST)
- Ilyas Yildirim (Sun Feb 06 2022 - 21:16:44 PST)
[AMBER] pH replica exchange MD (pH-REMD) in explicit solvent, using CUDA MPI in AMBER 18
- Vinicius Wilian Cruzeiro (Mon Feb 28 2022 - 09:40:05 PST)
- Laura Milena Pedraza-González (Mon Feb 28 2022 - 03:26:13 PST)
- Vinicius Wilian Cruzeiro (Fri Feb 25 2022 - 13:03:18 PST)
- Laura Milena Pedraza-González (Fri Feb 25 2022 - 12:48:55 PST)
- Vinicius Wilian Cruzeiro (Fri Feb 25 2022 - 10:46:47 PST)
- Laura Milena Pedraza-González (Fri Feb 25 2022 - 03:30:46 PST)
- Laura Milena Pedraza-González (Fri Feb 25 2022 - 01:55:52 PST)
- Vinicius Wilian Cruzeiro (Thu Feb 24 2022 - 15:17:31 PST)
- Laura Milena Pedraza-González (Thu Feb 24 2022 - 06:33:26 PST)
[AMBER] Potential PDB and .lib file atom order mismatch
- Carlos Simmerling (Mon Feb 14 2022 - 08:47:49 PST)
[AMBER] problem finding packmol.f90
- David A Case (Wed Feb 02 2022 - 07:07:00 PST)
[AMBER] problem in the protein-ligand system
- Alan (Thu Feb 10 2022 - 11:16:52 PST)
- Renato Araujo (Thu Feb 10 2022 - 10:35:58 PST)
- Alan (Thu Feb 10 2022 - 10:18:30 PST)
- Renato Araujo (Thu Feb 10 2022 - 05:52:19 PST)
[AMBER] Problem with make test.parallel during installation of parallel version of Amber
- David A Case (Thu Feb 10 2022 - 09:55:14 PST)
- Charlotta Lebedenko (Wed Feb 09 2022 - 16:55:54 PST)
[AMBER] Problems of sander.quick.cuda
- Vinicius Wilian Cruzeiro (Fri Feb 25 2022 - 10:53:31 PST)
- Jason Swails (Fri Feb 25 2022 - 06:30:50 PST)
- aa (Thu Feb 24 2022 - 23:17:57 PST)
- Vinicius Wilian Cruzeiro (Sun Feb 20 2022 - 19:06:19 PST)
- xmgign.126.com (Sun Feb 20 2022 - 17:12:13 PST)
[AMBER] Protocol to optimize bonded parameters for GAFF2
- ABEL Stephane (Thu Feb 17 2022 - 09:40:59 PST)
[AMBER] Query regarding 3DRISM calculation
- tluchko (Fri Feb 18 2022 - 08:15:44 PST)
- tluchko (Thu Feb 10 2022 - 15:54:00 PST)
- ABDUL BASIT (Thu Feb 10 2022 - 10:00:56 PST)
- David A Case (Thu Feb 10 2022 - 09:58:02 PST)
- ABDUL BASIT (Wed Feb 09 2022 - 20:55:13 PST)
- Rakesh Srivastava (Sat Feb 05 2022 - 09:06:50 PST)
- David A Case (Thu Feb 03 2022 - 10:00:53 PST)
- Rakesh Srivastava (Thu Feb 03 2022 - 06:31:54 PST)
[AMBER] Reg: Modified LYS residues - Can I use Gaff if so how to link with hybrid AMBERff14SB and GAFF
- Dr. Anselm Horn (Wed Feb 09 2022 - 12:13:33 PST)
- Lara rajam (Tue Feb 08 2022 - 12:01:03 PST)
[AMBER] Removing AmberTools binary files installed on .pyenv/shims
- Tony Myung Keun Cho (Tue Feb 22 2022 - 05:17:43 PST)
[AMBER] Restart using Nosé-Hoover
- GIULIA BIFFI (Thu Feb 17 2022 - 02:09:46 PST)
[AMBER] Running amber executable on multiple GPUs
- Adrian Roitberg (Tue Feb 15 2022 - 07:21:49 PST)
- Prithviraj Nandigrami (Tue Feb 15 2022 - 07:14:31 PST)
[AMBER] Running Umbrella Sampling simulations
- Osman, Roman (Fri Feb 18 2022 - 12:14:16 PST)
[AMBER] Same initial velocities with ig=NNN and NTT=1 (on GPU)?
- Dr. Anselm Horn (Wed Feb 09 2022 - 07:48:20 PST)
- Carlos Simmerling (Fri Feb 04 2022 - 10:53:01 PST)
- Dr. Anselm Horn (Fri Feb 04 2022 - 09:38:07 PST)
- Carlos Simmerling (Fri Feb 04 2022 - 09:21:47 PST)
- Dr. Anselm Horn (Fri Feb 04 2022 - 09:18:27 PST)
- Carlos Simmerling (Fri Feb 04 2022 - 09:11:14 PST)
- Adrian Roitberg (Fri Feb 04 2022 - 09:10:11 PST)
- Dr. Anselm Horn (Fri Feb 04 2022 - 09:01:03 PST)
- Carlos Simmerling (Fri Feb 04 2022 - 07:00:02 PST)
- Dr. Anselm Horn (Fri Feb 04 2022 - 06:08:41 PST)
[AMBER] Segmentation Fault (Core Dumped) in xLEaP
- Nathan Black (Mon Feb 28 2022 - 08:29:39 PST)
- Nathan Black (Mon Feb 28 2022 - 08:02:50 PST)
- Dr. Anselm Horn (Sun Feb 27 2022 - 12:52:34 PST)
- Nathan Black (Fri Feb 25 2022 - 12:50:49 PST)
- Carlos Simmerling (Fri Feb 25 2022 - 09:20:53 PST)
- Nathan Black (Fri Feb 25 2022 - 09:04:46 PST)
- Carlos Simmerling (Fri Feb 25 2022 - 08:02:58 PST)
- Nathan Black (Thu Feb 24 2022 - 16:32:22 PST)
- Nathan Black (Thu Feb 24 2022 - 14:33:36 PST)
- Carlos Simmerling (Thu Feb 24 2022 - 14:06:44 PST)
- Nathan Black (Thu Feb 24 2022 - 14:04:45 PST)
- Carlos Simmerling (Thu Feb 24 2022 - 13:48:39 PST)
- Nathan Black (Thu Feb 24 2022 - 13:40:53 PST)
[AMBER] Simulation of proteins with D-amino acids
- Piotr Cieplak (Thu Feb 10 2022 - 22:49:01 PST)
- Nathan Guerin (Tue Feb 08 2022 - 09:58:11 PST)
- Carlos Simmerling (Mon Feb 07 2022 - 18:04:49 PST)
- nguerin (Mon Feb 07 2022 - 17:17:05 PST)
[AMBER] Single-Molecule Mixing of Force Fields
- Nathan Black (Tue Feb 22 2022 - 09:16:48 PST)
- Dr. Anselm Horn (Tue Feb 22 2022 - 04:21:15 PST)
- Carlos Simmerling (Mon Feb 21 2022 - 10:03:51 PST)
- Nathan Black (Mon Feb 21 2022 - 09:54:32 PST)
- Dr. Anselm Horn (Mon Feb 21 2022 - 08:31:26 PST)
- Nathan Black (Sat Feb 19 2022 - 11:04:33 PST)
[AMBER] solvation failed with Amber 20
- Qinghua Liao (Thu Feb 10 2022 - 01:53:04 PST)
- Dr. Anselm Horn (Thu Feb 10 2022 - 00:08:41 PST)
- Qinghua Liao (Wed Feb 09 2022 - 15:23:58 PST)
[AMBER] Symmetric or mirrored boundary condition?
- David A Case (Wed Feb 09 2022 - 05:52:59 PST)
- Tucker Burgin (Tue Feb 08 2022 - 09:09:49 PST)
[AMBER] test cuda parallel error message
- David A Case (Mon Feb 07 2022 - 18:48:21 PST)
- Suguna Sakkiah (Mon Feb 07 2022 - 15:08:10 PST)
[AMBER] To know about the Forcefield of Pyrrolysine amino acid.
- PRIYANKA PUROHIT (Thu Feb 24 2022 - 00:38:16 PST)
[AMBER] trouble finding vdW parameters for methanol
- Carlos Simmerling (Tue Feb 08 2022 - 08:50:28 PST)
- Debarati DasGupta (Tue Feb 08 2022 - 08:48:02 PST)
- Carlos Simmerling (Tue Feb 08 2022 - 08:03:41 PST)
- Debarati DasGupta (Tue Feb 08 2022 - 07:56:12 PST)
- David A Case (Mon Feb 07 2022 - 18:45:05 PST)
- Debarati DasGupta (Mon Feb 07 2022 - 09:50:34 PST)
[AMBER] Unexpected TER chars with pdb4amber and phosphorylated amino acids
- Brian Radak (Thu Feb 10 2022 - 11:57:10 PST)
[AMBER] Unused parameters in tip4pew?
- Jason Swails (Wed Feb 16 2022 - 09:09:30 PST)
- Rosemary Millmore (Wed Feb 16 2022 - 08:40:05 PST)
[AMBER] Void bubbles forming in minimization with single nucleoside/solvent?
- Carlos Simmerling (Wed Feb 02 2022 - 11:50:26 PST)
- Kenneth Huang (Wed Feb 02 2022 - 10:05:52 PST)
[AMBER] when amber22 is going to be released?
- David A Case (Mon Feb 07 2022 - 03:46:48 PST)
- Albert (Sun Feb 06 2022 - 17:05:49 PST)
[AMBER] Workstation Recommendations
- Sushil Mishra (Mon Feb 21 2022 - 06:48:04 PST)
[AMBER] xleap problem
- Dr. Anselm Horn (Thu Feb 10 2022 - 02:36:11 PST)
- Ibrahim Said (Thu Feb 10 2022 - 00:42:50 PST)
- David A Case (Wed Feb 09 2022 - 13:16:55 PST)
- Clorice Reinhardt (Wed Feb 09 2022 - 11:27:36 PST)
- Ibrahim Said (Wed Feb 09 2022 - 11:14:29 PST)

Amber Archive Feb 2022 by subject