Amber Archive Aug 2020: by author

Aashish Bhatt
- [AMBER] azobenzene atoms name in amber format (Mon Aug 31 2020 - 04:42:26 PDT)
Adrian Roitberg
- Re: [AMBER] Unable to complete heating stage (Thu Aug 27 2020 - 10:00:30 PDT)
aishen
- Re: [AMBER] Attention: All CPPTRAJ Questions (Mon Aug 31 2020 - 12:35:38 PDT)
- Re: [AMBER] new to amber20 (Sun Aug 30 2020 - 00:53:16 PDT)
alex rayevsky
- [AMBER] novel residue from Glutamine (Tue Aug 25 2020 - 05:24:29 PDT)
Amanda Buyan
- Re: [AMBER] Amber20 with PLUMED not working with multiple CPUs (Tue Aug 11 2020 - 16:23:24 PDT)
- Re: [AMBER] Amber20 with PLUMED not working with multiple CPUs (Mon Aug 10 2020 - 21:23:23 PDT)
- [AMBER] Amber20 with PLUMED not working with multiple CPUs (Sun Aug 09 2020 - 16:25:13 PDT)
An Ta
- [AMBER] Stripping Protocol in Cpptraj (Thu Aug 27 2020 - 12:50:39 PDT)
angad sharma
- [AMBER] facing problem in 3DRISM (Fri Aug 28 2020 - 05:27:59 PDT)
- [AMBER] problem in 3DRISM (Fri Aug 07 2020 - 06:32:51 PDT)
ankita mehta
- [AMBER] Force Field (Fri Aug 21 2020 - 07:03:21 PDT)
- [AMBER] tleap error (Wed Aug 12 2020 - 09:43:03 PDT)
ATUL KUMAR
- Re: [AMBER] problem in 3DRISM (Fri Aug 07 2020 - 06:59:41 PDT)
Ayesha Fatima
- [AMBER] Fatal error atom type work around (Mon Aug 31 2020 - 04:32:19 PDT)
- Re: [AMBER] "Atom does not have a type" despite adding .frcmod parameters (Thu Aug 27 2020 - 17:55:26 PDT)
- Re: [AMBER] "Atom does not have a type" despite adding .frcmod parameters (Thu Aug 27 2020 - 15:42:55 PDT)
- Re: [AMBER] error while running tutorial B5 (Mon Aug 24 2020 - 09:19:50 PDT)
- Re: [AMBER] error while running tutorial B5 (Sun Aug 23 2020 - 23:44:50 PDT)
- [AMBER] error while running tutorial B5 (Sun Aug 23 2020 - 11:08:48 PDT)
- [AMBER] preparing complexes (Mon Aug 17 2020 - 13:25:14 PDT)
- Re: [AMBER] tleap.in error (Fri Aug 07 2020 - 06:14:08 PDT)
- [AMBER] tleap.in error (Thu Aug 06 2020 - 09:41:19 PDT)
- Re: [AMBER] open valence problem (Thu Aug 06 2020 - 06:41:56 PDT)
- Re: [AMBER] open valence problem (Thu Aug 06 2020 - 05:04:23 PDT)
- Re: [AMBER] open valence problem (Thu Aug 06 2020 - 04:10:35 PDT)
- [AMBER] open valence problem (Tue Aug 04 2020 - 07:34:19 PDT)
Bill Ross
- Re: [AMBER] amber14 cuda code does not work (Sun Aug 23 2020 - 08:30:19 PDT)
- Re: [AMBER] trouble with pdb4amber (Fri Aug 21 2020 - 07:15:52 PDT)
- Re: [AMBER] Force Field (Fri Aug 21 2020 - 07:11:30 PDT)
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value (Tue Aug 18 2020 - 04:36:07 PDT)
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value (Sun Aug 16 2020 - 01:56:15 PDT)
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value (Sun Aug 16 2020 - 01:27:22 PDT)
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value (Sat Aug 15 2020 - 21:21:03 PDT)
- Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) (Sun Aug 09 2020 - 23:27:45 PDT)
- Re: [AMBER] implicit solvent calculations with calcium ion (Thu Aug 06 2020 - 04:53:24 PDT)
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. (Thu Aug 06 2020 - 02:15:36 PDT)
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. (Thu Aug 06 2020 - 02:08:33 PDT)
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. (Wed Aug 05 2020 - 23:52:10 PDT)
- Re: [AMBER] Are Amber program can running using AMD processor? (Mon Aug 03 2020 - 21:43:46 PDT)
- Re: [AMBER] Are Amber program can running using AMD processor? (Mon Aug 03 2020 - 21:39:23 PDT)
- Re: [AMBER] Regarding the backup of amber nc files (Sun Aug 02 2020 - 23:19:03 PDT)
- Re: [AMBER] how to calculate net charge of "molecule" using the command "netCharge" (Sun Aug 02 2020 - 17:44:43 PDT)
Billiot, Eugene
- Re: [AMBER] how to calculate net charge of "molecule" using the command "netCharge" (Mon Aug 03 2020 - 11:33:59 PDT)
- [AMBER] how to calculate net charge of "molecule" using the command "netCharge" (Sun Aug 02 2020 - 16:40:27 PDT)
Bowleg, Jerrano
- Re: [AMBER] Force Field (Fri Aug 21 2020 - 07:08:07 PDT)
Camila Clemente
- Re: [AMBER] MMPBSA.py with saline environment (Fri Aug 28 2020 - 15:41:09 PDT)
- Re: [AMBER] MMPBSA.py with saline environment (Thu Aug 27 2020 - 10:21:20 PDT)
- [AMBER] MMPBSA.py with saline environment (Thu Aug 27 2020 - 07:10:24 PDT)
- Re: [AMBER] Request .nc to MMPBSA.py? (Tue Aug 25 2020 - 11:28:17 PDT)
- Re: [AMBER] Request .nc to MMPBSA.py? (Mon Aug 24 2020 - 10:55:59 PDT)
- [AMBER] Problem with MMPBSA.py (Sun Aug 23 2020 - 21:23:36 PDT)
- Re: [AMBER] Error searching for compatible GPU (Sun Aug 16 2020 - 09:00:53 PDT)
- [AMBER] Error searching for compatible GPU (Sat Aug 15 2020 - 18:01:37 PDT)
Camila Mara Clemente
- Re: [AMBER] Request .nc to MMPBSA.py? (Mon Aug 24 2020 - 11:16:36 PDT)
- [AMBER] Request .nc to MMPBSA.py? (Mon Aug 24 2020 - 10:38:37 PDT)
Carlos
- Re: [AMBER] amber14 cuda code does not work (Tue Aug 25 2020 - 08:28:22 PDT)
- Re: [AMBER] amber14 cuda code does not work (Sun Aug 23 2020 - 12:23:10 PDT)
- [AMBER] amber14 cuda code does not work (Sat Aug 22 2020 - 21:52:26 PDT)
Carlos Simmerling
- Re: [AMBER] ANTECHAMBER error: Fatal Error! Weird atomic valence (5) for atom (ID: 7, Name: C5). (Tue Aug 25 2020 - 03:44:57 PDT)
Charo del Genio
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber (Sat Aug 29 2020 - 06:52:09 PDT)
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber (Wed Aug 26 2020 - 08:38:37 PDT)
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber (Wed Aug 26 2020 - 06:57:38 PDT)
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber (Wed Aug 26 2020 - 02:22:59 PDT)
- [AMBER] Questions (and a small bug report) about SIRAH in Amber (Fri Aug 21 2020 - 13:43:18 PDT)
Christina Bergonzo
- Re: [AMBER] weird energy histograms with REMD (Wed Aug 05 2020 - 06:47:31 PDT)
Daniel Roe
- [AMBER] Attention: All CPPTRAJ Questions (Mon Aug 31 2020 - 09:55:20 PDT)
- Re: [AMBER] Time numbering problem with constant-pH simulations (Wed Aug 26 2020 - 06:47:13 PDT)
- Re: [AMBER] Time numbering problem with constant-pH simulations (Tue Aug 25 2020 - 12:22:47 PDT)
- Re: [AMBER] Time numbering problem with constant-pH simulations (Mon Aug 24 2020 - 17:57:07 PDT)
- Re: [AMBER] Time numbering problem with constant-pH simulations (Mon Aug 24 2020 - 16:57:44 PDT)
- Re: [AMBER] amber14 cuda code does not work (Mon Aug 24 2020 - 07:46:27 PDT)
- Re: [AMBER] converting prmtop to psf with improper and cross-term info stripped off (Fri Aug 21 2020 - 13:48:52 PDT)
- Re: [AMBER] Time numbering problem with constant-pH simulations (Tue Aug 18 2020 - 06:02:47 PDT)
- Re: [AMBER] Using cpptraj to generate rst7 files from trajectory (Wed Aug 12 2020 - 09:04:40 PDT)
- Re: [AMBER] Using cpptraj to generate rst7 files from trajectory (Wed Aug 12 2020 - 06:20:12 PDT)
- Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) (Wed Aug 12 2020 - 06:18:13 PDT)
- Re: [AMBER] weird energy histograms with REMD (Wed Aug 05 2020 - 06:15:14 PDT)
- Re: [AMBER] Usage of the Density Peaks Algorithm. (Tue Aug 04 2020 - 08:13:19 PDT)
- Re: [AMBER] Regarding RMSD calculation and Clustering (Tue Aug 04 2020 - 07:54:54 PDT)
- Re: [AMBER] Lipid bilayer imaging problem (Tue Aug 04 2020 - 07:29:01 PDT)
- Re: [AMBER] fixatomorder (Tue Aug 04 2020 - 07:27:20 PDT)
- Re: [AMBER] Problem installing AmberMD with MPI support on Cray XC40 (Tue Aug 04 2020 - 06:32:11 PDT)
- Re: [AMBER] Tracking lifetime distance by closest of specific water IDs? (Tue Aug 04 2020 - 06:28:49 PDT)
- Re: [AMBER] Structure Artifact After Autoimage (Tue Aug 04 2020 - 06:25:10 PDT)
David A Case
- Re: [AMBER] Fatal error atom type work around (Mon Aug 31 2020 - 12:53:01 PDT)
- Re: [AMBER] azobenzene atoms name in amber format (Mon Aug 31 2020 - 12:30:12 PDT)
- Re: [AMBER] "FATAL: Atom *** does not have a type" Error (Mon Aug 31 2020 - 05:23:29 PDT)
- Re: [AMBER] new to amber20 (Mon Aug 31 2020 - 05:19:30 PDT)
- Re: [AMBER] FATAL atom does not have a type crispr cas9 pdb (Mon Aug 31 2020 - 05:04:18 PDT)
- Re: [AMBER] "FATAL: Atom *** does not have a type" Error (Sat Aug 29 2020 - 10:23:59 PDT)
- Re: [AMBER] "Atom does not have a type" despite adding .frcmod parameters (Fri Aug 28 2020 - 05:04:32 PDT)
- Re: [AMBER] Fw: covalent molecule and modified residue parameters (Thu Aug 27 2020 - 18:03:23 PDT)
- Re: [AMBER] Help for building cross linking polymer using graphic antechamber (Thu Aug 27 2020 - 05:10:01 PDT)
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber (Mon Aug 24 2020 - 11:40:06 PDT)
- Re: [AMBER] Problem with MMPBSA.py (Mon Aug 24 2020 - 05:04:08 PDT)
- Re: [AMBER] error while running tutorial B5 (Sun Aug 23 2020 - 18:39:16 PDT)
- Re: [AMBER] amber14 cuda code does not work (Sun Aug 23 2020 - 07:33:26 PDT)
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber (Fri Aug 21 2020 - 19:06:09 PDT)
- Re: [AMBER] trouble with pdb4amber (Fri Aug 21 2020 - 09:59:07 PDT)
- Re: [AMBER] Force Field (Fri Aug 21 2020 - 09:47:47 PDT)
- Re: [AMBER] 转发: Amber20 install problem （Geng Dong） (Wed Aug 19 2020 - 19:00:31 PDT)
- Re: [AMBER] 转发: Amber20 install problem （Geng Dong） (Tue Aug 18 2020 - 19:28:34 PDT)
- Re: [AMBER] AMBER18 pmemd.MPI installation error (Tue Aug 18 2020 - 05:45:47 PDT)
- Re: [AMBER] preparing complexes (Tue Aug 18 2020 - 05:27:46 PDT)
- Re: [AMBER] Error searching for compatible GPU (Sun Aug 16 2020 - 05:04:08 PDT)
- Re: [AMBER] tleap error (Wed Aug 12 2020 - 12:30:40 PDT)
- Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) (Mon Aug 10 2020 - 04:57:40 PDT)
- Re: [AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming (Fri Aug 07 2020 - 17:41:25 PDT)
- Re: [AMBER] problem in 3DRISM (Fri Aug 07 2020 - 08:18:15 PDT)
- Re: [AMBER] Parmed: Residues cannot be part of 2 molecules! Molecule section will not be correctly set. (Thu Aug 06 2020 - 13:30:16 PDT)
- Re: [AMBER] tleap.in error (Thu Aug 06 2020 - 13:22:47 PDT)
- Re: [AMBER] asking about "timlim" in accelerated MD (Thu Aug 06 2020 - 13:19:30 PDT)
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. (Thu Aug 06 2020 - 04:52:31 PDT)
- Re: [AMBER] implicit solvent calculations with calcium ion (Thu Aug 06 2020 - 04:46:30 PDT)
- Re: [AMBER] conversion of tripose mol2 to amber type (Wed Aug 05 2020 - 13:07:20 PDT)
- Re: [AMBER] open valence problem (Tue Aug 04 2020 - 18:44:32 PDT)
- Re: [AMBER] conversion of tripose mol2 to amber type (Tue Aug 04 2020 - 18:37:09 PDT)
- Re: [AMBER] Regarding the backup of amber nc files (Mon Aug 03 2020 - 07:25:23 PDT)
- Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???) (Mon Aug 03 2020 - 07:16:16 PDT)
- Re: [AMBER] how to calculate net charge of "molecule" using the command "netCharge" (Mon Aug 03 2020 - 07:07:11 PDT)
David Cerutti
- Re: [AMBER] Missing (ATTN, need revision) and poor parameters (high penalty score) for small molecule parameters and hard time with paramfit (Sun Aug 23 2020 - 15:06:46 PDT)
- Re: [AMBER] Running Paramfit with 300 + structures (Fri Aug 14 2020 - 15:36:18 PDT)
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. (Thu Aug 06 2020 - 02:11:29 PDT)
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. (Thu Aug 06 2020 - 02:03:07 PDT)
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. (Thu Aug 06 2020 - 02:02:27 PDT)
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. (Wed Aug 05 2020 - 19:48:36 PDT)
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. (Mon Aug 03 2020 - 21:40:51 PDT)
Debarati DasGupta
- [AMBER] Amazon Cloud services and Amber (Wed Aug 12 2020 - 05:24:31 PDT)
Diego Morone
- Re: [AMBER] weird energy histograms with REMD (Wed Aug 05 2020 - 05:53:44 PDT)
- [AMBER] weird energy histograms with REMD (Wed Aug 05 2020 - 05:35:04 PDT)
Dmitry Karlov
- [AMBER] plumed does not work with pmemd.cuda but it works with sander (Wed Aug 26 2020 - 12:04:11 PDT)
Dr. Anselm Horn
- Re: [AMBER] novel residue from Glutamine (Tue Aug 25 2020 - 08:17:34 PDT)
- Re: [AMBER] gnuplot (Wed Aug 05 2020 - 02:50:48 PDT)
Elvis Martis
- Re: [AMBER] "FATAL: Atom *** does not have a type" Error (Fri Aug 28 2020 - 23:29:10 PDT)
- Re: [AMBER] MMPBSA.py with saline environment (Thu Aug 27 2020 - 20:27:46 PDT)
- Re: [AMBER] MMPBSA.py with saline environment (Thu Aug 27 2020 - 07:56:38 PDT)
- Re: [AMBER] Request .nc to MMPBSA.py? (Tue Aug 25 2020 - 20:03:44 PDT)
- Re: [AMBER] ANTECHAMBER error: Fatal Error! Weird atomic valence (5) for atom (ID: 7, Name: C5). (Tue Aug 25 2020 - 01:41:01 PDT)
- Re: [AMBER] Request .nc to MMPBSA.py? (Mon Aug 24 2020 - 11:18:20 PDT)
- Re: [AMBER] Request .nc to MMPBSA.py? (Mon Aug 24 2020 - 11:06:29 PDT)
- Re: [AMBER] Request .nc to MMPBSA.py? (Mon Aug 24 2020 - 10:49:45 PDT)
- Re: [AMBER] Problem with MMPBSA.py (Sun Aug 23 2020 - 22:37:58 PDT)
- Re: [AMBER] Problem with MMPBSA.py (Sun Aug 23 2020 - 22:36:06 PDT)
Erika Davidoff
- [AMBER] "Atom does not have a type" despite adding .frcmod parameters (Thu Aug 27 2020 - 12:56:25 PDT)
FLORA, JOSEPH
- [AMBER] no collective variables output for infe=1 and abfqmmm (Mon Aug 17 2020 - 18:52:20 PDT)
Fulbabu Sk
- [AMBER] Help for building two different salt concentration system using tLeap module (Thu Aug 27 2020 - 05:55:29 PDT)
gagandeep singh
- [AMBER] Fatal error on running GAMESS for parameters of FE ion (Thu Aug 06 2020 - 08:59:52 PDT)
- Re: [AMBER] Error in Gausian file preparation using MCPB.py (Sat Aug 01 2020 - 18:56:45 PDT)
- Re: [AMBER] Error in Gausian file preparation using MCPB.py (Fri Jul 31 2020 - 14:01:14 PDT)
German P. Barletta
- Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (Wed Aug 12 2020 - 12:16:19 PDT)
- Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) (Tue Aug 11 2020 - 16:46:27 PDT)
- [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) (Sun Aug 09 2020 - 13:43:20 PDT)
Gomez, Yessica
- Re: [AMBER] Problems with MC barostat (Fri Jul 31 2020 - 17:51:23 PDT)
Guadalupe Alvarez
- [AMBER] Change covar matrix precision when crdaction is used (Wed Aug 26 2020 - 12:56:39 PDT)
Guessregen, Stefan /DE
- [AMBER] EXTENDED DEADLINE for Submissions - 16th German Conference on Cheminformatics (GCC) and the SAMPL satellite workshop (Sun Aug 30 2020 - 23:16:41 PDT)
- [AMBER] CALL FOR PAPER - 16th German Conference on Cheminformatics (GCC) and the SAMPL satellite workshop (Sat Aug 08 2020 - 03:45:10 PDT)
Gustaf Olsson
- Re: [AMBER] "After the fact" lifetime analysis with CPPTRAJ (Mon Aug 31 2020 - 03:27:45 PDT)
- [AMBER] "After the fact" lifetime analysis with CPPTRAJ (Fri Aug 28 2020 - 05:11:52 PDT)
- [AMBER] Tutorial B0 (Thu Aug 27 2020 - 00:52:38 PDT)
- [AMBER] Fundamentals of LEaP Tutorial (Tue Aug 25 2020 - 05:36:19 PDT)
- Re: [AMBER] error while running tutorial B5 (Tue Aug 25 2020 - 00:24:14 PDT)
- Re: [AMBER] error while running tutorial B5 (Mon Aug 24 2020 - 01:03:58 PDT)
- Re: [AMBER] Amber20 install problem （Geng Dong） (Thu Aug 20 2020 - 00:45:32 PDT)
- [AMBER] Compiling AmberTools on macOS (Wed Aug 12 2020 - 07:08:23 PDT)
- Re: [AMBER] Amazon Cloud services and Amber (Wed Aug 12 2020 - 05:40:38 PDT)
- Re: [AMBER] Using cpptraj to generate rst7 files from trajectory (Tue Aug 11 2020 - 22:57:44 PDT)
- [AMBER] Defining/Selecting BLAS with cmake (Mon Aug 10 2020 - 03:19:03 PDT)
Hai Nguyen
- Re: [AMBER] trouble with pdb4amber (Fri Aug 21 2020 - 19:33:42 PDT)
Jakub Jalowiec
- Re: [AMBER] Problem installing AmberMD with MPI support on Cray XC40 (Wed Aug 12 2020 - 01:33:01 PDT)
Jatin Kashyap
- [AMBER] "FATAL: Atom *** does not have a type" Error (Fri Aug 28 2020 - 22:44:11 PDT)
Jenny 148
- [AMBER] Regarding the backup of amber nc files (Sun Aug 02 2020 - 22:44:34 PDT)
Jisha B
- [AMBER] FATAL atom does not have a type crispr cas9 pdb (Sat Aug 29 2020 - 20:37:47 PDT)
Jonee Lillard
- Re: [AMBER] Time numbering problem with constant-pH simulations (Wed Aug 26 2020 - 06:03:25 PDT)
- Re: [AMBER] Time numbering problem with constant-pH simulations (Tue Aug 25 2020 - 08:30:35 PDT)
- Re: [AMBER] Time numbering problem with constant-pH simulations (Tue Aug 25 2020 - 08:22:01 PDT)
- Re: [AMBER] Time numbering problem with constant-pH simulations (Sat Aug 22 2020 - 06:04:50 PDT)
- [AMBER] Time numbering problem with constant-pH simulations (Sat Aug 15 2020 - 07:31:14 PDT)
Kashyap, Jatin
- Re: [AMBER] "FATAL: Atom *** does not have a type" Error (Sat Aug 29 2020 - 21:45:39 PDT)
koushik kasavajhala
- Re: [AMBER] weird energy histograms with REMD (Wed Aug 05 2020 - 05:43:03 PDT)
Lachele Foley
- [AMBER] GlycoTools Webinar tomorrow (Thu Aug 13 2020 - 07:34:28 PDT)
Li, Min
- [AMBER] about pressure calculation in Amber18 (Sun Aug 09 2020 - 21:16:35 PDT)
Liao
- Re: [AMBER] Using cpptraj to generate rst7 files from trajectory (Wed Aug 12 2020 - 11:25:08 PDT)
- Re: [AMBER] Using cpptraj to generate rst7 files from trajectory (Wed Aug 12 2020 - 08:59:53 PDT)
- [AMBER] Using cpptraj to generate rst7 files from trajectory (Tue Aug 11 2020 - 14:47:47 PDT)
Lod King
- [AMBER] converting prmtop to psf with improper and cross-term info stripped off (Thu Aug 20 2020 - 13:22:41 PDT)
Luca Codutti
- Re: [AMBER] Amazon Cloud services and Amber (Wed Aug 12 2020 - 05:58:40 PDT)
Maghsoud, Yazdan
- [AMBER] Asking for Fe2-S2 cluster and Molybdopterin AMBER force field parameters (Mon Aug 31 2020 - 11:53:51 PDT)
Marek Maly
- Re: [AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files (Tue Aug 25 2020 - 10:07:48 PDT)
- [AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files (Thu Aug 20 2020 - 03:21:08 PDT)
Maria Nagan
- Re: [AMBER] "Atom does not have a type" despite adding .frcmod parameters (Thu Aug 27 2020 - 17:59:02 PDT)
- Re: [AMBER] "Atom does not have a type" despite adding .frcmod parameters (Thu Aug 27 2020 - 16:02:21 PDT)
- Re: [AMBER] Fundamentals of LEaP Tutorial (Tue Aug 25 2020 - 05:56:47 PDT)
Matias Machado
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber (Fri Aug 28 2020 - 09:57:40 PDT)
- Re: [AMBER] Help for building two different salt concentration system using tLeap module (Thu Aug 27 2020 - 07:33:09 PDT)
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber (Wed Aug 26 2020 - 08:27:43 PDT)
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber (Wed Aug 26 2020 - 06:07:09 PDT)
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber (Mon Aug 24 2020 - 09:09:09 PDT)
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber (Mon Aug 24 2020 - 07:26:57 PDT)
- Re: [AMBER] tleap.in error (Fri Aug 07 2020 - 06:26:46 PDT)
- Re: [AMBER] tleap.in error (Fri Aug 07 2020 - 06:00:06 PDT)
Mattia Cavallaro
- Re: [AMBER] trouble with pdb4amber (Sat Aug 22 2020 - 05:25:57 PDT)
- [AMBER] trouble with pdb4amber (Fri Aug 21 2020 - 07:10:45 PDT)
Mohamed M. Aboelnga
- [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme) using MCPB tool (Sun Aug 23 2020 - 08:31:58 PDT)
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) (Wed Aug 19 2020 - 06:20:40 PDT)
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) (Tue Aug 18 2020 - 09:10:11 PDT)
mohamed marzouk
- Re: [AMBER] Caping error (Thu Aug 06 2020 - 22:39:44 PDT)
MYRIAN TORRES RICO
- Re: [AMBER] gnuplot (Wed Aug 05 2020 - 04:23:31 PDT)
- [AMBER] gnuplot (Wed Aug 05 2020 - 01:25:03 PDT)
Neha Gandhi
- [AMBER] Few workflow-LIE (Tue Aug 18 2020 - 06:15:04 PDT)
neildancer
- Re: [AMBER] preparing complexes (Mon Aug 17 2020 - 20:18:11 PDT)
neildancer.sina.com
- [AMBER] Problem about ADP-Protein complex simulation (Sat Aug 08 2020 - 06:58:49 PDT)
Nikhil Maroli
- [AMBER] How to select groups for energy calculations-CPPtraj (Sun Aug 30 2020 - 12:44:25 PDT)
- Re: [AMBER] conversion of tripose mol2 to amber type (Wed Aug 05 2020 - 10:30:50 PDT)
- [AMBER] How to make amber/antechamber type mol2 from syble mol2 (Wed Aug 05 2020 - 00:05:03 PDT)
- [AMBER] conversion of tripose mol2 to amber type (Tue Aug 04 2020 - 05:21:08 PDT)
paraw
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber (Mon Aug 24 2020 - 09:45:37 PDT)
- [AMBER] Questions (and a small bug report) about SIRAH in Amber (Mon Aug 24 2020 - 08:19:42 PDT)
Pinky Mazumder
- Re: [AMBER] Help for building cross linking polymer using graphic antechamber (Wed Aug 26 2020 - 13:17:45 PDT)
- [AMBER] Help for building cross linking polymer using graphic antechamber (Wed Aug 26 2020 - 13:16:26 PDT)
Piotr Fajer
- [AMBER] implicit solvent calculations with calcium ion (Wed Aug 05 2020 - 17:56:06 PDT)
Pooja Kesari
- [AMBER] ANTECHAMBER error: Fatal Error! Weird atomic valence (5) for atom (ID: 7, Name: C5). (Tue Aug 25 2020 - 01:33:01 PDT)
Prathit Chatterjee
- [AMBER] Confusion regarding Center of mass coordinates for protein, with CPPTRAJ (Thu Aug 27 2020 - 04:58:48 PDT)
Qinghua Liao
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value (Sun Aug 16 2020 - 02:26:54 PDT)
Ram Koganti
- [AMBER] Help with MDCRD file for calculating binding energy (Fri Aug 07 2020 - 18:36:34 PDT)
Raman Preet Singh
- Re: [AMBER] Amazon Cloud services and Amber (Wed Aug 12 2020 - 05:47:36 PDT)
Ramanathan Rajesh
- Re: [AMBER] Unable to complete heating stage (Thu Aug 27 2020 - 10:56:05 PDT)
- [AMBER] Unable to complete heating stage (Thu Aug 27 2020 - 10:37:54 PDT)
Robin Betz
- Re: [AMBER] Running Paramfit with 300 + structures (Fri Aug 14 2020 - 15:12:12 PDT)
Rodrigo Galindo-Murillo
- Re: [AMBER] gnuplot (Wed Aug 05 2020 - 08:38:43 PDT)
Samuel A. Ratliff
- Re: [AMBER] Parmed: Residues cannot be part of 2 molecules! Molecule section will not be correctly set. (Fri Aug 07 2020 - 08:34:26 PDT)
- [AMBER] Parmed: Residues cannot be part of 2 molecules! Molecule section will not be correctly set. (Thu Aug 06 2020 - 10:10:58 PDT)
- Re: [AMBER] Issue heating system in equilibration step (Thu Aug 06 2020 - 09:58:04 PDT)
Samuel Himes
- [AMBER] Running Paramfit with 300 + structures (Fri Aug 14 2020 - 14:58:14 PDT)
Sarah Jane
- [AMBER] Fw: covalent molecule and modified residue parameters (Thu Aug 27 2020 - 12:44:59 PDT)
Scott Brozell
- Re: [AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files (Thu Aug 27 2020 - 14:43:01 PDT)
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber (Fri Aug 21 2020 - 18:21:46 PDT)
- Re: [AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files (Fri Aug 21 2020 - 15:02:13 PDT)
- Re: [AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files (Thu Aug 20 2020 - 18:02:00 PDT)
- Re: [AMBER] tleap.in error (Thu Aug 06 2020 - 13:26:11 PDT)
Setyanto Md
- Re: [AMBER] asking about "timlim" in accelerated MD (Thu Aug 06 2020 - 16:04:22 PDT)
- [AMBER] asking about "timlim" in accelerated MD (Thu Aug 06 2020 - 09:22:24 PDT)
- Re: [AMBER] Are Amber program can running using AMD processor? (Mon Aug 03 2020 - 22:40:31 PDT)
- [AMBER] Are Amber program can running using AMD processor? (Mon Aug 03 2020 - 20:25:18 PDT)
Shubhandra Tripathi
- [AMBER] AMBER18 pmemd.MPI installation error (Mon Aug 17 2020 - 06:43:47 PDT)
Thomas Cheatham
- Re: [AMBER] Amazon Cloud services and Amber (Wed Aug 12 2020 - 15:37:20 PDT)
Tyler Luchko (Lists)
- Re: [AMBER] facing problem in 3DRISM (Fri Aug 28 2020 - 07:26:41 PDT)
Vaibhav Dixit
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) (Wed Aug 19 2020 - 06:56:04 PDT)
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) (Tue Aug 18 2020 - 23:11:21 PDT)
viktor drobot
- Re: [AMBER] plumed does not work with pmemd.cuda but it works with sander (Wed Aug 26 2020 - 12:07:10 PDT)
- Re: [AMBER] trouble with pdb4amber (Fri Aug 21 2020 - 07:33:39 PDT)
- Re: [AMBER] Amber20 with PLUMED not working with multiple CPUs (Tue Aug 11 2020 - 00:19:20 PDT)
- Re: [AMBER] Amber20 with PLUMED not working with multiple CPUs (Mon Aug 10 2020 - 00:25:30 PDT)
Állan Ferrari
- [AMBER] Missing (ATTN, need revision) and poor parameters (high penalty score) for small molecule parameters and hard time with paramfit (Sat Aug 22 2020 - 13:59:45 PDT)
东庚
- [AMBER] 转发: Amber20 install problem （Geng Dong） (Tue Aug 18 2020 - 18:25:04 PDT)
李奕言
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value (Tue Aug 18 2020 - 04:31:47 PDT)
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value (Sun Aug 16 2020 - 01:21:50 PDT)
- [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value (Sat Aug 15 2020 - 21:00:28 PDT)
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. (Wed Aug 05 2020 - 23:43:57 PDT)
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. (Wed Aug 05 2020 - 18:58:58 PDT)
- [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. (Sun Aug 02 2020 - 20:21:55 PDT)
辛志宏
- Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???) (Mon Aug 03 2020 - 18:59:17 PDT)
- Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???) (Sun Aug 02 2020 - 21:04:16 PDT)

Amber Archive Aug 2020 by author