Amber Archive Oct 2020: by author

Abdul Basit
- [AMBER] pmemd.cuda and CPU cores (Tue Oct 27 2020 - 20:13:46 PDT)
Abdul-Rashid III Sampaco
- [AMBER] MMGBSA/MMPBSA Help (Sat Oct 03 2020 - 04:33:44 PDT)
Abhilash J
- Re: [AMBER] Adding catalytic Magnesium ion (Sat Oct 17 2020 - 14:41:57 PDT)
Adrian Roitberg
- Re: [AMBER] how find Es from mdout to estimate vertical energy gap (Sat Oct 31 2020 - 09:28:25 PDT)
- Re: [AMBER] how find Es from mdout to estimate vertical energy gap (Fri Oct 30 2020 - 10:11:02 PDT)
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs (Fri Oct 09 2020 - 09:44:49 PDT)
aishen
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd (Thu Oct 15 2020 - 23:45:47 PDT)
- [AMBER] about translation (Sat Oct 03 2020 - 01:21:57 PDT)
- [AMBER] pmemd (Thu Oct 01 2020 - 13:50:45 PDT)
- [AMBER] pmemd (Thu Oct 01 2020 - 09:44:55 PDT)
aishen.free.fr
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd (Fri Oct 16 2020 - 06:16:44 PDT)
Alejandro Cagnoni
- [AMBER] mdout error (Tue Oct 20 2020 - 04:54:13 PDT)
- [AMBER] mdout issue (Thu Oct 15 2020 - 07:01:53 PDT)
Amit Sharma (Asstt. Prof., MCARS)
- [AMBER] Help with parameterization of non-standard amino acid (Wed Oct 28 2020 - 05:43:59 PDT)
An Ta
- Re: [AMBER] Verbose - Output File Information Not Changing (Wed Oct 07 2020 - 17:09:14 PDT)
- Re: [AMBER] Verbose - Output File Information Not Changing (Wed Oct 07 2020 - 16:17:29 PDT)
- [AMBER] Verbose - Output File Information Not Changing (Wed Oct 07 2020 - 11:55:43 PDT)
Ari Zeida
- [AMBER] image protein complex iwrap=1 (Fri Oct 02 2020 - 07:21:41 PDT)
Asaf Farhi
- Re: [AMBER] Question about force field for proteins (Fri Oct 16 2020 - 15:04:49 PDT)
- Re: [AMBER] Question about force field for proteins (Sat Oct 10 2020 - 11:49:32 PDT)
- Re: [AMBER] Question about force field for proteins (Mon Oct 05 2020 - 08:42:33 PDT)
- [AMBER] Question about force field for proteins (Mon Oct 05 2020 - 08:31:10 PDT)
Ayesha Fatima
- [AMBER] error 403 (Thu Oct 22 2020 - 10:57:21 PDT)
Batuhan Kav
- Re: [AMBER] Changing lj_radius without changing lj_14_radius (Mon Oct 26 2020 - 09:22:52 PDT)
- Re: [AMBER] Changing lj_radius without changing lj_14_radius (Thu Oct 22 2020 - 01:34:22 PDT)
- [AMBER] Changing lj_radius without changing lj_14_radius (Mon Oct 19 2020 - 08:23:32 PDT)
bgostyns.cbmm.lodz.pl
- Re: [AMBER] Problems with using pdb4amber (and possibly other programs) on Ubuntu 20.04 (Thu Oct 08 2020 - 04:11:20 PDT)
- [AMBER] Problems with using pdb4amber (and possibly other programs) on Ubuntu 20.04 (Wed Oct 07 2020 - 06:52:03 PDT)
Bill Abbott
- Re: [AMBER] pmemd with hybrid mpi/mp (Tue Oct 27 2020 - 13:13:32 PDT)
- [AMBER] pmemd with hybrid mpi/mp (Tue Oct 27 2020 - 12:28:53 PDT)
Bill Ross
- Re: [AMBER] Tri-coordination environment in zinc (Thu Oct 29 2020 - 23:59:57 PDT)
- Re: [AMBER] cellulose crystal structure ( cellulose bundles) (Thu Oct 29 2020 - 10:34:27 PDT)
- Re: [AMBER] How to import (.pdb) files into xleap of AMBER generated by Cellulose builder (Thu Oct 29 2020 - 10:28:28 PDT)
- Re: [AMBER] Adding Ions (Tue Oct 20 2020 - 06:48:33 PDT)
- Re: [AMBER] Creating a coordinate bond in Leap (Sat Oct 17 2020 - 05:30:18 PDT)
- Re: [AMBER] Creating a coordinate bond in Leap (Fri Oct 16 2020 - 22:13:13 PDT)
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd (Thu Oct 15 2020 - 21:41:27 PDT)
- Re: [AMBER] Amber performance (Tue Oct 06 2020 - 16:13:54 PDT)
Billiot, Eugene
- [AMBER] calculating differences in binding energy for enantiomers to amino acid based surfactants (Tue Oct 20 2020 - 05:45:16 PDT)
BLUNTZER Marie
- Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule (Tue Oct 13 2020 - 07:45:22 PDT)
- Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule (Mon Oct 12 2020 - 05:42:34 PDT)
- [AMBER] Fw: partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule (Mon Oct 12 2020 - 04:16:01 PDT)
- Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule (Mon Oct 12 2020 - 04:09:32 PDT)
Carlos Simmerling
- Re: [AMBER] NMR restraints (Sat Oct 31 2020 - 05:42:30 PDT)
- Re: [AMBER] NMR restraints (Fri Oct 30 2020 - 14:11:50 PDT)
- Re: [AMBER] CO2 (Wed Oct 28 2020 - 12:37:06 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Sat Oct 24 2020 - 12:58:16 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Fri Oct 23 2020 - 10:28:58 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Fri Oct 23 2020 - 07:34:22 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Fri Oct 23 2020 - 05:27:34 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Thu Oct 22 2020 - 06:06:06 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Wed Oct 21 2020 - 06:32:50 PDT)
- Re: [AMBER] controversy in PBSA and GBSA results (Tue Oct 20 2020 - 05:34:39 PDT)
- Re: [AMBER] Question about force field for proteins (Sun Oct 11 2020 - 04:27:02 PDT)
- Re: [AMBER] ERROR: The file contained 14 atoms not in residue templates (Thu Oct 08 2020 - 12:48:34 PDT)
- Re: [AMBER] Hitting the supercomputer wall limit before completion of minimization step (Mon Oct 05 2020 - 11:52:19 PDT)
- Re: [AMBER] Hitting the supercomputer wall limit before completion of minimization step (Mon Oct 05 2020 - 08:38:43 PDT)
- Re: [AMBER] Question about force field for proteins (Mon Oct 05 2020 - 08:36:49 PDT)
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference (Sat Oct 03 2020 - 06:16:25 PDT)
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference (Fri Oct 02 2020 - 09:30:26 PDT)
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference (Fri Oct 02 2020 - 08:06:47 PDT)
Daniel Roe
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Fri Oct 23 2020 - 10:19:28 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Fri Oct 23 2020 - 07:29:46 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Fri Oct 23 2020 - 04:28:37 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Fri Oct 23 2020 - 02:36:20 PDT)
- Re: [AMBER] AmberMdPrep github cpptraj not sourced (Wed Oct 21 2020 - 03:38:33 PDT)
- Re: [AMBER] NAMD trajectory analysis with cpptraj (Sat Oct 17 2020 - 00:05:42 PDT)
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd (Fri Oct 16 2020 - 12:21:42 PDT)
- Re: [AMBER] rms(d) or (f) per residue (Fri Oct 16 2020 - 10:32:11 PDT)
- Re: [AMBER] rms(d) or (f) per residue (Fri Oct 16 2020 - 10:06:25 PDT)
- Re: [AMBER] cpptraj's hbond shows hbonds with carbon hydrogens (Thu Oct 15 2020 - 15:48:27 PDT)
- Re: [AMBER] RMSD, Rg density map (Wed Oct 14 2020 - 11:48:51 PDT)
- Re: [AMBER] Permute dihedrals (Fri Oct 09 2020 - 06:02:22 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using (Wed Oct 07 2020 - 08:35:37 PDT)
- Re: [AMBER] RMSD of ligand in pocket (Wed Oct 07 2020 - 08:02:28 PDT)
- Re: [AMBER] Fwd: Imaging issues with cpptraj (Wed Oct 07 2020 - 07:53:32 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using (Wed Oct 07 2020 - 07:52:13 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using (Wed Oct 07 2020 - 07:50:38 PDT)
- Re: [AMBER] Compiling CPPTRAJ from GitHub (Wed Oct 07 2020 - 07:47:57 PDT)
- Re: [AMBER] Compiling CPPTRAJ from GitHub (Mon Oct 05 2020 - 07:07:46 PDT)
- Re: [AMBER] image protein complex iwrap=1 (Sun Oct 04 2020 - 06:51:56 PDT)
- Re: [AMBER] RMSD of ligand in pocket (Sun Oct 04 2020 - 06:48:10 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using (Sun Oct 04 2020 - 06:46:05 PDT)
- Re: [AMBER] Compiling CPPTRAJ from GitHub (Fri Oct 02 2020 - 08:41:39 PDT)
David A Case
- Re: [AMBER] NMR restraints (Fri Oct 30 2020 - 18:21:41 PDT)
- Re: [AMBER] MM/PBSA after minimization (Fri Oct 30 2020 - 04:38:53 PDT)
- Re: [AMBER] Force field for IDP (Fri Oct 30 2020 - 04:33:20 PDT)
- Re: [AMBER] cellulose crystal structure ( cellulose bundles) (Thu Oct 29 2020 - 05:05:03 PDT)
- Re: [AMBER] Amber20 and RNA simulations (Wed Oct 28 2020 - 04:58:52 PDT)
- Re: [AMBER] pmemd.cuda and CPU cores (Wed Oct 28 2020 - 04:41:22 PDT)
- Re: [AMBER] pmemd with hybrid mpi/mp (Tue Oct 27 2020 - 13:04:24 PDT)
- Re: [AMBER] Amber20: Ampere microarchitecture support and next Amber release (Mon Oct 26 2020 - 17:55:55 PDT)
- Re: [AMBER] mmpbsa error (Mon Oct 26 2020 - 17:48:53 PDT)
- Re: [AMBER] mmpbsa error (Mon Oct 26 2020 - 06:26:32 PDT)
- Re: [AMBER] amber14 and amber16 are not working in new installation (Mon Oct 26 2020 - 06:23:20 PDT)
- Re: [AMBER] Trouble installing pbsa cuda code (Sat Oct 24 2020 - 10:18:29 PDT)
- Re: [AMBER] doubt charges (Fri Oct 23 2020 - 05:38:41 PDT)
- Re: [AMBER] drms comparison in sander during minimization? (Fri Oct 23 2020 - 05:31:32 PDT)
- Re: [AMBER] Trouble installing pbsa cuda code (Thu Oct 22 2020 - 12:59:18 PDT)
- Re: [AMBER] Is the amber website down? 9am EST (Thu Oct 22 2020 - 12:42:47 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Thu Oct 22 2020 - 05:47:51 PDT)
- Re: [AMBER] drms comparison in sander during minimization? (Thu Oct 22 2020 - 05:42:27 PDT)
- Re: [AMBER] installing Amber18 and AmberTools20 (Thu Oct 22 2020 - 05:37:10 PDT)
- Re: [AMBER] Adding Ions (Thu Oct 22 2020 - 05:21:51 PDT)
- Re: [AMBER] TI not compatible with GB on GPU (Thu Oct 22 2020 - 05:04:32 PDT)
- Re: [AMBER] Adding Ions (Wed Oct 21 2020 - 05:40:45 PDT)
- Re: [AMBER] AMBER16 problem (Tue Oct 20 2020 - 10:59:46 PDT)
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler (Tue Oct 20 2020 - 10:50:49 PDT)
- Re: [AMBER] mm-pbsa calculation: SA Bomb in circle(): Stored surface arcs over limit (Mon Oct 19 2020 - 04:47:09 PDT)
- Re: [AMBER] MD error (Mon Oct 19 2020 - 04:42:58 PDT)
- Re: [AMBER] Adding missing residues in a pdb file using tleap (Mon Oct 19 2020 - 04:39:14 PDT)
- Re: [AMBER] Bond: Maximum coordination exceeded (Mon Oct 19 2020 - 04:37:02 PDT)
- Re: [AMBER] Amber20 compiling warning (Mon Oct 19 2020 - 04:29:31 PDT)
- Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros (Sun Oct 18 2020 - 05:37:19 PDT)
- Re: [AMBER] Fwd: AMBER Digest, Vol 3153, Issue 1 (Fri Oct 16 2020 - 05:04:20 PDT)
- Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? (Thu Oct 15 2020 - 11:32:41 PDT)
- Re: [AMBER] Query about using MMPBSA.py to calculate the binding free energy for a ligand bound enzyme (Thu Oct 15 2020 - 11:29:26 PDT)
- Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros (Thu Oct 15 2020 - 06:43:25 PDT)
- Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? (Thu Oct 15 2020 - 05:13:28 PDT)
- Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros (Thu Oct 15 2020 - 05:10:07 PDT)
- Re: [AMBER] Installation of AMBER20 on CentOS 7 (Wed Oct 14 2020 - 12:20:55 PDT)
- Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros (Tue Oct 13 2020 - 08:05:30 PDT)
- Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule (Mon Oct 12 2020 - 05:06:31 PDT)
- Re: [AMBER] Verbose - Output File Information Not Changing (Fri Oct 09 2020 - 05:01:19 PDT)
- Re: [AMBER] Cannot run NPT (Thu Oct 08 2020 - 05:04:46 PDT)
- Re: [AMBER] Cannot run NPT (Wed Oct 07 2020 - 08:17:36 PDT)
- Re: [AMBER] Problems with using pdb4amber (and possibly other programs) on Ubuntu 20.04 (Wed Oct 07 2020 - 08:15:35 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using (Wed Oct 07 2020 - 08:05:22 PDT)
- Re: [AMBER] A100 and RTX3090 Benchmarks (Tue Oct 06 2020 - 05:26:26 PDT)
- Re: [AMBER] How does one build MMPBSA.py.MPI on a Centos 7 system? (Mon Oct 05 2020 - 12:53:39 PDT)
- Re: [AMBER] Compiling CPPTRAJ from GitHub (Mon Oct 05 2020 - 06:58:23 PDT)
- Re: [AMBER] RMSD of ligand in pocket (Sun Oct 04 2020 - 17:54:09 PDT)
- Re: [AMBER] image protein complex iwrap=1 (Fri Oct 02 2020 - 08:43:53 PDT)
- Re: [AMBER] Compiling CPPTRAJ from GitHub (Fri Oct 02 2020 - 08:34:48 PDT)
- Re: [AMBER] partial charges for modified nucleotide (Fri Oct 02 2020 - 08:31:00 PDT)
- Re: [AMBER] Error: Failed to generate parameters (Fri Oct 02 2020 - 08:26:38 PDT)
- Re: [AMBER] Query regarding Dialanine peptide 2d ABMD tutorial in the NFE category (Fri Oct 02 2020 - 08:19:45 PDT)
- Re: [AMBER] Error: Failed to generate parameters (Thu Oct 01 2020 - 13:45:02 PDT)
- Re: [AMBER] pmemd (Thu Oct 01 2020 - 13:40:41 PDT)
- Re: [AMBER] Modification of dihedral torsion potential (Thu Oct 01 2020 - 05:03:36 PDT)
David Cerutti
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs (Fri Oct 09 2020 - 09:41:08 PDT)
David Poole
- [AMBER] Permute dihedrals (Fri Oct 09 2020 - 04:40:53 PDT)
Debarati DasGupta
- Re: [AMBER] NMR restraints (Sat Oct 31 2020 - 07:46:15 PDT)
- Re: [AMBER] NMR restraints (Sat Oct 31 2020 - 05:54:14 PDT)
- Re: [AMBER] NMR restraints (Sat Oct 31 2020 - 05:40:45 PDT)
- [AMBER] NMR restraints (Fri Oct 30 2020 - 12:37:48 PDT)
- [AMBER] Is the amber website down? 9am EST (Thu Oct 22 2020 - 06:13:12 PDT)
- Re: [AMBER] TI not compatible with GB on GPU (Wed Oct 21 2020 - 07:46:07 PDT)
- Re: [AMBER] TI not compatible with GB on GPU (Wed Oct 21 2020 - 07:45:14 PDT)
- Re: [AMBER] TI not compatible with GB on GPU (Wed Oct 21 2020 - 05:21:46 PDT)
- Re: [AMBER] RMSD of ligand in pocket (Sun Oct 18 2020 - 08:05:42 PDT)
- Re: [AMBER] RMSD of ligand in pocket (Wed Oct 07 2020 - 16:03:08 PDT)
- Re: [AMBER] RMSD of ligand in pocket (Mon Oct 05 2020 - 05:16:53 PDT)
- Re: [AMBER] RMSD of ligand in pocket (Sun Oct 04 2020 - 06:55:41 PDT)
- [AMBER] RMSD of ligand in pocket (Sat Oct 03 2020 - 08:08:20 PDT)
Delwakkada Liyanage, Senal Dinuka
- Re: [AMBER] Amber TI - crgmask (Thu Oct 29 2020 - 08:16:23 PDT)
- [AMBER] Amber TI - crgmask (Wed Oct 28 2020 - 09:02:42 PDT)
- [AMBER] TI calculation input clarification (Tue Oct 27 2020 - 10:00:51 PDT)
- [AMBER] Using parmchk2 with GLYCAM_06j.dat (Tue Oct 13 2020 - 12:44:58 PDT)
DHEERAJ CHITARA
- [AMBER] Normalized eigen values (Thu Oct 29 2020 - 09:51:27 PDT)
divyabharathi korlepara
- [AMBER] Fwd: MMPBSA calculations with 1 explicit water molecule (Thu Oct 22 2020 - 11:01:31 PDT)
Dmitry Karlov
- [AMBER] usage of nmr (between COMs) restraints with pmem.cuda (Sun Oct 04 2020 - 06:57:55 PDT)
Dr. Anselm Horn
- Re: [AMBER] How to import (.pdb) files into xleap of AMBER generated by Cellulose builder (Thu Oct 29 2020 - 03:24:11 PDT)
- Re: [AMBER] Help with parameterization of non-standard amino acid (Wed Oct 28 2020 - 07:57:34 PDT)
- Re: [AMBER] doubt charges (Fri Oct 23 2020 - 08:28:58 PDT)
- Re: [AMBER] doubt charges (Fri Oct 23 2020 - 01:28:05 PDT)
- Re: [AMBER] pmemd (Fri Oct 02 2020 - 03:20:42 PDT)
Elvis Martis
- Re: [AMBER] Xleap error (Thu Oct 29 2020 - 03:26:34 PDT)
- Re: [AMBER] Cannot access amber website (Thu Oct 22 2020 - 08:44:27 PDT)
- Re: [AMBER] Creating a coordinate bond in Leap (Fri Oct 16 2020 - 22:10:59 PDT)
- Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? (Fri Oct 16 2020 - 19:24:00 PDT)
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd (Thu Oct 15 2020 - 22:31:45 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using (Wed Oct 07 2020 - 07:52:26 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using (Wed Oct 07 2020 - 05:40:39 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using (Mon Oct 05 2020 - 21:06:15 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using (Sun Oct 04 2020 - 09:31:39 PDT)
- Re: [AMBER] pmemd (Thu Oct 01 2020 - 09:49:36 PDT)
Emmett Leddin
- Re: [AMBER] Loading R.E.D server parameters into xleap (Fri Oct 16 2020 - 10:11:59 PDT)
- Re: [AMBER] Loading R.E.D server parameters into xleap (Fri Oct 16 2020 - 05:05:09 PDT)
Erik Zuiderweg
- Re: [AMBER] not writing restart file (Fri Oct 09 2020 - 03:57:55 PDT)
- [AMBER] not writing restart file (Thu Oct 08 2020 - 09:17:41 PDT)
Farkhad Maksudov
- [AMBER] partial charges for modified nucleotide (Thu Oct 01 2020 - 18:28:28 PDT)
Filip Fratev
- Re: [AMBER] A100 and RTX3090 Benchmarks (Tue Oct 06 2020 - 01:44:54 PDT)
gagandeep singh
- Re: [AMBER] doubt charges (Fri Oct 23 2020 - 06:27:09 PDT)
George M. Giambasu
- Re: [AMBER] Amber20 compilation issue (related to boost?) (Thu Oct 08 2020 - 20:25:18 PDT)
Gerald Monard
- Re: [AMBER] Which OS/Amber combinations are supported? (Mon Oct 05 2020 - 23:41:35 PDT)
German P. Barletta
- [AMBER] cpptraj's hbond shows hbonds with carbon hydrogens (Fri Oct 16 2020 - 13:03:50 PDT)
- [AMBER] cpptraj's hbond shows hbonds with carbon hydrogens (Thu Oct 15 2020 - 12:53:21 PDT)
- [AMBER] NVIDIA GeForce RTX 3080 GPUs (Sun Oct 11 2020 - 13:10:54 PDT)
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs (Ross Walker) (Sat Oct 10 2020 - 12:48:39 PDT)
Giulio Poli
- Re: [AMBER] R: mm-pbsa calculation (Wed Oct 28 2020 - 01:47:20 PDT)
Grant Keller
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd (Fri Oct 16 2020 - 10:40:46 PDT)
Gustaf Olsson
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Mon Oct 26 2020 - 01:21:15 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Mon Oct 26 2020 - 00:46:07 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Sat Oct 24 2020 - 12:49:30 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Fri Oct 23 2020 - 10:27:05 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Fri Oct 23 2020 - 10:23:56 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Fri Oct 23 2020 - 04:12:43 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Fri Oct 23 2020 - 02:26:05 PDT)
- Re: [AMBER] server issues 403 on ambermd.org (Thu Oct 22 2020 - 23:51:35 PDT)
- Re: [AMBER] Adding Ions (Thu Oct 22 2020 - 05:27:14 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Thu Oct 22 2020 - 02:27:13 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Thu Oct 22 2020 - 01:53:17 PDT)
- Re: [AMBER] Adding Ions (Thu Oct 22 2020 - 01:01:09 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Thu Oct 22 2020 - 00:10:34 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Wed Oct 21 2020 - 05:36:30 PDT)
- Re: [AMBER] Adding Ions (Wed Oct 21 2020 - 05:26:56 PDT)
- [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP (Wed Oct 21 2020 - 01:10:10 PDT)
- Re: [AMBER] Adding Ions (Wed Oct 21 2020 - 00:04:40 PDT)
- [AMBER] Adding Ions (Tue Oct 20 2020 - 05:56:08 PDT)
- Re: [AMBER] Compiling CPPTRAJ from GitHub (Thu Oct 08 2020 - 05:37:36 PDT)
- Re: [AMBER] Compiling CPPTRAJ from GitHub (Tue Oct 06 2020 - 02:28:30 PDT)
- Re: [AMBER] Compiling CPPTRAJ from GitHub (Tue Oct 06 2020 - 02:22:08 PDT)
- Re: [AMBER] Compiling CPPTRAJ from GitHub (Tue Oct 06 2020 - 02:00:32 PDT)
- Re: [AMBER] Compiling CPPTRAJ from GitHub (Mon Oct 05 2020 - 00:09:07 PDT)
- Re: [AMBER] Compiling CPPTRAJ from GitHub (Fri Oct 02 2020 - 05:06:43 PDT)
- [AMBER] Compiling CPPTRAJ from GitHub (Fri Oct 02 2020 - 03:53:11 PDT)
Gustavo Seabra
- Re: [AMBER] MCPB with OPC water? (Thu Oct 22 2020 - 17:11:19 PDT)
- Re: [AMBER] CPPTRAJ: Cluster structures keeping only one water, by position? (Fri Oct 09 2020 - 15:10:23 PDT)
- [AMBER] CPPTRAJ: Cluster structures keeping only one water, by position? (Fri Oct 09 2020 - 11:14:59 PDT)
h_sahakyan.mb.sci.am
- [AMBER] MM/PBSA after minimization (Thu Oct 29 2020 - 12:56:21 PDT)
- [AMBER] controversy in PBSA and GBSA results (Tue Oct 20 2020 - 05:27:05 PDT)
- [AMBER] controversy in PBSA and GBSA results (Wed Oct 07 2020 - 06:19:19 PDT)
- [AMBER] controversy in PBSA and GBSA results (Mon Oct 05 2020 - 09:04:26 PDT)
- [AMBER] controversy in PBSA and GBSA results (Sun Oct 04 2020 - 22:28:30 PDT)
- Re: [AMBER] controversy in PBSA and GBSA results (Wed Sep 30 2020 - 23:32:19 PDT)
- Re: [AMBER] controversy in PBSA and GBSA results (Wed Sep 30 2020 - 21:16:05 PDT)
Hai Nguyen
- Re: [AMBER] Conda installation of AmberTools (Mon Oct 12 2020 - 09:54:35 PDT)
- Re: [AMBER] Problems with using pdb4amber (and possibly other programs) on Ubuntu 20.04 (Wed Oct 07 2020 - 14:36:38 PDT)
Hamed S. Hayatshahi
- [AMBER] How does one build MMPBSA.py.MPI on a Centos 7 system? (Mon Oct 05 2020 - 12:30:44 PDT)
- Re: [AMBER] MMPBSA.py TypeError: a bytes-like object is required, not 'str' (Mon Oct 05 2020 - 11:15:06 PDT)
James Kress
- Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule (Mon Oct 12 2020 - 15:52:51 PDT)
Jason Hogrefe
- [AMBER] AMBER 20 Benchmarks on NVIDIA RTX 3080/3090 and more (Mon Oct 26 2020 - 15:26:13 PDT)
Jatin Kashyap
- [AMBER] ERROR: The file contained 14 atoms not in residue templates (Thu Oct 08 2020 - 12:28:14 PDT)
- Re: [AMBER] Hitting the supercomputer wall limit before completion of minimization step (Mon Oct 05 2020 - 09:25:13 PDT)
- [AMBER] Hitting the supercomputer wall limit before completion of minimization step (Mon Oct 05 2020 - 08:28:44 PDT)
- Re: [AMBER] Error: Failed to generate parameters (Thu Oct 01 2020 - 13:55:14 PDT)
- [AMBER] Error: Failed to generate parameters (Thu Oct 01 2020 - 09:57:17 PDT)
Jenny 148
- [AMBER] Creating a coordinate bond in Leap (Fri Oct 16 2020 - 21:53:54 PDT)
Jisha B
- [AMBER] Xleap error (Thu Oct 29 2020 - 02:17:22 PDT)
- Re: [AMBER] Adding catalytic Magnesium ion (Sat Oct 17 2020 - 03:22:48 PDT)
- [AMBER] Adding catalytic Magnesium ion (Thu Oct 15 2020 - 15:10:17 PDT)
Jonathan Gabriel Canan Gomez
- [AMBER] Amber performance (Tue Oct 06 2020 - 15:56:22 PDT)
Jorge Iulek
- Re: [AMBER] process_mdout.perl for pmemd (Sun Oct 18 2020 - 10:50:59 PDT)
- [AMBER] process_mdout.perl for pmemd (Sat Oct 17 2020 - 14:31:07 PDT)
Juraj Dobias
- Re: [AMBER] Amber TI - crgmask (Fri Oct 30 2020 - 03:39:02 PDT)
- Re: [AMBER] Amber TI - crgmask (Thu Oct 29 2020 - 02:04:50 PDT)
- Re: [AMBER] Adding catalytic Magnesium ion (Mon Oct 19 2020 - 00:27:50 PDT)
- Re: [AMBER] Cannot run NPT (Thu Oct 08 2020 - 04:21:35 PDT)
- Re: [AMBER] RMSD of ligand in pocket (Mon Oct 05 2020 - 05:32:31 PDT)
Kazuo Ohta
- Re: [AMBER] Error building Amber (Tue Oct 20 2020 - 19:08:05 PDT)
Kehinde Idowu
- Re: [AMBER] MD error (Mon Oct 19 2020 - 07:58:48 PDT)
- [AMBER] MD error (Sun Oct 18 2020 - 14:24:14 PDT)
Kenneth Huang
- Re: [AMBER] drms comparison in sander during minimization? (Thu Oct 22 2020 - 20:59:05 PDT)
- [AMBER] drms comparison in sander during minimization? (Wed Oct 21 2020 - 15:03:40 PDT)
- Re: [AMBER] partial charges for modified nucleotide (Fri Oct 02 2020 - 17:36:31 PDT)
Kevin Keane
- [AMBER] Which OS/Amber combinations are supported? (Mon Oct 05 2020 - 13:06:37 PDT)
Kraus, Sebastian
- [AMBER] Amber20: Ampere microarchitecture support and Amber release in 2021 (Tue Oct 27 2020 - 00:36:28 PDT)
- [AMBER] Amber20: Ampere microarchitecture support and next Amber release (Mon Oct 26 2020 - 12:18:42 PDT)
Lang,Lijun
- [AMBER] Cannot access amber website (Thu Oct 22 2020 - 08:13:11 PDT)
Liao
- Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? (Fri Oct 16 2020 - 14:30:45 PDT)
- Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? (Thu Oct 15 2020 - 07:54:31 PDT)
- [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? (Tue Oct 13 2020 - 11:29:23 PDT)
Loo Kang
- [AMBER] Bacteria cell membrane PDB (Mon Oct 19 2020 - 20:06:53 PDT)
Luka Bilić
- Re: [AMBER] Amber20 installation for MPI, CUDA issues. (Fri Oct 30 2020 - 03:30:45 PDT)
- [AMBER] Amber20 installation for MPI, CUDA issues. (Thu Oct 29 2020 - 12:38:15 PDT)
Madhur Aggarwal
- [AMBER] RMSD (non mass-weighted) as collective variable in Amber-18 (Sun Oct 18 2020 - 14:20:09 PDT)
Marcelo Andrade Chagas
- [AMBER] amber14 and amber16 are not working in new installation (Fri Oct 23 2020 - 19:31:47 PDT)
Margareta Hellmann
- [AMBER] Different atomic partial charges on OD1/OD2 (Mon Oct 05 2020 - 07:59:37 PDT)
Mariangela Dametto
- Re: [AMBER] Problem in AMBER18 Installation (Thu Oct 01 2020 - 09:58:09 PDT)
Mariano Curti
- Re: [AMBER] Prmtop for protein + 2 identical ligands has wrong dihedral parameters for the second ligand. LEaP bug? (Mon Oct 26 2020 - 02:18:33 PDT)
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd (Fri Oct 16 2020 - 00:01:56 PDT)
Matias Machado
- Re: [AMBER] Changing lj_radius without changing lj_14_radius (Mon Oct 26 2020 - 14:43:38 PDT)
- Re: [AMBER] Changing lj_radius without changing lj_14_radius (Thu Oct 22 2020 - 07:43:42 PDT)
- Re: [AMBER] Changing lj_radius without changing lj_14_radius (Wed Oct 21 2020 - 11:25:38 PDT)
- Re: [AMBER] Adding Ions (Wed Oct 21 2020 - 10:22:20 PDT)
- Re: [AMBER] [External] Re: Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT (Sat Oct 03 2020 - 09:00:54 PDT)
- Re: [AMBER] Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT (Thu Oct 01 2020 - 05:58:33 PDT)
Michele Vanini
- [AMBER] Problem with acpype (Sat Oct 31 2020 - 02:08:54 PDT)
- Re: [AMBER] CO2 (Wed Oct 28 2020 - 12:20:17 PDT)
- [AMBER] CO2 (Wed Oct 28 2020 - 09:55:40 PDT)
Mike Mazanetz
- Re: [AMBER] AMBER 20 Benchmarks on NVIDIA RTX 3080/3090 and more (Tue Oct 27 2020 - 03:40:10 PDT)
- [AMBER] server issues 403 on ambermd.org (Thu Oct 22 2020 - 06:49:11 PDT)
- Re: [AMBER] NVIDIA GeForce RTX 3090 GPUs (Thu Oct 22 2020 - 05:11:35 PDT)
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs (Sat Oct 10 2020 - 13:26:06 PDT)
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs (Fri Oct 09 2020 - 10:23:33 PDT)
- [AMBER] NVIDIA GeForce RTX 3080 GPUs (Fri Oct 09 2020 - 08:36:46 PDT)
mohamed marzouk
- [AMBER] Force field for IDP (Thu Oct 29 2020 - 08:31:29 PDT)
- Re: [AMBER] RMSD, Rg density map (Tue Oct 20 2020 - 20:17:58 PDT)
- Re: [AMBER] RMSD, Rg density map (Tue Oct 20 2020 - 11:06:36 PDT)
- Re: [AMBER] RMSD, Rg density map (Fri Oct 16 2020 - 09:57:45 PDT)
- [AMBER] RMSD, Rg density map (Mon Oct 12 2020 - 11:00:45 PDT)
- Re: [AMBER] Cannot run NPT (Mon Oct 12 2020 - 10:45:54 PDT)
- Re: [AMBER] Cannot run NPT (Wed Oct 07 2020 - 19:41:01 PDT)
- [AMBER] Cannot run NPT (Wed Oct 07 2020 - 07:05:56 PDT)
MR. RABINDRANATH PAUL
- Re: [AMBER] Constant Force SMD simulation (Thu Oct 29 2020 - 21:55:21 PDT)
mukesh raval
- [AMBER] Conda installation of AmberTools (Sat Oct 10 2020 - 21:00:54 PDT)
MYRIAN TORRES RICO
- Re: [AMBER] mmpbsa error (Tue Oct 27 2020 - 01:37:12 PDT)
- Re: [AMBER] mmpbsa error (Mon Oct 26 2020 - 10:30:43 PDT)
- [AMBER] mmpbsa error (Mon Oct 26 2020 - 05:53:47 PDT)
- Re: [AMBER] doubt charges (Mon Oct 26 2020 - 02:15:27 PDT)
- Re: [AMBER] doubt charges (Mon Oct 26 2020 - 02:11:53 PDT)
- Re: [AMBER] doubt charges (Fri Oct 23 2020 - 07:10:55 PDT)
- Re: [AMBER] doubt charges (Fri Oct 23 2020 - 05:30:26 PDT)
- [AMBER] doubt charges (Fri Oct 23 2020 - 01:11:27 PDT)
- [AMBER] MMPBS decomposition error (Wed Oct 21 2020 - 02:05:27 PDT)
Naxhije Berisha
- [AMBER] Is there a way to analyze contact maps of mixtures of more than 2 components? (Fri Oct 23 2020 - 10:44:52 PDT)
Neha Gandhi
- Re: [AMBER] [GaMD-discuss] GaMD (Sun Oct 25 2020 - 17:11:36 PDT)
- [AMBER] GaMD (Thu Oct 22 2020 - 15:30:03 PDT)
Nick Palmer
- Re: [AMBER] [External] Re: Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT (Thu Oct 01 2020 - 16:16:21 PDT)
Niel Henriksen
- Re: [AMBER] CPPTRAJ: Cluster structures keeping only one water, by position? (Fri Oct 09 2020 - 14:41:34 PDT)
Nisha Amarnath Jonniya
- [AMBER] Query regarding ion constraint in MD simulations (Sat Oct 03 2020 - 19:33:58 PDT)
Pandey Anwesh
- [AMBER] Installation of AMBER20 on CentOS 7 (Wed Oct 14 2020 - 06:53:31 PDT)
Pavlína Pokorná
- [AMBER] NOE analysis with cpptraj (Mon Oct 19 2020 - 06:17:47 PDT)
Pengfei Li
- Re: [AMBER] KeyError: 'H262' (Thu Oct 22 2020 - 15:32:52 PDT)
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) (Thu Oct 22 2020 - 14:36:01 PDT)
- Re: [AMBER] Tri-coordination environment in zinc (Thu Oct 22 2020 - 14:22:53 PDT)
- Re: [AMBER] Prmtop for protein + 2 identical ligands has wrong dihedral parameters for the second ligand. LEaP bug? (Thu Oct 22 2020 - 14:19:21 PDT)
- Re: [AMBER] ddikick.x error during Fe3+ ion parameter derivation using Gamess (Thu Oct 22 2020 - 14:14:09 PDT)
- Re: [AMBER] MCPB with OPC water? (Thu Oct 22 2020 - 13:59:34 PDT)
Piia Kokkonen
- Re: [AMBER] Amber20 and RNA simulations (Wed Oct 28 2020 - 05:22:05 PDT)
- [AMBER] Amber20 and RNA simulations (Wed Oct 28 2020 - 03:31:13 PDT)
Pinky Mazumder
- Re: [AMBER] How to import (.pdb) files into xleap of AMBER generated by Cellulose builder (Thu Oct 29 2020 - 09:58:46 PDT)
- Re: [AMBER] cellulose crystal structure ( cellulose bundles) (Thu Oct 29 2020 - 09:54:09 PDT)
- [AMBER] cellulose crystal structure ( cellulose bundles) (Thu Oct 29 2020 - 00:59:00 PDT)
- [AMBER] How to import (.pdb) files into xleap of AMBER generated by Cellulose builder (Wed Oct 28 2020 - 22:47:59 PDT)
Qing Lv
- [AMBER] Additional restraints in Umbrella sampling? (Thu Oct 01 2020 - 18:29:39 PDT)
Qinghua Liao
- Re: [AMBER] not writing restart file (Thu Oct 08 2020 - 09:20:35 PDT)
- [AMBER] REST2 in Amber (Mon Oct 05 2020 - 08:30:05 PDT)
Raman Preet Singh
- Re: [AMBER] CO2 (Wed Oct 28 2020 - 23:41:03 PDT)
- Re: [AMBER] CO2 (Wed Oct 28 2020 - 10:38:01 PDT)
Ray Luo
- Re: [AMBER] System preparation for MMPBSA.py (Fri Oct 30 2020 - 08:07:32 PDT)
- Re: [AMBER] Fwd: MMPBSA calculations with 1 explicit water molecule (Fri Oct 30 2020 - 08:02:45 PDT)
- Re: [AMBER] MMGBSA/MMPBSA Help (Fri Oct 30 2020 - 07:42:37 PDT)
- Re: [AMBER] controversy in PBSA and GBSA results (Tue Oct 20 2020 - 09:54:08 PDT)
- Re: [AMBER] controversy in PBSA and GBSA results (Wed Oct 07 2020 - 10:35:08 PDT)
- Re: [AMBER] controversy in PBSA and GBSA results (Wed Oct 07 2020 - 10:08:33 PDT)
- Re: [AMBER] controversy in PBSA and GBSA results (Wed Oct 07 2020 - 10:06:39 PDT)
- Re: [AMBER] controversy in PBSA and GBSA results (Mon Oct 05 2020 - 07:39:59 PDT)
- Re: [AMBER] MMPBSA.py TypeError: a bytes-like object is required, not 'str' (Thu Oct 01 2020 - 20:16:16 PDT)
Rodrigo Galindo-Murillo
- Re: [AMBER] process_mdout.perl for pmemd (Sat Oct 17 2020 - 14:45:44 PDT)
Ross Walker
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs (Ross Walker) (Sat Oct 10 2020 - 14:21:47 PDT)
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs (Sat Oct 10 2020 - 06:58:21 PDT)
- Re: [AMBER] Amber performance (Tue Oct 06 2020 - 16:19:45 PDT)
- Re: [AMBER] A100 and RTX3090 Benchmarks (Tue Oct 06 2020 - 10:31:45 PDT)
- Re: [AMBER] A100 and RTX3090 Benchmarks (Tue Oct 06 2020 - 10:13:48 PDT)
sangita kachhap
- Re: [AMBER] NAMD trajectory analysis with cpptraj (Sat Oct 17 2020 - 02:53:29 PDT)
- [AMBER] NAMD trajectory analysis with cpptraj (Fri Oct 16 2020 - 12:35:39 PDT)
Sarah Jane
- [AMBER] Bond: Maximum coordination exceeded (Sun Oct 18 2020 - 11:21:45 PDT)
- [AMBER] QMMM SCC-DFTB: Convergence could not be achieved (Wed Oct 07 2020 - 10:22:46 PDT)
SATYAJIT KHATUA
- Re: [AMBER] Tri-coordination environment in zinc (Thu Oct 29 2020 - 22:39:20 PDT)
- [AMBER] System preparation for MMPBSA.py (Mon Oct 26 2020 - 21:29:12 PDT)
- [AMBER] Metalloprotein-ligand complex modelling for MMPBSA.py (Mon Oct 19 2020 - 00:59:36 PDT)
- [AMBER] Fwd: AMBER Digest, Vol 3153, Issue 1 (Thu Oct 15 2020 - 21:59:05 PDT)
- [AMBER] Query about using MMPBSA.py to calculate the binding free energy for a ligand bound enzyme (Thu Oct 15 2020 - 09:41:54 PDT)
Scott Brozell
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler (Fri Oct 30 2020 - 13:47:02 PDT)
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler (Wed Oct 21 2020 - 16:04:20 PDT)
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler (Tue Oct 20 2020 - 14:37:31 PDT)
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler (Mon Oct 19 2020 - 19:10:10 PDT)
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler (Mon Oct 19 2020 - 18:44:09 PDT)
Seibold, Steve Allan
- [AMBER] installing Amber18 and AmberTools20 (Wed Oct 21 2020 - 10:40:43 PDT)
- Re: [AMBER] AMBER16 problem (Wed Oct 21 2020 - 10:08:17 PDT)
- [AMBER] AMBER16 problem (Tue Oct 20 2020 - 07:56:20 PDT)
- Re: [AMBER] rms(d) or (f) per residue (Sat Oct 17 2020 - 05:01:36 PDT)
- Re: [AMBER] rms(d) or (f) per residue (Fri Oct 16 2020 - 10:21:58 PDT)
- [AMBER] rms(d) or (f) per residue (Fri Oct 16 2020 - 09:51:09 PDT)
Serena Vittorio
- [AMBER] R: mm-pbsa calculation (Mon Oct 19 2020 - 02:36:36 PDT)
- [AMBER] mm-pbsa calculation: SA Bomb in circle(): Stored surface arcs over limit (Mon Oct 19 2020 - 01:27:56 PDT)
- [AMBER] mm-pbsa calculation (Fri Oct 16 2020 - 09:21:24 PDT)
SHAUNAK BADANI
- Re: [AMBER] Query regarding Dialanine peptide 2d ABMD tutorial in the NFE category (Thu Oct 01 2020 - 13:26:28 PDT)
somdev pahari
- Re: [AMBER] PMF calculation (Thu Oct 15 2020 - 10:11:28 PDT)
Sruthi Sudhakar
- Re: [AMBER] Loading R.E.D server parameters into xleap (Fri Oct 16 2020 - 06:12:44 PDT)
- [AMBER] Loading R.E.D server parameters into xleap (Fri Oct 16 2020 - 02:50:13 PDT)
Suchetana Gupta
- Re: [AMBER] R: mm-pbsa calculation (Tue Oct 27 2020 - 22:21:26 PDT)
- Re: [AMBER] mm-pbsa calculation (Sun Oct 18 2020 - 00:13:36 PDT)
- [AMBER] Fwd: MMGBSA Ligand Mask issues (Wed Oct 14 2020 - 05:17:22 PDT)
- [AMBER] MMGBSA Ligand Mask issues (Tue Oct 13 2020 - 03:03:31 PDT)
- Re: [AMBER] Fwd: Imaging issues with cpptraj (Wed Oct 07 2020 - 00:12:36 PDT)
- Re: [AMBER] Fwd: Imaging issues with cpptraj (Tue Oct 06 2020 - 23:56:51 PDT)
- [AMBER] Fwd: Imaging issues with cpptraj (Tue Oct 06 2020 - 21:43:51 PDT)
- [AMBER] Imaging issues with cpptraj (Tue Oct 06 2020 - 00:09:41 PDT)
Suman Chakrabarty
- Re: [AMBER] Amber20 compilation issue (related to boost?) (Fri Oct 09 2020 - 02:35:46 PDT)
- [AMBER] Amber20 compilation issue (related to boost?) (Wed Oct 07 2020 - 23:07:08 PDT)
SUNITA MUDULI
- [AMBER] Adding missing residues in a pdb file using tleap (Sun Oct 18 2020 - 12:14:01 PDT)
Thomas Cheatham
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference (Thu Oct 08 2020 - 16:37:23 PDT)
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference (Wed Oct 07 2020 - 16:17:10 PDT)
Tom Wang
- [AMBER] Amber20 compiling warning (Sun Oct 18 2020 - 05:40:44 PDT)
Tru Huynh
- Re: [AMBER] Trouble installing pbsa cuda code (Thu Oct 22 2020 - 14:09:32 PDT)
Vaibhav Dixit
- Re: [AMBER] how find Es from mdout to estimate vertical energy gap (Fri Oct 30 2020 - 13:56:58 PDT)
- Re: [AMBER] how find Es from mdout to estimate vertical energy gap (Fri Oct 30 2020 - 13:20:58 PDT)
- [AMBER] how find Es from mdout to estimate vertical energy gap (Fri Oct 30 2020 - 10:05:07 PDT)
- Re: [AMBER] a metal bound Met (Wed Oct 28 2020 - 18:31:06 PDT)
- Re: [AMBER] correct md-input & prmtop for TI calculations (Mon Oct 26 2020 - 03:47:15 PDT)
- Re: [AMBER] TI not compatible with GB on GPU (Thu Oct 22 2020 - 02:29:55 PDT)
- [AMBER] correct md-input & prmtop for TI calculations (Thu Oct 22 2020 - 02:27:55 PDT)
- Re: [AMBER] TI not compatible with GB on GPU (Wed Oct 21 2020 - 23:52:56 PDT)
- Re: [AMBER] TI not compatible with GB on GPU (Wed Oct 21 2020 - 05:59:26 PDT)
- Re: [AMBER] AmberMdPrep github cpptraj not sourced (Wed Oct 21 2020 - 04:37:06 PDT)
- [AMBER] TI not compatible with GB on GPU (Tue Oct 20 2020 - 02:27:07 PDT)
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd (Thu Oct 15 2020 - 22:50:00 PDT)
- [AMBER] assess which structures are similar between two MD-trajectories (Wed Oct 14 2020 - 20:51:04 PDT)
- Re: [AMBER] AmberMdPrep github cpptraj not sourced (Fri Oct 09 2020 - 17:30:17 PDT)
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference (Wed Oct 07 2020 - 17:03:46 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using (Wed Oct 07 2020 - 16:43:25 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using (Wed Oct 07 2020 - 06:47:17 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using (Wed Oct 07 2020 - 01:57:52 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using (Mon Oct 05 2020 - 21:16:18 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using (Mon Oct 05 2020 - 20:56:51 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using (Sun Oct 04 2020 - 09:15:12 PDT)
- [AMBER] cpptraj unable to write pdb files using (Sat Oct 03 2020 - 21:32:46 PDT)
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference (Sat Oct 03 2020 - 06:29:12 PDT)
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference (Fri Oct 02 2020 - 14:12:32 PDT)
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference (Fri Oct 02 2020 - 08:42:28 PDT)
- [AMBER] how to use one prmtop for two trajectories with just one ion difference (Fri Oct 02 2020 - 07:55:35 PDT)
viktor
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd (Fri Oct 16 2020 - 04:27:32 PDT)
Vishal Singh
- Re: [AMBER] Constant Force SMD simulation (Thu Oct 29 2020 - 22:07:42 PDT)
- [AMBER] Constant Force SMD simulation (Thu Oct 29 2020 - 21:05:24 PDT)
- [AMBER] Steered MD at constant force (Mon Oct 26 2020 - 05:15:01 PDT)
- [AMBER] Steered MD at constant force (Mon Oct 19 2020 - 05:28:49 PDT)
Vlad Cojocaru
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler (Fri Oct 23 2020 - 01:28:11 PDT)
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler (Wed Oct 21 2020 - 04:31:27 PDT)
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler (Tue Oct 20 2020 - 07:46:37 PDT)
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler (Tue Oct 20 2020 - 04:37:59 PDT)
- [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler (Mon Oct 19 2020 - 10:47:43 PDT)
Wesley Michael Botello-Smith
- Re: [AMBER] Trouble installing pbsa cuda code (Fri Oct 23 2020 - 20:32:39 PDT)
- [AMBER] Trouble installing pbsa cuda code (Thu Oct 22 2020 - 11:47:41 PDT)
Wu Xu
- Re: [AMBER] a metal bound Met (Wed Oct 28 2020 - 18:41:39 PDT)
- [AMBER] a metal bound Met (Wed Oct 28 2020 - 12:33:18 PDT)
- Re: [AMBER] KeyError: 'H262' (Fri Oct 23 2020 - 18:57:32 PDT)
- Re: [AMBER] KeyError: 'H262' (Thu Oct 22 2020 - 20:09:03 PDT)
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd (Fri Oct 16 2020 - 19:36:23 PDT)
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd (Fri Oct 16 2020 - 05:46:11 PDT)
- [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd (Thu Oct 15 2020 - 21:23:17 PDT)
- [AMBER] KeyError: 'H262' (Thu Oct 15 2020 - 20:25:27 PDT)
Állan Ferrari
- Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros (Thu Oct 15 2020 - 07:11:40 PDT)
- Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros (Thu Oct 15 2020 - 06:26:08 PDT)
- Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros (Wed Oct 14 2020 - 12:57:44 PDT)
- [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros (Tue Oct 13 2020 - 07:07:53 PDT)
سید حامد سادات حیاتشاهی
- [AMBER] MMPBSA.py TypeError: a bytes-like object is required, not 'str' (Thu Oct 01 2020 - 13:52:28 PDT)

Amber Archive Oct 2020 by author