Amber Archive Dec 2018: by author

Aashish Bhatt
- Re: [AMBER] RESP charge calculation (Mon Dec 10 2018 - 02:54:14 PST)
Akshay Prabhakant
- Re: [AMBER] Axis of a helix as a collective variable (Thu Dec 20 2018 - 19:24:06 PST)
- Re: [AMBER] Axis of a helix as a collective variable (Thu Dec 20 2018 - 09:30:14 PST)
- [AMBER] Axis of a helix as a collective variable (Thu Dec 20 2018 - 09:13:26 PST)
- [AMBER] info on trajectory files (Wed Dec 19 2018 - 01:14:59 PST)
- [AMBER] error on equilibriation (Tue Dec 18 2018 - 07:55:10 PST)
Alan
- Re: [AMBER] Acpype related problem : topology for GROMACS (Mon Dec 17 2018 - 07:26:36 PST)
- Re: [AMBER] Acpype related problem : topology for GROMACS (Mon Dec 17 2018 - 01:24:12 PST)
Alex Spasic
- Re: [AMBER] Obtaining contact maps with cpptraj (Tue Dec 04 2018 - 12:25:22 PST)
Alfredo Quevedo
- Re: [AMBER] using sander in Xeon Phi (Wed Dec 12 2018 - 14:03:07 PST)
- [AMBER] using sander in Xeon Phi (Wed Dec 12 2018 - 13:29:12 PST)
andreas.tosstorff.cup.uni-muenchen.de
- [AMBER] Fatty acid ester parameter file (Mon Dec 10 2018 - 13:28:06 PST)
Angew Chemie
- [AMBER] stapled peptide- PDB bond atom problem (Mon Dec 03 2018 - 08:45:08 PST)
Anthony Bogetti
- [AMBER] Simulating a DNA Double helix with a mutated base pair (Tue Dec 18 2018 - 08:43:11 PST)
anthonycruzpr
- Re: [AMBER] GIST calculation on NAMD-generated trajectory (Wed Dec 12 2018 - 15:42:11 PST)
Antoine MARION
- Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF (Wed Dec 05 2018 - 02:16:12 PST)
- Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF (Tue Dec 04 2018 - 06:22:56 PST)
Asma Abro
- Re: [AMBER] CUDA test failure (Mon Dec 17 2018 - 06:33:42 PST)
- [AMBER] CUDA test failure (Sun Dec 16 2018 - 23:22:47 PST)
Baker, Joseph
- Re: [AMBER] Lipid NMR order parameters (Sun Dec 16 2018 - 16:59:48 PST)
Bellesis, Andrew G
- [AMBER] Testing AMBER16 installation in parallel; possible bug in testing scripts (Fri Dec 21 2018 - 12:56:46 PST)
- [AMBER] Error when installing AMBER16 (Thu Dec 13 2018 - 09:55:38 PST)
Bill Ross
- Re: [AMBER] FATAL Error: Atom does not have a type (Thu Dec 27 2018 - 04:07:32 PST)
- Re: [AMBER] regarding G-quadraplex (Mon Dec 24 2018 - 05:12:36 PST)
- Re: [AMBER] Amber18 compilation error on a Linux CPU cluster (Sun Dec 23 2018 - 11:17:50 PST)
- Re: [AMBER] ACE (Thu Dec 20 2018 - 03:05:42 PST)
- Re: [AMBER] ACE (Thu Dec 20 2018 - 02:39:23 PST)
- [AMBER] CUDA bootstrap site (Wed Dec 19 2018 - 20:05:59 PST)
- Re: [AMBER] amd running error (Mon Dec 17 2018 - 23:52:38 PST)
- Re: [AMBER] CUDA test failure (Sun Dec 16 2018 - 23:42:35 PST)
- Re: [AMBER] Acpype related problem : topology for GROMACS (Sun Dec 16 2018 - 18:48:27 PST)
- Re: [AMBER] Acpype related problem : topology for GROMACS (Sun Dec 16 2018 - 06:10:07 PST)
- Re: [AMBER] strange line between protein chains (Thu Dec 13 2018 - 10:25:55 PST)
- Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??) (Mon Dec 10 2018 - 03:22:59 PST)
- Re: [AMBER] minimization difficulties (Mon Dec 03 2018 - 03:10:05 PST)
- Re: [AMBER] TUTORIAL (Mon Dec 03 2018 - 03:05:37 PST)
- Re: [AMBER] TUTORIAL (Mon Dec 03 2018 - 02:44:42 PST)
- Re: [AMBER] TUTORIAL (Mon Dec 03 2018 - 02:24:26 PST)
Bin Sun
- Re: [AMBER] GIST calculation on NAMD-generated trajectory (Thu Dec 13 2018 - 11:57:19 PST)
- Re: [AMBER] GIST calculation on NAMD-generated trajectory (Thu Dec 13 2018 - 11:55:14 PST)
- [AMBER] GIST calculation on NAMD-generated trajectory (Tue Dec 11 2018 - 11:52:48 PST)
Brian Radak
- Re: [AMBER] vdwmeth (Sat Dec 08 2018 - 07:15:34 PST)
- Re: [AMBER] vdwmeth (Fri Dec 07 2018 - 11:44:59 PST)
Casalini Tommaso
- [AMBER] Ris: Ris: Extracting PDBs every 'N" ns (Sun Dec 02 2018 - 08:02:03 PST)
- [AMBER] Ris: Extracting PDBs every 'N" ns (Sun Dec 02 2018 - 07:45:16 PST)
Chang Woon Jang
- Re: [AMBER] Missing gaff parameters for epoxy ring (Tue Dec 18 2018 - 09:29:23 PST)
- [AMBER] Missing gaff parameters for epoxy ring (Mon Dec 17 2018 - 15:07:09 PST)
changseo park
- [AMBER] Too much comparisons failed for test_at_parallel (Tue Dec 18 2018 - 04:07:28 PST)
Charu Sharma (JRF)
- [AMBER] regarding G-quadraplex (Mon Dec 24 2018 - 04:31:18 PST)
- [AMBER] mpi (Thu Dec 20 2018 - 22:04:44 PST)
- [AMBER] regarding graph saving in JPEG (Wed Dec 05 2018 - 03:41:05 PST)
- Re: [AMBER] TUTORIAL (Mon Dec 03 2018 - 02:53:05 PST)
- Re: [AMBER] TUTORIAL (Mon Dec 03 2018 - 02:34:12 PST)
- [AMBER] TUTORIAL (Mon Dec 03 2018 - 01:54:35 PST)
Chhaya Singh
- [AMBER] Cpptraj usage (Tue Dec 04 2018 - 14:16:01 PST)
Christina Bergonzo
- Re: [AMBER] Include bound ions as part of the receptor molecule in MMPBSA.py (Thu Dec 06 2018 - 05:34:21 PST)
Cruzeiro,Vinicius Wilian D
- Re: [AMBER] cpin file format issue in production run (Fri Dec 21 2018 - 06:58:25 PST)
Daniel Roe
- Re: [AMBER] MD Analysis - Consistency (Fri Dec 28 2018 - 06:33:39 PST)
- Re: [AMBER] Amber18 compilation error on a Linux CPU cluster (Fri Dec 28 2018 - 06:24:47 PST)
- Re: [AMBER] All Energy Calculations in AMBER18. (Fri Dec 28 2018 - 06:21:01 PST)
- Re: [AMBER] constant dieletcric (Fri Dec 28 2018 - 06:06:51 PST)
- Re: [AMBER] Problems calculating self diffusion coefficient of water (Fri Dec 21 2018 - 12:04:39 PST)
- Re: [AMBER] Lipid NMR order parameters (Fri Dec 21 2018 - 11:46:00 PST)
- Re: [AMBER] Total energy of glycan simulation is postive (Fri Dec 21 2018 - 05:49:55 PST)
- Re: [AMBER] Problems modifing box lengths in a .rst file. (Tue Dec 18 2018 - 09:18:14 PST)
- Re: [AMBER] Problems modifing box lengths in a .rst file. (Mon Dec 17 2018 - 10:59:54 PST)
- Re: [AMBER] Problems modifing box lengths in a .rst file. (Mon Dec 17 2018 - 09:13:53 PST)
- Re: [AMBER] GIST calculation on NAMD-generated trajectory (Thu Dec 13 2018 - 11:59:00 PST)
- Re: [AMBER] GIST calculation on NAMD-generated trajectory (Wed Dec 12 2018 - 17:40:08 PST)
- Re: [AMBER] GBSA error (Wed Dec 12 2018 - 08:45:20 PST)
- Re: [AMBER] Size limit for amber (Wed Dec 12 2018 - 08:01:26 PST)
- Re: [AMBER] GIST calculation on NAMD-generated trajectory (Wed Dec 12 2018 - 07:58:30 PST)
- Re: [AMBER] Minimisation and periodic boundaries (Mon Dec 10 2018 - 06:37:06 PST)
- Re: [AMBER] Cpptraj usage (Mon Dec 10 2018 - 06:34:28 PST)
- Re: [AMBER] Ptraj Command not found. (Mon Dec 10 2018 - 06:04:30 PST)
- Re: [AMBER] AMBER18 Update Fail (AmberTools Update.10) (Fri Dec 07 2018 - 05:21:33 PST)
- Re: [AMBER] Linear Interaction Energy (Mon Dec 03 2018 - 12:50:03 PST)
- Re: [AMBER] Minimisation and periodic boundaries. (Mon Dec 03 2018 - 12:21:16 PST)
- Re: [AMBER] Obtaining contact maps with cpptraj (Mon Dec 03 2018 - 12:14:13 PST)
- Re: [AMBER] cpptraj error (Mon Dec 03 2018 - 11:23:50 PST)
- Re: [AMBER] Extracting PDBs every 'N" ns (Mon Dec 03 2018 - 11:14:20 PST)
David A Case
- Re: [AMBER] HMR 4fs error. (Mon Dec 31 2018 - 04:49:22 PST)
- Re: [AMBER] Total energy of glycan simulation is postive (Fri Dec 21 2018 - 06:00:12 PST)
- Re: [AMBER] mpi (Fri Dec 21 2018 - 05:57:34 PST)
- Re: [AMBER] Amber18 compilation error on a Linux CPU cluster (Thu Dec 20 2018 - 04:54:07 PST)
- Re: [AMBER] Too much comparisons failed for test_at_parallel (Tue Dec 18 2018 - 09:15:46 PST)
- Re: [AMBER] Simulating a DNA Double helix with a mutated base pair (Tue Dec 18 2018 - 09:10:33 PST)
- Re: [AMBER] Missing gaff parameters for epoxy ring (Tue Dec 18 2018 - 05:21:49 PST)
- Re: [AMBER] Problems modifing box lengths in a .rst file. (Tue Dec 18 2018 - 05:18:52 PST)
- Re: [AMBER] Query regarding the internal energy of protein. (Mon Dec 17 2018 - 05:34:56 PST)
- Re: [AMBER] AMBER16 re-installation problem (Mon Dec 17 2018 - 05:31:09 PST)
- Re: [AMBER] CUDA test failure (Mon Dec 17 2018 - 05:21:33 PST)
- Re: [AMBER] DOi for Amber 2017 (Mon Dec 17 2018 - 05:13:28 PST)
- Re: [AMBER] Acpype related problem : topology for GROMACS (Mon Dec 17 2018 - 05:13:01 PST)
- Re: [AMBER] strange line between protein chains (Thu Dec 13 2018 - 09:45:30 PST)
- Re: [AMBER] using sander in Xeon Phi (Thu Dec 13 2018 - 09:42:41 PST)
- Re: [AMBER] PSF file generation for heme and hydrogen peroxide (Thu Dec 13 2018 - 05:25:10 PST)
- Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??) (Tue Dec 11 2018 - 10:31:15 PST)
- Re: [AMBER] Reading Amber-generated NetCDF files using python (Tue Dec 11 2018 - 04:49:04 PST)
- Re: [AMBER] How to get the jac.restrt？ (Tue Dec 11 2018 - 04:46:36 PST)
- Re: [AMBER] amber12 install problem (Tue Dec 11 2018 - 04:41:21 PST)
- Re: [AMBER] Calculate the conduct rate from PMF (Mon Dec 10 2018 - 10:41:29 PST)
- Re: [AMBER] Size limit for amber (Mon Dec 10 2018 - 10:34:30 PST)
- Re: [AMBER] Backbone position restraints as a group (Thu Dec 06 2018 - 06:12:04 PST)
- Re: [AMBER] numpy related problem in amber (Thu Dec 06 2018 - 06:01:57 PST)
- Re: [AMBER] tleap does not add OXT when I load a crystal structure (Thu Dec 06 2018 - 05:57:53 PST)
- Re: [AMBER] regarding graph saving in JPEG (Wed Dec 05 2018 - 05:08:50 PST)
- Re: [AMBER] stapled peptide- PDB bond atom problem (Mon Dec 03 2018 - 10:17:07 PST)
- Re: [AMBER] minimization difficulties (Mon Dec 03 2018 - 07:05:32 PST)
David Case
- Re: [AMBER] multiconformational respgen with fixed charges and gcc 4.8 (Sun Dec 30 2018 - 06:06:28 PST)
- Re: [AMBER] compilation error AMBER16 (Thu Dec 27 2018 - 12:56:06 PST)
- Re: [AMBER] TI method with combination of restrained MD in pmemd.cuda of AMBER18 (Thu Dec 27 2018 - 06:25:54 PST)
- Re: [AMBER] FATAL Error: Atom does not have a type (Wed Dec 26 2018 - 18:35:33 PST)
- Re: [AMBER] Calculation of Hbond energy (Tue Dec 25 2018 - 14:42:48 PST)
- Re: [AMBER] Testing AMBER16 installation in parallel; possible bug in testing scripts (Sat Dec 22 2018 - 14:22:54 PST)
- Re: [AMBER] Query regarding force field (Sat Dec 15 2018 - 18:04:32 PST)
- Re: [AMBER] ligand charges for md (Sun Dec 09 2018 - 13:08:51 PST)
- Re: [AMBER] Dear AMBER members, (Sun Dec 09 2018 - 05:39:56 PST)
- Re: [AMBER] vdwmeth (Sat Dec 08 2018 - 08:11:02 PST)
- Re: [AMBER] AMBER18 Update Fail (AmberTools Update.10) (Sat Dec 08 2018 - 08:09:00 PST)
- Re: [AMBER] thermostat on solvent (Thu Dec 06 2018 - 19:04:46 PST)
- Re: [AMBER] Strange TIP3P solvent box distortions in Amber 18 with Mg2+, but no MG (Thu Dec 06 2018 - 19:02:59 PST)
- Re: [AMBER] tleap does not add OXT when I load a crystal structure (Wed Dec 05 2018 - 18:22:26 PST)
- Re: [AMBER] Ambiguous interfaces in generic interface (Wed Dec 05 2018 - 18:14:38 PST)
- Re: [AMBER] Extracting PDBs every 'N" ns (Sun Dec 02 2018 - 11:40:27 PST)
David Cerutti
- Re: [AMBER] ACE (Thu Dec 20 2018 - 02:44:02 PST)
- Re: [AMBER] Problems modifing box lengths in a .rst file. (Tue Dec 18 2018 - 09:44:56 PST)
- Re: [AMBER] AMBER18 on RTX 2080Ti (Mon Dec 17 2018 - 19:37:48 PST)
- Re: [AMBER] AMBER18 on RTX 2080Ti (Fri Dec 14 2018 - 18:01:31 PST)
- Re: [AMBER] AMBER18 on RTX 2080Ti (Fri Dec 14 2018 - 15:09:21 PST)
- Re: [AMBER] Strange TIP3P solvent box distortions in Amber 18 with Mg2+ (Thu Dec 06 2018 - 12:32:55 PST)
- Re: [AMBER] tleap does not add OXT when I load a crystal structure (Wed Dec 05 2018 - 16:40:21 PST)
David Sáez
- [AMBER] DOi for Amber 2017 (Sun Dec 16 2018 - 12:30:41 PST)
Debostuti Ghoshdastidar
- Re: [AMBER] Reading Amber-generated NetCDF files using python (Tue Dec 11 2018 - 22:21:03 PST)
- Re: [AMBER] Reading Amber-generated NetCDF files using python (Tue Dec 11 2018 - 22:17:10 PST)
- Re: [AMBER] Reading Amber-generated NetCDF files using python (Tue Dec 11 2018 - 04:22:39 PST)
- [AMBER] Reading Amber-generated NetCDF files using python (Mon Dec 10 2018 - 23:16:28 PST)
dhaval patel
- Re: [AMBER] ligand charges for md (Fri Dec 21 2018 - 21:23:04 PST)
DHEERAJ CHITARA
- [AMBER] All Energy Calculations in AMBER18. (Tue Dec 25 2018 - 05:58:19 PST)
Dr. Anselm Horn
- Re: [AMBER] info on trajectory files (Wed Dec 19 2018 - 02:12:01 PST)
Elvis Martis
- Re: [AMBER] FATAL Error: Atom does not have a type (Tue Dec 25 2018 - 20:57:22 PST)
- Re: [AMBER] mpi (Thu Dec 20 2018 - 22:08:08 PST)
- [AMBER] Re: How to get the jac.restrt？ (Tue Dec 11 2018 - 00:53:45 PST)
- [AMBER] Re: How to get the jac.restrt？ (Mon Dec 10 2018 - 20:48:15 PST)
- Re: [AMBER] numpy related problem in amber (Wed Dec 05 2018 - 20:52:32 PST)
- Re: [AMBER] RMSD vs RMSF (Sun Dec 02 2018 - 20:51:24 PST)
Eric Lang
- Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF (Wed Dec 05 2018 - 01:55:43 PST)
- Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF (Tue Dec 04 2018 - 08:10:14 PST)
- [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF (Tue Dec 04 2018 - 03:36:20 PST)
Fabian Glaser
- Re: [AMBER] ligand charges for md (Tue Dec 11 2018 - 08:33:08 PST)
- [AMBER] ligand charges for md (Sun Dec 09 2018 - 08:15:56 PST)
Farial Tavakoli
- [AMBER] Fwd: constant dieletcric (Thu Dec 27 2018 - 22:15:25 PST)
- [AMBER] constant dieletcric (Tue Dec 25 2018 - 05:05:23 PST)
- [AMBER] MMPBSA (Fri Dec 14 2018 - 07:26:48 PST)
- [AMBER] mmpbsa (Thu Dec 13 2018 - 08:59:04 PST)
Ghoreishi, Delaram
- Re: [AMBER] GPU download(upload) only a small subset of coordinates (Wed Dec 26 2018 - 10:22:41 PST)
- Re: [AMBER] Can a Nudged elastic band (NEB) job run on a single GPU? (Fri Dec 07 2018 - 13:10:03 PST)
- Re: [AMBER] Can a Nudged elastic band (NEB) job run on a single GPU? (Fri Dec 07 2018 - 11:49:08 PST)
Goetz, Andreas
- Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF (Wed Dec 05 2018 - 11:38:02 PST)
- Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF (Tue Dec 04 2018 - 11:48:59 PST)
Gustaf Olsson
- Re: [AMBER] amd running error (Mon Dec 17 2018 - 23:25:57 PST)
- Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??) (Mon Dec 17 2018 - 06:21:04 PST)
- Re: [AMBER] sander: command not found (Fri Dec 14 2018 - 05:14:10 PST)
- Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??) (Tue Dec 11 2018 - 05:41:57 PST)
- Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??) (Mon Dec 10 2018 - 04:32:36 PST)
Hai Nguyen
- Re: [AMBER] numpy related problem in amber (Thu Dec 06 2018 - 23:30:28 PST)
Han, Jaebeom
- [AMBER] ff12pol in Amber 18 (Thu Dec 20 2018 - 12:37:34 PST)
Hosein Geraili Daronkola
- Re: [AMBER] vdwmeth (Fri Dec 07 2018 - 14:46:04 PST)
- Re: [AMBER] vdwmeth (Fri Dec 07 2018 - 10:16:49 PST)
- Re: [AMBER] vdwmeth (Fri Dec 07 2018 - 07:55:42 PST)
- [AMBER] vdwmeth (Fri Dec 07 2018 - 06:58:46 PST)
Hunter Wilson
- Re: [AMBER] MCPB.py Modelling Question (Sat Dec 29 2018 - 14:17:11 PST)
- [AMBER] MCPB.py Modelling Question (Sun Dec 16 2018 - 12:48:07 PST)
Ibrahim M. Moustafa
- Re: [AMBER] Size limit for amber (Wed Dec 12 2018 - 10:42:14 PST)
- Re: [AMBER] Size limit for amber (Mon Dec 10 2018 - 10:44:41 PST)
- [AMBER] Size limit for amber (Mon Dec 10 2018 - 09:27:09 PST)
ilhan.yavuz
- [AMBER] AMBER16 re-installation problem (Mon Dec 17 2018 - 01:06:30 PST)
jacob wick
- [AMBER] GBSA error (Tue Dec 11 2018 - 21:45:32 PST)
- [AMBER] GBSA error (Tue Dec 11 2018 - 00:49:15 PST)
Jag Silwal
- Re: [AMBER] Extracting PDBs every 'N" ns (Mon Dec 03 2018 - 02:25:11 PST)
- Re: [AMBER] Ris: Extracting PDBs every 'N" ns (Sun Dec 02 2018 - 07:54:44 PST)
- [AMBER] Extracting PDBs every 'N" ns (Sun Dec 02 2018 - 07:16:15 PST)
Jinfeng Chen
- [AMBER] MCPB.py problems For atom (.R<AL1 380>.A<CL2 1>) could not find vdW (or other) parameters for type (Y1) (Mon Dec 03 2018 - 03:42:29 PST)
Jinfeng Huang
- [AMBER] Antechamber give a different total charge from net charge that I specified by -nc (Tue Dec 04 2018 - 10:42:41 PST)
Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] Strange TIP3P solvent box - reference to the tutorial (Fri Dec 07 2018 - 05:25:54 PST)
- Re: [AMBER] Strange TIP3P solvent box distortions in Amber 18 with Mg2+, but no MG (Thu Dec 06 2018 - 13:56:21 PST)
- [AMBER] Strange TIP3P solvent box distortions in Amber 18 with Mg2+ (Thu Dec 06 2018 - 12:21:19 PST)
kegohda2kegohda.mx5.canvas.ne.jp
- Re: [AMBER] TI method with combination of restrained MD in pmemd.cuda of AMBER18 (Fri Dec 28 2018 - 04:41:53 PST)
- [AMBER] TI method with combination of restrained MD in pmemd.cuda of AMBER18 (Wed Dec 26 2018 - 05:11:59 PST)
Keiran Corbett
- [AMBER] ACE (Thu Dec 20 2018 - 00:22:58 PST)
- Re: [AMBER] Include bound ions as part of the receptor molecule in MMPBSA.py (Thu Dec 06 2018 - 00:11:17 PST)
- [AMBER] Delta G pb and Delta G Sa (Mon Dec 03 2018 - 08:00:11 PST)
Kimia Sh
- [AMBER] minimization difficulties (Mon Dec 03 2018 - 02:46:16 PST)
Leena Aggarwal
- Re: [AMBER] How to add ff99sb*ildn? (Fri Dec 21 2018 - 20:51:50 PST)
- Re: [AMBER] Query regarding the internal energy of protein. (Mon Dec 17 2018 - 22:14:46 PST)
- [AMBER] Query regarding the internal energy of protein. (Mon Dec 17 2018 - 02:09:29 PST)
Li, Dailin
- [AMBER] 答复: Can a Nudged elastic band (NEB) job run on a single GPU? (Fri Dec 07 2018 - 14:16:11 PST)
- [AMBER] 答复: Can a Nudged elastic band (NEB) job run on a single GPU? (Fri Dec 07 2018 - 12:09:15 PST)
- [AMBER] Can a Nudged elastic band (NEB) job run on a single GPU? (Fri Dec 07 2018 - 11:11:49 PST)
lorenaz
- Re: [AMBER] Backbone position restraints as a group (Thu Dec 06 2018 - 06:33:07 PST)
- [AMBER] Backbone position restraints as a group (Wed Dec 05 2018 - 00:49:57 PST)
Lucas Bandeira
- Re: [AMBER] Problems calculating self diffusion coefficient of water (Sat Dec 22 2018 - 05:30:37 PST)
- Re: [AMBER] Problems calculating self diffusion coefficient of water (Thu Dec 20 2018 - 02:21:04 PST)
- [AMBER] Problems calculating self diffusion coefficient of water (Wed Dec 19 2018 - 09:13:07 PST)
- Re: [AMBER] Problems modifing box lengths in a .rst file. (Wed Dec 19 2018 - 07:25:34 PST)
- Re: [AMBER] Problems modifing box lengths in a .rst file. (Tue Dec 18 2018 - 07:29:31 PST)
- Re: [AMBER] Problems modifing box lengths in a .rst file. (Mon Dec 17 2018 - 10:18:00 PST)
- Re: [AMBER] Problems modifing box lengths in a .rst file. (Mon Dec 17 2018 - 08:45:46 PST)
- [AMBER] Problems modifing box lengths in a .rst file. (Mon Dec 17 2018 - 08:43:04 PST)
M RCC
- [AMBER] HMR 4fs error. (Mon Dec 31 2018 - 02:06:51 PST)
Mac Kevin Braza
- Re: [AMBER] FATAL Error: Atom does not have a type (Thu Dec 27 2018 - 02:58:26 PST)
- [AMBER] Fwd: FATAL Error: Atom does not have a type (Tue Dec 25 2018 - 20:38:01 PST)
- [AMBER] FATAL Error: Atom does not have a type (Tue Dec 25 2018 - 20:36:55 PST)
Manju Sah
- [AMBER] cpin file format issue in production run (Fri Dec 21 2018 - 03:45:32 PST)
Margarita I. Bernal-Uruchurtu
- [AMBER] lambda option in SEBOMD (Mon Dec 17 2018 - 05:15:38 PST)
- Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??) (Tue Dec 11 2018 - 05:35:29 PST)
- Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??) (Tue Dec 11 2018 - 05:26:28 PST)
- [AMBER] Problems with installation on Mac with Mojave. (cpptraj??) (Mon Dec 10 2018 - 03:18:10 PST)
maya nair
- [AMBER] sander: command not found (Fri Dec 14 2018 - 04:54:50 PST)
Meng Wu
- [AMBER] Calculate the conduct rate from PMF (Thu Dec 06 2018 - 18:51:13 PST)
- Re: [AMBER] water-induced force on substrate along time (Wed Dec 05 2018 - 17:31:15 PST)
- [AMBER] water-induced force on substrate along time (Wed Dec 05 2018 - 04:27:45 PST)
Midhun K Madhu
- [AMBER] How to add ff99sb*ildn? (Fri Dec 21 2018 - 07:22:33 PST)
Mlynsky Vojtech
- Re: [AMBER] AMBER18 on RTX 2080Ti (Fri Dec 21 2018 - 07:25:43 PST)
MOHD HOMAIDUR RAHMAN
- [AMBER] Calculation of Hbond energy (Tue Dec 25 2018 - 07:33:58 PST)
Nanjie Deng
- Re: [AMBER] Include bound ions as part of the receptor molecule in MMPBSA.py (Thu Dec 06 2018 - 19:44:42 PST)
- [AMBER] Include bound ions as part of the receptor molecule in MMPBSA.py (Wed Dec 05 2018 - 13:27:11 PST)
Nisha Amarnath Jonniya
- [AMBER] amd running error (Mon Dec 17 2018 - 22:01:20 PST)
Núbia Prates
- Re: [AMBER] strange line between protein chains (Fri Dec 14 2018 - 04:54:40 PST)
- [AMBER] strange line between protein chains (Thu Dec 13 2018 - 07:20:42 PST)
Osman, Roman
- Re: [AMBER] Axis of a helix as a collective variable (Thu Dec 20 2018 - 10:54:03 PST)
Pavithra Support
- [AMBER] Ptraj Command not found. (Sun Dec 09 2018 - 18:37:37 PST)
Pedro H. Oliveira
- [AMBER] Ambiguous interfaces in generic interface (Wed Dec 05 2018 - 13:36:24 PST)
Pengfei Li
- Re: [AMBER] MCPB.py Modelling Question (Fri Dec 21 2018 - 14:21:27 PST)
- Re: [AMBER] MCPB.py problems For atom (.R<AL1 380>.A<CL2 1>) could not find vdW (or other) parameters for type (Y1) (Sat Dec 08 2018 - 18:34:00 PST)
- Re: [AMBER] RESP charge calculation (Sat Dec 08 2018 - 18:27:17 PST)
Pratul Agarwal
- Re: [AMBER] Testing AMBER16 installation in parallel; possible bug in testing scripts (Fri Dec 21 2018 - 15:04:38 PST)
- Re: [AMBER] Axis of a helix as a collective variable (Thu Dec 20 2018 - 21:35:17 PST)
- Re: [AMBER] Axis of a helix as a collective variable (Thu Dec 20 2018 - 15:19:18 PST)
- Re: [AMBER] Axis of a helix as a collective variable (Thu Dec 20 2018 - 12:23:53 PST)
- Re: [AMBER] AMBER18 on RTX 2080Ti (Tue Dec 18 2018 - 09:43:59 PST)
- Re: [AMBER] Simulating a DNA Double helix with a mutated base pair (Tue Dec 18 2018 - 09:07:55 PST)
- Re: [AMBER] error on equilibriation (Tue Dec 18 2018 - 08:09:00 PST)
- Re: [AMBER] AMBER18 on RTX 2080Ti (Mon Dec 17 2018 - 17:16:31 PST)
- Re: [AMBER] Query regarding the internal energy of protein. (Mon Dec 17 2018 - 07:37:58 PST)
- Re: [AMBER] CUDA test failure (Mon Dec 17 2018 - 06:10:09 PST)
- Re: [AMBER] AMBER18 on RTX 2080Ti (Fri Dec 14 2018 - 15:29:57 PST)
- Re: [AMBER] strange line between protein chains (Fri Dec 14 2018 - 12:18:02 PST)
- Re: [AMBER] strange line between protein chains (Thu Dec 13 2018 - 09:25:19 PST)
- Re: [AMBER] Reading Amber-generated NetCDF files using python (Tue Dec 11 2018 - 04:33:57 PST)
- Re: [AMBER] Reading Amber-generated NetCDF files using python (Tue Dec 11 2018 - 04:18:26 PST)
- Re: [AMBER] Ptraj Command not found. (Sun Dec 09 2018 - 18:59:43 PST)
Qasim Pars
- [AMBER] amber12 install problem (Mon Dec 10 2018 - 11:46:57 PST)
Qinghua Liao
- Re: [AMBER] Obtaining necessary *.top for MMPBSA.py (Mon Dec 31 2018 - 07:12:16 PST)
Rajarshi Roy
- Re: [AMBER] Total energy of glycan simulation is postive (Sat Dec 22 2018 - 02:26:38 PST)
- [AMBER] Total energy of glycan simulation is postive (Fri Dec 21 2018 - 03:38:30 PST)
Rajbinder Kaur Virk
- Re: [AMBER] cpptraj error (Tue Dec 04 2018 - 01:18:29 PST)
- Re: [AMBER] cpptraj error (Sun Dec 02 2018 - 22:16:28 PST)
Rakesh Srivastava
- Re: [AMBER] Query regarding force field (Sat Dec 15 2018 - 22:46:30 PST)
- [AMBER] Query regarding force field (Sat Dec 15 2018 - 08:05:19 PST)
Ray Luo
- Re: [AMBER] ff12pol in Amber 18 (Thu Dec 20 2018 - 14:51:45 PST)
Ross Walker
- Re: [AMBER] AMBER18 on RTX 2080Ti (Mon Dec 17 2018 - 17:55:22 PST)
Rui Sun
- Re: [AMBER] AMBER18 on RTX 2080Ti (Tue Dec 18 2018 - 02:56:02 PST)
- Re: [AMBER] AMBER18 on RTX 2080Ti (Mon Dec 17 2018 - 16:46:59 PST)
- [AMBER] AMBER18 on RTX 2080Ti (Fri Dec 14 2018 - 14:53:23 PST)
- Re: [AMBER] AMBER18 Update Fail (AmberTools Update.10) (Fri Dec 07 2018 - 11:28:56 PST)
- [AMBER] AMBER18 Update Fail (AmberTools Update.10) (Fri Dec 07 2018 - 01:31:50 PST)
Saeed Izadi
- Re: [AMBER] Problems calculating self diffusion coefficient of water (Wed Dec 19 2018 - 12:52:06 PST)
Seibold, Steve Allan
- Re: [AMBER] compilation error AMBER16 (Fri Dec 28 2018 - 07:52:56 PST)
- [AMBER] compilation error AMBER16 (Thu Dec 27 2018 - 11:31:20 PST)
Seketoulie Keretsu
- Re: [AMBER] Acpype related problem : topology for GROMACS (Mon Dec 17 2018 - 08:04:12 PST)
- Re: [AMBER] Acpype related problem : topology for GROMACS (Mon Dec 17 2018 - 05:20:09 PST)
- Re: [AMBER] Acpype related problem : topology for GROMACS (Sun Dec 16 2018 - 21:11:33 PST)
- [AMBER] is acpype compatible with amber 2018?? parmchk2 and not parmchk available (Sun Dec 16 2018 - 21:07:04 PST)
- Re: [AMBER] Acpype related problem : topology for GROMACS (Sun Dec 16 2018 - 16:31:42 PST)
- [AMBER] Acpype related problem : topology for GROMACS (Sun Dec 16 2018 - 05:58:08 PST)
- Re: [AMBER] numpy related problem in amber (Fri Dec 07 2018 - 03:05:46 PST)
- Re: [AMBER] AMBER18 Update Fail (AmberTools Update.10) (Fri Dec 07 2018 - 03:04:19 PST)
- Re: [AMBER] numpy related problem in amber (Thu Dec 06 2018 - 22:02:39 PST)
- [AMBER] numpy related problem in amber (Wed Dec 05 2018 - 20:05:22 PST)
senal dinuka
- [AMBER] MD Analysis - Consistency (Sat Dec 22 2018 - 22:10:44 PST)
Stejskal, Lenka
- Re: [AMBER] Minimisation and periodic boundaries (Wed Dec 05 2018 - 08:11:44 PST)
Stephan Schott
- Re: [AMBER] multiconformational respgen with fixed charges and gcc 4.8 (Sun Dec 30 2018 - 16:38:16 PST)
- [AMBER] multiconformational respgen with fixed charges and gcc 4.8 (Sat Dec 22 2018 - 15:39:56 PST)
Sundar
- [AMBER] Obtaining necessary *.top for MMPBSA.py (Mon Dec 31 2018 - 06:08:46 PST)
- Re: [AMBER] Amber18 compilation error on a Linux CPU cluster (Mon Dec 24 2018 - 17:16:49 PST)
- Re: [AMBER] Amber18 compilation error on a Linux CPU cluster (Sun Dec 23 2018 - 10:40:59 PST)
- Re: [AMBER] Amber18 compilation error on a Linux CPU cluster (Sat Dec 22 2018 - 20:21:07 PST)
- [AMBER] Amber18 compilation error on a Linux CPU cluster (Wed Dec 19 2018 - 21:47:23 PST)
- [AMBER] cation-pi and amber FF (Wed Dec 19 2018 - 21:36:45 PST)
Thomas Evangelidis
- Re: [AMBER] tleap does not add OXT when I load a crystal structure (Thu Dec 06 2018 - 02:09:31 PST)
- [AMBER] tleap does not add OXT when I load a crystal structure (Wed Dec 05 2018 - 15:23:47 PST)
Thomas Fox
- [AMBER] resp charge fitting (Fri Dec 14 2018 - 08:14:41 PST)
Tom Kurtzman
- Re: [AMBER] Problems calculating self diffusion coefficient of water (Thu Dec 20 2018 - 05:13:30 PST)
- Re: [AMBER] GIST calculation on NAMD-generated trajectory (Tue Dec 18 2018 - 10:26:27 PST)
Vlad Cojocaru
- Re: [AMBER] How to add ff99sb*ildn? (Fri Dec 21 2018 - 07:43:22 PST)
wangjianing_mail
- [AMBER] q (Sat Dec 29 2018 - 04:19:24 PST)
Wesley Michael Botello-Smith
- [AMBER] Problem running tiMerge (parmed) (Fri Dec 21 2018 - 09:15:47 PST)
- Re: [AMBER] Axis of a helix as a collective variable (Thu Dec 20 2018 - 15:11:25 PST)
- Re: [AMBER] Axis of a helix as a collective variable (Thu Dec 20 2018 - 10:37:24 PST)
- Re: [AMBER] Delta G pb and Delta G Sa (Mon Dec 03 2018 - 10:19:41 PST)
Xiaoyu Wang
- [AMBER] RMSD vs RMSF (Sun Dec 02 2018 - 16:28:45 PST)
张浩淼
- [AMBER] GPU download(upload) only a small subset of coordinates (Wed Dec 26 2018 - 01:12:02 PST)
王茜茜
- Re: [AMBER] How to get the jac.restrt？ (Tue Dec 11 2018 - 06:14:24 PST)
- Re: [AMBER] How to get the jac.restrt？ (Tue Dec 11 2018 - 01:08:18 PST)
- Re: [AMBER] How to get the jac.restrt？ (Mon Dec 10 2018 - 22:53:26 PST)
- [AMBER] How to get the jac.restrt？ (Mon Dec 10 2018 - 19:37:04 PST)
대학원/일반대학원 생명과학부
- [AMBER] PSF file generation for heme and hydrogen peroxide (Wed Dec 12 2018 - 18:37:09 PST)
- [AMBER] Dear AMBER members, (Sat Dec 08 2018 - 07:46:31 PST)

Amber Archive Dec 2018 by author