Amber Archive Aug 2016: by author

Abhilash J
- Re: [AMBER] Two ion problem with mcpb.py (Thu Aug 18 2016 - 21:19:44 PDT)
- Re: [AMBER] Two ion problem with mcpb.py (Thu Aug 18 2016 - 12:17:50 PDT)
- [AMBER] Two ion problem with mcpb.py (Fri Aug 12 2016 - 10:11:55 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 14:19:11 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 14:00:32 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 13:44:56 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 13:27:52 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 13:04:45 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 12:45:35 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 12:18:33 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 12:06:33 PDT)
- [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 07:55:00 PDT)
Aditya Padhi
- [AMBER] Generating parameter and topology files for a protein with multiple Zinc ions (Tue Aug 23 2016 - 18:00:15 PDT)
Adrian Roitberg
- Re: [AMBER] Regarding the use of sed command to replace water (Wed Aug 31 2016 - 12:58:29 PDT)
- Re: [AMBER] QM/MM energy units? (Wed Aug 31 2016 - 08:56:48 PDT)
- Re: [AMBER] frozen geometry setting? (Tue Aug 30 2016 - 12:14:29 PDT)
- Re: [AMBER] problem upon optimization (Thu Aug 25 2016 - 08:14:34 PDT)
- Re: [AMBER] WHAM analysis (Sat Aug 20 2016 - 11:17:23 PDT)
- Re: [AMBER] secondary structure graph vs Time (Thu Aug 11 2016 - 09:26:20 PDT)
- Re: [AMBER] secondary structure graph vs Time (Thu Aug 11 2016 - 09:05:01 PDT)
- Re: [AMBER] for what kind of post simulation analysis I need to do reweighing? (Tue Aug 09 2016 - 08:04:05 PDT)
- Re: [AMBER] restraining mean square displacements (Fri Aug 05 2016 - 12:54:33 PDT)
- Re: [AMBER] unreadable crd files (Thu Aug 04 2016 - 15:31:29 PDT)
Albert
- [AMBER] concerns on membrane protein restrain (Fri Aug 19 2016 - 11:39:35 PDT)
- Re: [AMBER] about lipids retrain (Wed Aug 17 2016 - 05:26:59 PDT)
- [AMBER] about lipids retrain (Wed Aug 17 2016 - 02:45:19 PDT)
- Re: [AMBER] lipid simulation with Lipid14 FF failed (Tue Aug 16 2016 - 06:07:56 PDT)
- [AMBER] lipid simulation with Lipid14 FF failed (Tue Aug 16 2016 - 03:00:50 PDT)
- [AMBER] job failed (Sat Aug 13 2016 - 23:37:26 PDT)
- Re: [AMBER] job suspended (Fri Aug 12 2016 - 08:15:42 PDT)
- [AMBER] job suspended (Fri Aug 12 2016 - 06:33:22 PDT)
- Re: [AMBER] GPU MPI failed (Thu Aug 11 2016 - 06:20:37 PDT)
- [AMBER] GPU MPI failed (Thu Aug 11 2016 - 01:37:52 PDT)
- Re: [AMBER] intel MPI failed (Tue Aug 09 2016 - 06:00:17 PDT)
- Re: [AMBER] intel MPI failed (Mon Aug 08 2016 - 23:12:00 PDT)
- Re: [AMBER] intel MPI failed (Mon Aug 08 2016 - 07:39:38 PDT)
- Re: [AMBER] intel MPI failed (Mon Aug 08 2016 - 07:26:47 PDT)
- [AMBER] intel MPI failed (Mon Aug 08 2016 - 06:40:54 PDT)
- [AMBER] which forcefield it is? (Mon Aug 01 2016 - 23:38:43 PDT)
Alfredo Quevedo
- Re: [AMBER] Tutorial B5 - Loading CRO from ccif file (Fri Aug 19 2016 - 10:49:05 PDT)
- [AMBER] Tutorial B5 - Loading CRO from ccif file (Fri Aug 19 2016 - 07:26:42 PDT)
amir sadeghi
- [AMBER] Amber Force Fields (Wed Aug 31 2016 - 12:33:48 PDT)
Amrullah13
- [AMBER] (no subject) (Sat Aug 27 2016 - 18:51:50 PDT)
Amy Rice
- Re: [AMBER] WHAM analysis (Sat Aug 20 2016 - 08:41:00 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Fri Aug 12 2016 - 10:46:30 PDT)
- Re: [AMBER] 3 trajectory MMPBSA free energy calculation (Wed Aug 10 2016 - 08:34:15 PDT)
- Re: [AMBER] Amber14 FEW for 3 trajectory free energy (Fri Aug 05 2016 - 08:21:50 PDT)
- Re: [AMBER] which forcefield it is? (Tue Aug 02 2016 - 09:17:43 PDT)
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion (Mon Aug 01 2016 - 12:35:03 PDT)
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion (Mon Aug 01 2016 - 12:06:53 PDT)
Andrew Schaub
- Re: [AMBER] Checking modeling after MCPB and unable to fix atom order using cpptraj (Tue Aug 23 2016 - 22:56:02 PDT)
- [AMBER] Checking modeling after MCPB and unable to fix atom order using cpptraj (Tue Aug 23 2016 - 22:15:58 PDT)
Andrew.Warden.csiro.au
- Re: [AMBER] parmchk vs parmchk2 (Thu Aug 04 2016 - 18:08:21 PDT)
- [AMBER] parmchk vs parmchk2 (Tue Aug 02 2016 - 21:53:09 PDT)
Aravind Ravichandran
- [AMBER] Temperature Shoot-up in TMD (Fri Aug 19 2016 - 00:26:24 PDT)
Aronica, Pietro
- [AMBER] Alanine scan of nonnatural amino acid (Tue Aug 23 2016 - 02:21:37 PDT)
- [AMBER] LEaP and PARMSETs (Thu Aug 18 2016 - 01:49:50 PDT)
ATUL KUMAR
- Re: [AMBER] Problem in charge generation through antechamber (Thu Aug 18 2016 - 23:11:14 PDT)
- Re: [AMBER] Problem in charge generation through antechamber (Thu Aug 18 2016 - 12:43:07 PDT)
- [AMBER] Problem in charge generation through antechamber (Thu Aug 18 2016 - 11:53:45 PDT)
Ayesha Fatima
- Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water (Mon Aug 08 2016 - 16:36:48 PDT)
Baker, Joseph
- Re: [AMBER] Issues compiling Amber with CUDA support (Sat Aug 27 2016 - 21:48:21 PDT)
- Re: [AMBER] Issues compiling Amber with CUDA support (Sat Aug 27 2016 - 13:10:31 PDT)
Bence Hégely
- Re: [AMBER] Checking AmberTools16 installation (Tue Aug 30 2016 - 07:37:58 PDT)
- Re: [AMBER] Checking AmberTools16 installation (Fri Aug 26 2016 - 07:19:10 PDT)
- [AMBER] Checking AmberTools16 installation (Thu Aug 25 2016 - 11:53:11 PDT)
bharat gupta
- Re: [AMBER] SMD simulation (Sun Aug 07 2016 - 22:44:08 PDT)
Bilal Nizami
- Re: [AMBER] output of MMPBSA.py (Thu Aug 25 2016 - 03:54:19 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Sat Aug 13 2016 - 01:11:11 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Fri Aug 12 2016 - 00:15:01 PDT)
Bill Ross
- Re: [AMBER] change the atom charge in a restart simulations (Wed Aug 31 2016 - 02:54:44 PDT)
- Re: [AMBER] frozen geometry setting? (Tue Aug 30 2016 - 12:32:16 PDT)
- Re: [AMBER] frozen geometry setting? (Tue Aug 30 2016 - 11:59:10 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Sat Aug 27 2016 - 15:33:52 PDT)
- Re: [AMBER] repair mdcrd? (Thu Aug 25 2016 - 15:48:11 PDT)
- [AMBER] repair mdcrd? (Thu Aug 25 2016 - 13:26:01 PDT)
- Re: [AMBER] Problem with rst7 (Thu Aug 25 2016 - 02:41:46 PDT)
- Re: [AMBER] Generating parameter and topology files for a protein with multiple Zinc ions (Wed Aug 24 2016 - 21:19:37 PDT)
- Re: [AMBER] Generating topology and parameter file for a peptide (Wed Aug 24 2016 - 00:57:27 PDT)
- Re: [AMBER] Sigma and epsilon vdw parameters (Mon Aug 22 2016 - 15:58:45 PDT)
- Re: [AMBER] Adaptively Biased MD Simulations of type "distance" using "FLOODING" (Mon Aug 22 2016 - 03:54:06 PDT)
- Re: [AMBER] Adaptively Biased MD Simulations of type "distance" using "FLOODING" (Mon Aug 22 2016 - 03:45:53 PDT)
- Re: [AMBER] solid surface simulation in amber (Mon Aug 22 2016 - 03:07:59 PDT)
- Re: [AMBER] solid surface simulation in amber (Fri Aug 19 2016 - 18:35:12 PDT)
- Re: [AMBER] solid surface simulation in amber (Fri Aug 19 2016 - 14:06:40 PDT)
- Re: [AMBER] Temperature Shoot-up in TMD (Fri Aug 19 2016 - 00:20:52 PDT)
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server (Thu Aug 18 2016 - 02:24:14 PDT)
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server (Thu Aug 18 2016 - 02:17:30 PDT)
- Re: [AMBER] solid surface simulation in amber (Thu Aug 18 2016 - 01:55:20 PDT)
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server (Thu Aug 18 2016 - 01:49:43 PDT)
- Re: [AMBER] solid surface simulation in amber (Thu Aug 18 2016 - 01:36:32 PDT)
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server (Wed Aug 17 2016 - 23:40:44 PDT)
- Re: [AMBER] RMSd (Wed Aug 17 2016 - 23:18:53 PDT)
- Re: [AMBER] Restarting a crushed run (Tue Aug 16 2016 - 14:24:52 PDT)
- Re: [AMBER] Restarting a crushed run (Tue Aug 16 2016 - 12:40:07 PDT)
- Re: [AMBER] Restarting a crushed run (Tue Aug 16 2016 - 12:12:05 PDT)
- Re: [AMBER] solid surface simulation in amber (Tue Aug 16 2016 - 01:27:51 PDT)
- Re: [AMBER] solid surface simulation in amber (Tue Aug 16 2016 - 00:33:02 PDT)
- Re: [AMBER] How to fix the wall of the water box in amber (Sun Aug 07 2016 - 02:01:46 PDT)
- Re: [AMBER] How to fix the wall of the water box in amber (Sat Aug 06 2016 - 18:59:00 PDT)
- Re: [AMBER] Sander bomb: how to create a larger box (Mon Aug 01 2016 - 05:11:10 PDT)
- Re: [AMBER] Sander bomb: how to create a larger box (Mon Aug 01 2016 - 04:32:22 PDT)
Bruno Falcone
- Re: [AMBER] Problem in charge generation through antechamber (Fri Aug 19 2016 - 07:47:05 PDT)
- Re: [AMBER] Problem in charge generation through antechamber (Thu Aug 18 2016 - 12:58:42 PDT)
- Re: [AMBER] Problem in charge generation through antechamber (Thu Aug 18 2016 - 12:33:49 PDT)
- Re: [AMBER] save Hessian nmode mmpbsa (Thu Aug 04 2016 - 08:45:51 PDT)
- [AMBER] save Hessian nmode mmpbsa (Wed Aug 03 2016 - 09:51:23 PDT)
Budhathoki, Dipesh
- Re: [AMBER] Regarding the use of sed command to replace water (Wed Aug 31 2016 - 14:54:40 PDT)
- [AMBER] Regarding the use of sed command to replace water (Wed Aug 31 2016 - 12:52:37 PDT)
Carlos Simmerling
- Re: [AMBER] Amber Force Fields (Wed Aug 31 2016 - 17:34:12 PDT)
- Re: [AMBER] lowering the temperature (Wed Aug 31 2016 - 04:02:04 PDT)
- Re: [AMBER] lowering the temperature (Tue Aug 30 2016 - 17:19:14 PDT)
- Re: [AMBER] SEP parameter with ff15ipq (Fri Aug 26 2016 - 06:35:52 PDT)
- Re: [AMBER] Problem with rst7 (Thu Aug 25 2016 - 04:31:25 PDT)
- Re: [AMBER] Problem with rst7 (Thu Aug 25 2016 - 03:33:54 PDT)
- Re: [AMBER] Temperature Shoot-up in TMD (Fri Aug 19 2016 - 04:50:38 PDT)
- Re: [AMBER] umbrella sampling restraining both angle and distance (Sun Aug 14 2016 - 07:55:57 PDT)
- Re: [AMBER] Question of Parameter Defaults (Sat Aug 13 2016 - 07:37:00 PDT)
- Re: [AMBER] umbrella sampling restraining both angle and distance (Fri Aug 12 2016 - 15:22:27 PDT)
- Re: [AMBER] Implicit solvent in pmemd.cuda (Fri Aug 05 2016 - 09:31:42 PDT)
Cecilia Lindgren
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server (Thu Aug 18 2016 - 03:40:21 PDT)
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server (Thu Aug 18 2016 - 02:03:43 PDT)
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server (Thu Aug 18 2016 - 01:35:54 PDT)
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server (Wed Aug 17 2016 - 23:11:15 PDT)
- [AMBER] MD simulation with non natural amino acid, parameterized using the RED server (Wed Aug 17 2016 - 05:56:24 PDT)
Chi Jin
- Re: [AMBER] WHAM analysis (Sat Aug 20 2016 - 11:13:41 PDT)
- Re: [AMBER] WHAM analysis (Sat Aug 20 2016 - 00:30:05 PDT)
- [AMBER] CHARM force field (Mon Aug 15 2016 - 13:48:12 PDT)
- [AMBER] correlated dihedral force constant (Tue Aug 02 2016 - 12:46:23 PDT)
Chitrak Gupta
- [AMBER] Amber B5 tutorial (Fri Aug 12 2016 - 11:10:05 PDT)
- [AMBER] antechamber cannot match patching atoms of amino acid (Wed Aug 10 2016 - 15:26:24 PDT)
- [AMBER] Implicit solvent in pmemd.cuda (Fri Aug 05 2016 - 08:54:58 PDT)
Christina Bergonzo
- Re: [AMBER] for what kind of post simulation analysis I need to do reweighing? (Tue Aug 09 2016 - 09:18:41 PDT)
Christopher Jesudason
- [AMBER] Off , mol2 and frcmod files (Tue Aug 09 2016 - 04:40:25 PDT)
Corum, Katharine W
- Re: [AMBER] Regarding the use of sed command to replace water (Wed Aug 31 2016 - 12:57:43 PDT)
- Re: [AMBER] QM/MM energy units? (Wed Aug 31 2016 - 08:58:56 PDT)
- [AMBER] QM/MM energy units? (Wed Aug 31 2016 - 08:52:45 PDT)
- [AMBER] QM region has an odd number of electrons (Wed Aug 17 2016 - 14:22:53 PDT)
- Re: [AMBER] QM/MM stops at step 2114 (Tue Aug 16 2016 - 06:40:23 PDT)
- [AMBER] QM/MM stops at step 2114 (Mon Aug 15 2016 - 08:08:25 PDT)
- Re: [AMBER] Converting rst to pdb (Tue Aug 09 2016 - 16:26:09 PDT)
- [AMBER] Converting rst to pdb (Tue Aug 09 2016 - 14:01:58 PDT)
- Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water (Tue Aug 09 2016 - 07:53:51 PDT)
- Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water (Tue Aug 09 2016 - 07:20:05 PDT)
- [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water (Mon Aug 08 2016 - 14:33:12 PDT)
Damiano Spadoni
- Re: [AMBER] Multihist in watershell command (Wed Aug 31 2016 - 08:45:21 PDT)
- [AMBER] Multihist in watershell command (Fri Aug 26 2016 - 05:26:24 PDT)
Daniel Mermelstein
- Re: [AMBER] Regarding the free energy calculation (Fri Aug 19 2016 - 11:32:23 PDT)
Daniel Roe
- Re: [AMBER] autoimage bug? (Wed Aug 31 2016 - 06:22:55 PDT)
- Re: [AMBER] Problem with atommap function in cpptraj (v16) (Wed Aug 31 2016 - 06:12:00 PDT)
- Re: [AMBER] Problem with atommap function in cpptraj (v16) (Fri Aug 26 2016 - 13:40:24 PDT)
- Re: [AMBER] Regarding hbond bridgeout (Fri Aug 26 2016 - 13:24:08 PDT)
- Re: [AMBER] Multihist in watershell command (Fri Aug 26 2016 - 11:11:06 PDT)
- Re: [AMBER] begin time read from input coords (Fri Aug 26 2016 - 03:17:33 PDT)
- Re: [AMBER] repair mdcrd? (Thu Aug 25 2016 - 16:56:44 PDT)
- Re: [AMBER] Frac in cpptraj hydrogen bond command. (Sun Aug 21 2016 - 05:55:13 PDT)
- Re: [AMBER] MASK with distance in AMBER. (Wed Aug 17 2016 - 09:38:20 PDT)
- Re: [AMBER] Accelerated MD -- cudaMemcpy error (Tue Aug 16 2016 - 07:58:59 PDT)
- Re: [AMBER] solid surface simulation in amber (Tue Aug 16 2016 - 07:58:05 PDT)
- Re: [AMBER] Fwd: cpptraj issues (Tue Aug 16 2016 - 07:56:01 PDT)
- Re: [AMBER] error in sander and sander.mpi running (Tue Aug 16 2016 - 07:52:01 PDT)
- Re: [AMBER] secondary structure graph vs Time (Mon Aug 15 2016 - 14:15:24 PDT)
- Re: [AMBER] Accelerated MD -- cudaMemcpy error (Mon Aug 15 2016 - 11:01:27 PDT)
- Re: [AMBER] Fwd: cpptraj issues (Mon Aug 15 2016 - 10:45:40 PDT)
- Re: [AMBER] cpptraj issues (Fri Aug 12 2016 - 10:56:20 PDT)
- Re: [AMBER] MASK with distance in AMBER. (Fri Aug 12 2016 - 10:54:05 PDT)
- Re: [AMBER] Converting rst to pdb (Tue Aug 09 2016 - 14:22:17 PDT)
- Re: [AMBER] intel MPI failed (Mon Aug 08 2016 - 07:37:26 PDT)
- Re: [AMBER] intel MPI failed (Mon Aug 08 2016 - 07:16:04 PDT)
- Re: [AMBER] QMMM MD, Simulation does not start (Sun Aug 07 2016 - 14:42:01 PDT)
- Re: [AMBER] error in runing mdout_analyzer.py (Thu Aug 04 2016 - 08:05:51 PDT)
- Re: [AMBER] error running production with restraint. (Thu Aug 04 2016 - 08:04:48 PDT)
- Re: [AMBER] Amber´14 Solvent box simulation, something went wrong!! (Thu Aug 04 2016 - 08:02:28 PDT)
- Re: [AMBER] error in runing mdout_analyzer.py (Wed Aug 03 2016 - 21:25:23 PDT)
- Re: [AMBER] Amber´14 Solvent box simulation, something went wrong!! (Wed Aug 03 2016 - 12:30:45 PDT)
- Re: [AMBER] Cyana3.97 to Amber15 pdb conversion (Wed Aug 03 2016 - 12:26:52 PDT)
- Re: [AMBER] gbsa parameter (Wed Aug 03 2016 - 12:23:03 PDT)
- Re: [AMBER] HBond command (Tue Aug 02 2016 - 08:49:18 PDT)
- Re: [AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?) (Tue Aug 02 2016 - 08:25:42 PDT)
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion (Mon Aug 01 2016 - 12:24:37 PDT)
- Re: [AMBER] Difference of two trajectories (Mon Aug 01 2016 - 10:27:33 PDT)
- Re: [AMBER] Calculating Salt bridge interactions- Protein and RNA (Mon Aug 01 2016 - 10:26:14 PDT)
- Re: [AMBER] hydrogen bond occupancy plot cpptraj (Mon Aug 01 2016 - 10:23:57 PDT)
David A Case
- Re: [AMBER] Regarding the use of sed command to replace water (Wed Aug 31 2016 - 13:38:16 PDT)
- Re: [AMBER] change the atom charge in a restart simulations (Wed Aug 31 2016 - 05:32:25 PDT)
- Re: [AMBER] frozen geometry setting? (Tue Aug 30 2016 - 08:26:12 PDT)
- Re: [AMBER] errors in doing TI tutorial calculation (Mon Aug 29 2016 - 12:25:59 PDT)
- Re: [AMBER] begin time read from input coords (Fri Aug 26 2016 - 06:11:04 PDT)
- Re: [AMBER] Fw: Problems to calculate frequencies (Thu Aug 25 2016 - 06:40:56 PDT)
- Re: [AMBER] SEP parameter with ff15ipq (Thu Aug 25 2016 - 06:33:47 PDT)
- Re: [AMBER] minimum restraint_wt. (Tue Aug 23 2016 - 04:49:54 PDT)
- Re: [AMBER] Tutorial B5 - Loading CRO from ccif file (Fri Aug 19 2016 - 10:43:15 PDT)
- Re: [AMBER] solid surface simulation in amber (Fri Aug 19 2016 - 07:54:01 PDT)
- Re: [AMBER] Problem in charge generation through antechamber (Thu Aug 18 2016 - 12:43:09 PDT)
- Re: [AMBER] a bug in leaprc.gaff2 file (Thu Aug 18 2016 - 11:07:07 PDT)
- Re: [AMBER] a bug in leaprc.gaff2 file (Thu Aug 18 2016 - 06:22:25 PDT)
- Re: [AMBER] solid surface simulation in amber (Thu Aug 18 2016 - 06:13:05 PDT)
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server (Wed Aug 17 2016 - 07:13:46 PDT)
- Re: [AMBER] about lipids retrain (Wed Aug 17 2016 - 04:48:00 PDT)
- Re: [AMBER] parmchk2 issue (Tue Aug 16 2016 - 14:15:52 PDT)
- Re: [AMBER] lipid simulation with Lipid14 FF failed (Tue Aug 16 2016 - 05:11:16 PDT)
- Re: [AMBER] parmchk2 issue (Tue Aug 16 2016 - 05:09:37 PDT)
- Re: [AMBER] solid surface simulation in amber (Tue Aug 16 2016 - 05:04:29 PDT)
- Re: [AMBER] bellymask option. (Tue Aug 16 2016 - 04:59:16 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Tue Aug 16 2016 - 04:57:21 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Mon Aug 15 2016 - 13:32:38 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Mon Aug 15 2016 - 10:00:30 PDT)
- Re: [AMBER] QM/MM stops at step 2114 (Mon Aug 15 2016 - 09:13:44 PDT)
- Re: [AMBER] parmchk2 issue (Mon Aug 15 2016 - 09:06:35 PDT)
- Re: [AMBER] solid surface simulation in amber (Mon Aug 15 2016 - 04:39:23 PDT)
- Re: [AMBER] job failed (Sun Aug 14 2016 - 06:03:23 PDT)
- Re: [AMBER] Question of Parameter Defaults (Sat Aug 13 2016 - 12:48:59 PDT)
- Re: [AMBER] Amber B5 tutorial (Fri Aug 12 2016 - 12:22:25 PDT)
- Re: [AMBER] job suspended (Fri Aug 12 2016 - 08:11:28 PDT)
- Re: [AMBER] Optimal force constant for AMBER (Fri Aug 12 2016 - 07:40:46 PDT)
- Re: [AMBER] amber pdb > 100,000 atoms (Fri Aug 12 2016 - 05:42:19 PDT)
- Re: [AMBER] Regarding antechamber command Error (Fri Aug 12 2016 - 05:34:01 PDT)
- Re: [AMBER] LINMIN FAILURE on large protein minimization with GB and explicit (Fri Aug 12 2016 - 05:27:23 PDT)
- Re: [AMBER] Regarding antechamber command Error (Thu Aug 11 2016 - 12:38:51 PDT)
- Re: [AMBER] GPU MPI failed (Thu Aug 11 2016 - 05:15:16 PDT)
- Re: [AMBER] antechamber cannot match patching atoms of amino acid (Thu Aug 11 2016 - 05:05:53 PDT)
- Re: [AMBER] Regarding antechamber command Error (Thu Aug 11 2016 - 04:52:43 PDT)
- [AMBER] paper describing the ff15ipq protein force field is now available (Wed Aug 10 2016 - 11:11:08 PDT)
- Re: [AMBER] simultaneous use of ibelly=1 and ntr=1 (Tue Aug 09 2016 - 12:33:05 PDT)
- Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water (Tue Aug 09 2016 - 12:30:04 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM (Tue Aug 09 2016 - 12:27:00 PDT)
- Re: [AMBER] Off , mol2 and frcmod files (Tue Aug 09 2016 - 06:56:40 PDT)
- Re: [AMBER] query regarding restraint on specific residues. (Tue Aug 09 2016 - 05:02:10 PDT)
- Re: [AMBER] {AMBER} installation on mac osx 10.11.6 hanging when configuring NetCDF (Tue Aug 09 2016 - 05:00:39 PDT)
- Re: [AMBER] intel MPI failed (Tue Aug 09 2016 - 04:55:04 PDT)
- Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water (Tue Aug 09 2016 - 04:52:06 PDT)
- Re: [AMBER] copy charges using Python API (Mon Aug 08 2016 - 05:16:13 PDT)
- Re: [AMBER] copy charges using Python API (Sun Aug 07 2016 - 09:13:06 PDT)
- Re: [AMBER] Extend of manual modulation-Connecting two molecules methodology (Sat Aug 06 2016 - 19:27:23 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM (Fri Aug 05 2016 - 06:50:55 PDT)
- Re: [AMBER] error running production with restraint. (Fri Aug 05 2016 - 04:55:29 PDT)
- Re: [AMBER] MMPBSA.py TrajError: Could not find number of frames in .mdcrd (Fri Aug 05 2016 - 04:49:56 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM (Thu Aug 04 2016 - 14:38:07 PDT)
- Re: [AMBER] Generate Polymer parameters (Wed Aug 03 2016 - 16:47:17 PDT)
- Re: [AMBER] Cyana3.97 to Amber15 pdb conversion (Wed Aug 03 2016 - 16:41:13 PDT)
- Re: [AMBER] parmchk vs parmchk2 (Wed Aug 03 2016 - 16:34:34 PDT)
- Re: [AMBER] EM in vacuum (Wed Aug 03 2016 - 16:22:18 PDT)
- Re: [AMBER] EVB calculations of proton transfer (Tue Aug 02 2016 - 07:38:37 PDT)
- Re: [AMBER] subject: parametrization of Force field (Tue Aug 02 2016 - 07:36:09 PDT)
- Re: [AMBER] Use two different force fields in Amber (Tue Aug 02 2016 - 07:34:33 PDT)
- Re: [AMBER] EEL become ****** in minimization (Mon Aug 01 2016 - 08:04:15 PDT)
- Re: [AMBER] EEL energy of QM/MM-GBSA (Mon Aug 01 2016 - 07:58:39 PDT)
- Re: [AMBER] Sander bomb: how to create a larger box (Mon Aug 01 2016 - 07:57:05 PDT)
- [AMBER] EVB calculations of proton transfer (Mon Aug 01 2016 - 07:52:43 PDT)
David Cerutti
- Re: [AMBER] SEP parameter with ff15ipq (Thu Aug 25 2016 - 07:18:37 PDT)
- Re: [AMBER] paper describing the ff15ipq protein force field is now available (Wed Aug 10 2016 - 11:55:11 PDT)
- Re: [AMBER] EEL become ****** in minimization (Sun Jul 31 2016 - 22:04:36 PDT)
Dd H
- Re: [AMBER] Simulation Time (Wed Aug 24 2016 - 04:31:07 PDT)
diaby
- [AMBER] interaction entropy instead of normal mode analysis (Tue Aug 02 2016 - 06:57:10 PDT)
Dmitry Suplatov
- Re: [AMBER] Restarting a crushed run (Tue Aug 16 2016 - 13:27:34 PDT)
- Re: [AMBER] Restarting a crushed run (Tue Aug 16 2016 - 12:45:23 PDT)
- [AMBER] Accelerated MD -- cudaMemcpy error (Fri Aug 12 2016 - 13:53:07 PDT)
- [AMBER] EM in vacuum (Tue Aug 02 2016 - 13:52:17 PDT)
DmitryASuplatov
- [AMBER] What cutoff you use in Amber simulations? (Fri Aug 19 2016 - 04:35:40 PDT)
- [AMBER] Restarting a crushed run (Tue Aug 16 2016 - 09:43:44 PDT)
- Re: [AMBER] Accelerated MD -- cudaMemcpy error (Tue Aug 16 2016 - 04:05:38 PDT)
- Re: [AMBER] Accelerated MD -- cudaMemcpy error (Mon Aug 15 2016 - 03:52:14 PDT)
DOCENTE ANTISTIO ANIBAL ALVIS AMADOR
- [AMBER] subject: parametrization of Force field (Mon Aug 01 2016 - 07:50:08 PDT)
Dr. Andreas W. Goetz
- Re: [AMBER] changing atom type (Wed Aug 31 2016 - 14:15:35 PDT)
- Re: [AMBER] QM region has an odd number of electrons (Wed Aug 17 2016 - 16:33:24 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM (Tue Aug 09 2016 - 15:39:00 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM (Sat Aug 06 2016 - 13:18:13 PDT)
- Re: [AMBER] QMMM MD, Simulation does not start (Fri Aug 05 2016 - 14:31:45 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM (Fri Aug 05 2016 - 14:17:21 PDT)
- Re: [AMBER] amber16/test/qmmm_DFTB (Thu Aug 04 2016 - 23:27:47 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM (Thu Aug 04 2016 - 23:15:40 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM (Thu Aug 04 2016 - 12:17:15 PDT)
Elisa Pieri
- Re: [AMBER] Problem with rst7 (Thu Aug 25 2016 - 04:04:18 PDT)
- [AMBER] Problem with rst7 (Thu Aug 25 2016 - 02:12:46 PDT)
- [AMBER] cpptraj on pH-REMD (Wed Aug 24 2016 - 04:19:10 PDT)
Emmanuel
- [AMBER] Adaptively Biased MD Simulations of type "distance" using "FLOODING" (Mon Aug 22 2016 - 03:32:05 PDT)
Erik Davis
- Re: [AMBER] Combining single structure NMR pdb files into an ensemble. (Wed Aug 17 2016 - 06:05:24 PDT)
- [AMBER] Combining single structure NMR pdb files into an ensemble. (Tue Aug 16 2016 - 13:38:05 PDT)
- Re: [AMBER] Cyana3.97 to Amber15 pdb conversion (Fri Aug 05 2016 - 11:01:46 PDT)
- [AMBER] Cyana3.97 to Amber15 pdb conversion (Wed Aug 03 2016 - 08:09:35 PDT)
Fabrício Bracht
- Re: [AMBER] Question about usage of external QM in QM/MM (Tue Aug 09 2016 - 13:26:01 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM (Tue Aug 09 2016 - 07:13:42 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM (Tue Aug 09 2016 - 07:07:55 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM (Fri Aug 05 2016 - 18:30:56 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM (Fri Aug 05 2016 - 11:06:18 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM (Thu Aug 04 2016 - 19:04:46 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM (Thu Aug 04 2016 - 13:03:56 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM (Thu Aug 04 2016 - 12:29:35 PDT)
- [AMBER] Question about usage of external QM in QM/MM (Thu Aug 04 2016 - 10:59:10 PDT)
Feng Pan
- Re: [AMBER] Adaptively Biased MD Simulations of type "distance" using "FLOODING" (Mon Aug 22 2016 - 08:25:24 PDT)
Filip Persson
- [AMBER] autoimage bug? (Mon Aug 29 2016 - 05:36:24 PDT)
FyD
- Re: [AMBER] Problem in charge generation through antechamber (Sat Aug 20 2016 - 02:08:20 PDT)
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server (Sat Aug 20 2016 - 01:55:11 PDT)
- Re: [AMBER] antechamber cannot match patching atoms of amino acid (Fri Aug 12 2016 - 01:12:01 PDT)
giulia palermo
- Re: [AMBER] problem upon optimization (Thu Aug 25 2016 - 15:34:15 PDT)
- [AMBER] problem upon optimization (Thu Aug 25 2016 - 08:12:39 PDT)
Hai Nguyen
- Re: [AMBER] Amber Force Fields (Wed Aug 31 2016 - 12:40:45 PDT)
- Re: [AMBER] changing atom type (Wed Aug 31 2016 - 08:41:22 PDT)
- Re: [AMBER] Checking AmberTools16 installation (Tue Aug 30 2016 - 10:07:17 PDT)
- Re: [AMBER] Checking AmberTools16 installation (Tue Aug 30 2016 - 09:30:49 PDT)
- Re: [AMBER] Checking AmberTools16 installation (Mon Aug 29 2016 - 10:09:08 PDT)
- Re: [AMBER] (no subject) (Sat Aug 27 2016 - 20:34:02 PDT)
- Re: [AMBER] Multihist in watershell command (Fri Aug 26 2016 - 10:35:39 PDT)
- Re: [AMBER] repair mdcrd? (Thu Aug 25 2016 - 13:47:07 PDT)
- Re: [AMBER] Checking AmberTools16 installation (Thu Aug 25 2016 - 12:45:01 PDT)
- Re: [AMBER] Generating topology and parameter file for a peptide (Tue Aug 23 2016 - 23:37:14 PDT)
- Re: [AMBER] Checking modeling after MCPB and unable to fix atom order using cpptraj (Tue Aug 23 2016 - 22:44:43 PDT)
- Re: [AMBER] Output Files (Mon Aug 22 2016 - 20:33:37 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Mon Aug 22 2016 - 10:17:51 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Mon Aug 22 2016 - 09:40:38 PDT)
- Re: [AMBER] percentages of protein secondary structure. (Fri Aug 19 2016 - 07:51:53 PDT)
- Re: [AMBER] Problem when visualizing bonds in VMD (Thu Aug 18 2016 - 15:12:22 PDT)
- Re: [AMBER] RMSd (Wed Aug 17 2016 - 21:11:05 PDT)
- Re: [AMBER] Combining single structure NMR pdb files into an ensemble. (Tue Aug 16 2016 - 13:45:14 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Mon Aug 15 2016 - 10:15:04 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Mon Aug 15 2016 - 09:50:41 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Fri Aug 12 2016 - 11:49:05 PDT)
- Re: [AMBER] not sure if this is an ERROR in installation please suggest (Fri Aug 12 2016 - 06:36:34 PDT)
- Re: [AMBER] not sure if this is an ERROR in installation please suggest (Thu Aug 11 2016 - 22:11:31 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 14:06:31 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 13:36:56 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 13:16:30 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 13:13:53 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 12:52:46 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 12:41:34 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 12:12:35 PDT)
- Re: [AMBER] Amber16 installation error. (Thu Aug 11 2016 - 11:54:41 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Thu Aug 11 2016 - 11:49:15 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Thu Aug 11 2016 - 11:32:25 PDT)
- Re: [AMBER] Converting rst to pdb (Tue Aug 09 2016 - 14:09:46 PDT)
- Re: [AMBER] copy charges using Python API (Mon Aug 08 2016 - 12:06:07 PDT)
- Re: [AMBER] Implicit solvent in pmemd.cuda (Fri Aug 05 2016 - 09:05:47 PDT)
- Re: [AMBER] unreadable crd files (Thu Aug 04 2016 - 21:05:07 PDT)
- Re: [AMBER] gbsa parameter (Wed Aug 03 2016 - 09:33:14 PDT)
Hannes Loeffler
- Re: [AMBER] errors in doing TI tutorial calculation (Mon Aug 29 2016 - 12:26:33 PDT)
- Re: [AMBER] begin time read from input coords (Fri Aug 26 2016 - 08:34:45 PDT)
- Re: [AMBER] begin time read from input coords (Fri Aug 26 2016 - 05:01:40 PDT)
- [AMBER] begin time read from input coords (Fri Aug 26 2016 - 01:10:09 PDT)
- Re: [AMBER] 22.1.6.1. Free Energy using linear scaling 22.1.6.2.Absolute free energy using soft core, (Wed Aug 24 2016 - 04:58:58 PDT)
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server (Thu Aug 18 2016 - 02:19:35 PDT)
- Re: [AMBER] parmchk2 issue (Tue Aug 16 2016 - 06:47:21 PDT)
- Re: [AMBER] parmchk2 issue (Tue Aug 16 2016 - 01:35:08 PDT)
- [AMBER] parmchk2 issue (Mon Aug 15 2016 - 08:06:38 PDT)
- Re: [AMBER] parmchk vs parmchk2 (Mon Aug 15 2016 - 00:39:45 PDT)
Harshavardhan Khare
- Re: [AMBER] Does Scaled MD require NVT ensemble? (Fri Aug 19 2016 - 22:01:53 PDT)
- [AMBER] Does Scaled MD require NVT ensemble? (Thu Aug 18 2016 - 23:20:40 PDT)
Hirdesh Kumar
- Re: [AMBER] restraint does not work in mininmization (Tue Aug 30 2016 - 01:02:56 PDT)
- Re: [AMBER] GPU peer support disabled (Thu Aug 11 2016 - 14:11:38 PDT)
- [AMBER] GPU peer support disabled (Thu Aug 11 2016 - 13:53:22 PDT)
Ilkow, Veronica
- [AMBER] Cpptraj-PCA Warning (Fri Aug 05 2016 - 07:15:50 PDT)
Indrajit Deb
- [AMBER] Regarding hbond bridgeout (Wed Aug 24 2016 - 09:04:17 PDT)
Irem Altan
- [AMBER] restraining mean square displacements (Fri Aug 05 2016 - 12:52:35 PDT)
Jacopo Sgrignani
- Re: [AMBER] QM/MM energy units? (Wed Aug 31 2016 - 08:56:24 PDT)
- [AMBER] changing atom type (Wed Aug 31 2016 - 08:16:37 PDT)
JAIME RUBIO MARTINEZ
- Re: [AMBER] InVacuoWithDielc (Tue Aug 02 2016 - 00:32:58 PDT)
Jason Swails
- Re: [AMBER] changing atom type (Wed Aug 31 2016 - 09:00:20 PDT)
- Re: [AMBER] (no subject) (Mon Aug 29 2016 - 08:27:33 PDT)
- Re: [AMBER] MMPBSA.py CalcError on ligand contribution only (Thu Aug 25 2016 - 17:19:27 PDT)
- Re: [AMBER] MMPBSA.py CalcError on ligand contribution only (Thu Aug 25 2016 - 10:35:26 PDT)
- Re: [AMBER] problem upon optimization (Thu Aug 25 2016 - 10:34:44 PDT)
- Re: [AMBER] cpptraj on pH-REMD (Wed Aug 24 2016 - 19:34:16 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Tue Aug 23 2016 - 09:25:45 PDT)
- Re: [AMBER] Alanine scan of nonnatural amino acid (Tue Aug 23 2016 - 09:21:07 PDT)
- Re: [AMBER] What cutoff you use in Amber simulations? (Fri Aug 19 2016 - 05:57:48 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Fri Aug 19 2016 - 05:51:35 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Thu Aug 18 2016 - 05:18:47 PDT)
- Re: [AMBER] Problem when visualizing bonds in VMD (Wed Aug 17 2016 - 13:17:27 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Mon Aug 15 2016 - 18:56:04 PDT)
- Re: [AMBER] CHARM force field (Mon Aug 15 2016 - 18:50:22 PDT)
- Re: [AMBER] copy charges using Python API (Sun Aug 07 2016 - 06:05:35 PDT)
- Re: [AMBER] Error with nmode calculations (Fri Aug 05 2016 - 12:10:33 PDT)
- Re: [AMBER] 180 degrees of angle in AMBER 10 (Thu Aug 04 2016 - 13:30:36 PDT)
- Re: [AMBER] Getting free energy (difference) from GPU simulations (Thu Aug 04 2016 - 11:09:44 PDT)
- Re: [AMBER] interaction entropy instead of normal mode analysis (Thu Aug 04 2016 - 11:03:44 PDT)
- Re: [AMBER] Is there a way to disable electrostatic solute-solvent interactions in PMEMD? (Thu Aug 04 2016 - 11:02:00 PDT)
- Re: [AMBER] save Hessian nmode mmpbsa (Thu Aug 04 2016 - 10:56:37 PDT)
Jingyi Yan
- [AMBER] running RISM/MD on multi processors (Tue Aug 02 2016 - 14:26:16 PDT)
JoAnne Babula
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Mon Aug 22 2016 - 17:56:23 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Mon Aug 22 2016 - 09:58:21 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Mon Aug 22 2016 - 09:04:27 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Mon Aug 22 2016 - 08:54:16 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Mon Aug 22 2016 - 08:33:56 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Mon Aug 22 2016 - 07:19:03 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Fri Aug 12 2016 - 11:41:21 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Fri Aug 12 2016 - 10:38:24 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Fri Aug 12 2016 - 10:34:41 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Thu Aug 11 2016 - 11:41:31 PDT)
- [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Thu Aug 11 2016 - 08:21:11 PDT)
- Re: [AMBER] 3 trajectory MMPBSA free energy calculation (Wed Aug 10 2016 - 11:04:44 PDT)
- [AMBER] 3 trajectory MMPBSA free energy calculation (Wed Aug 10 2016 - 07:47:45 PDT)
- Re: [AMBER] Amber14 FEW for 3 trajectory free energy (Tue Aug 09 2016 - 11:02:24 PDT)
- [AMBER] Amber14 FEW for 3 trajectory free energy (Fri Aug 05 2016 - 07:32:22 PDT)
kenfack cyril
- Re: [AMBER] EVB calculations of proton transfer (Mon Aug 01 2016 - 14:05:09 PDT)
konda003 .
- [AMBER] Generate Polymer parameters (Wed Aug 03 2016 - 12:58:24 PDT)
Kostas Bourandas
- Re: [AMBER] Extend of manual modulation-Connecting two molecules methodology (Mon Aug 08 2016 - 19:56:53 PDT)
- [AMBER] Extend of manual modulation-Connecting two molecules methodology (Sat Aug 06 2016 - 13:32:44 PDT)
Leandro Bortot
- Re: [AMBER] MMPBSA.py CalcError on ligand contribution only (Thu Aug 25 2016 - 12:51:54 PDT)
- [AMBER] MMPBSA.py CalcError on ligand contribution only (Thu Aug 25 2016 - 07:43:11 PDT)
leila karami
- [AMBER] error in sander and sander.mpi running (Sun Aug 14 2016 - 05:24:31 PDT)
- [AMBER] error in sander and sander.mpi running (Sun Aug 14 2016 - 04:11:11 PDT)
li he
- [AMBER] Is there any CG martini parameter for K+? (Wed Aug 17 2016 - 11:18:34 PDT)
macc_200
- [AMBER] unreadable crd files (Thu Aug 04 2016 - 14:47:48 PDT)
Marc van der Kamp
- Re: [AMBER] amber pdb > 100,000 atoms (Fri Aug 12 2016 - 01:19:18 PDT)
- Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water (Tue Aug 09 2016 - 07:43:13 PDT)
Markus Kaukonen
- [AMBER] output of MMPBSA.py (Thu Aug 25 2016 - 03:43:20 PDT)
- [AMBER] 22.1.6.1. Free Energy using linear scaling 22.1.6.2.Absolute free energy using soft core, (Wed Aug 24 2016 - 01:01:45 PDT)
- [AMBER] amber16/test/qmmm_DFTB (Thu Aug 04 2016 - 23:13:12 PDT)
maryam azimzadehirani
- Re: [AMBER] MMPBSA.py TrajError: Could not find number of frames in .mdcrd (Mon Aug 08 2016 - 00:27:58 PDT)
- [AMBER] MMPBSA.py TrajError: Could not find number of frames in .mdcrd (Thu Aug 04 2016 - 20:52:07 PDT)
Michael Shokhen
- Re: [AMBER] frozen geometry setting? (Wed Aug 31 2016 - 06:34:36 PDT)
- Re: [AMBER] frozen geometry setting? (Tue Aug 30 2016 - 12:12:33 PDT)
- Re: [AMBER] frozen geometry setting? (Tue Aug 30 2016 - 11:55:56 PDT)
- [AMBER] frozen geometry setting? (Tue Aug 30 2016 - 07:32:09 PDT)
- [AMBER] restraint does not work in mininmization (Tue Aug 30 2016 - 00:48:54 PDT)
Ming Tang
- Re: [AMBER] How to fix the wall of the water box in amber (Sat Aug 06 2016 - 22:34:11 PDT)
- [AMBER] How to fix the wall of the water box in amber (Sat Aug 06 2016 - 18:17:18 PDT)
mirko hennig
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Sat Aug 27 2016 - 15:32:25 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Sat Aug 27 2016 - 09:52:04 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Tue Aug 16 2016 - 07:53:42 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Tue Aug 16 2016 - 00:18:10 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Mon Aug 15 2016 - 11:00:40 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Mon Aug 15 2016 - 10:03:04 PDT)
- [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Mon Aug 15 2016 - 09:26:56 PDT)
- Re: [AMBER] {AMBER} installation on mac osx 10.11.6 hanging when configuring NetCDF (Tue Aug 09 2016 - 08:29:50 PDT)
- [AMBER] {AMBER} installation on mac osx 10.11.6 hanging when configuring NetCDF (Tue Aug 09 2016 - 00:53:23 PDT)
Neha Gandhi
- [AMBER] Sigma and epsilon vdw parameters (Mon Aug 22 2016 - 15:28:44 PDT)
- Re: [AMBER] solid surface simulation in amber (Mon Aug 22 2016 - 03:17:23 PDT)
- Re: [AMBER] solid surface simulation in amber (Mon Aug 22 2016 - 02:00:52 PDT)
- Re: [AMBER] solid surface simulation in amber (Fri Aug 19 2016 - 18:28:18 PDT)
- Re: [AMBER] solid surface simulation in amber (Fri Aug 19 2016 - 01:57:24 PDT)
- Re: [AMBER] solid surface simulation in amber (Thu Aug 18 2016 - 01:48:12 PDT)
- Re: [AMBER] solid surface simulation in amber (Thu Aug 18 2016 - 01:27:28 PDT)
- Re: [AMBER] solid surface simulation in amber (Tue Aug 16 2016 - 06:17:47 PDT)
- Re: [AMBER] solid surface simulation in amber (Tue Aug 16 2016 - 01:00:20 PDT)
- Re: [AMBER] solid surface simulation in amber (Mon Aug 15 2016 - 22:25:46 PDT)
- [AMBER] solid surface simulation in amber (Sun Aug 14 2016 - 23:59:57 PDT)
- [AMBER] amber pdb > 100,000 atoms (Fri Aug 12 2016 - 00:53:28 PDT)
- [AMBER] solvate hexagonal box (Wed Aug 03 2016 - 22:29:52 PDT)
Nhai
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan (Sat Aug 27 2016 - 15:07:14 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Mon Aug 22 2016 - 08:38:38 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation (Mon Aug 22 2016 - 08:31:42 PDT)
- Re: [AMBER] Problem when visualizing bonds in VMD (Fri Aug 19 2016 - 14:53:17 PDT)
- Re: [AMBER] percentages of protein secondary structure. (Thu Aug 18 2016 - 22:32:00 PDT)
- Re: [AMBER] job suspended (Fri Aug 12 2016 - 08:26:09 PDT)
nida baig
- Re: [AMBER] error in runing mdout_analyzer.py (Wed Aug 03 2016 - 21:39:05 PDT)
- [AMBER] error in runing mdout_analyzer.py (Wed Aug 03 2016 - 21:10:04 PDT)
Osman, Roman
- Re: [AMBER] autocorr of hydrogen bonds (Tue Aug 30 2016 - 14:41:38 PDT)
- [AMBER] autocorr of hydrogen bonds (Mon Aug 29 2016 - 06:05:06 PDT)
Parviz Seifpanahi Shabane
- Re: [AMBER] MASK with distance in AMBER. (Tue Aug 16 2016 - 11:23:32 PDT)
- Re: [AMBER] secondary structure graph vs Time (Tue Aug 16 2016 - 08:45:59 PDT)
- Re: [AMBER] secondary structure graph vs Time (Mon Aug 15 2016 - 13:28:43 PDT)
- [AMBER] MASK with distance in AMBER. (Fri Aug 12 2016 - 08:48:32 PDT)
- Re: [AMBER] secondary structure graph vs Time (Thu Aug 11 2016 - 09:16:59 PDT)
- [AMBER] secondary structure graph vs Time (Thu Aug 11 2016 - 09:03:01 PDT)
Pengfei Li
- Re: [AMBER] Generating parameter and topology files for a protein with multiple Zinc ions (Sat Aug 27 2016 - 13:55:54 PDT)
- Re: [AMBER] Copper +1 and membrane with LJ 12-6-4 potential (Sat Aug 27 2016 - 13:48:22 PDT)
- Re: [AMBER] Two ion problem with mcpb.py (Thu Aug 18 2016 - 18:18:35 PDT)
- Re: [AMBER] Is there any CG martini parameter for K+? (Wed Aug 17 2016 - 13:40:33 PDT)
- Re: [AMBER] Two ion problem with mcpb.py (Tue Aug 16 2016 - 07:40:46 PDT)
- Re: [AMBER] does AMBER already have Pt parameters for modeling cisplatin like compounds? (Wed Aug 10 2016 - 06:37:06 PDT)
Pengzhi Zhang
- [AMBER] 180 degrees of angle in AMBER 10 (Wed Aug 03 2016 - 13:07:26 PDT)
Plotnikov, Nikolay
- [AMBER] Is there a way to disable electrostatic solute-solvent interactions in PMEMD? (Thu Aug 04 2016 - 08:27:25 PDT)
Prajwal Nandekar
- Re: [AMBER] secondary structure graph vs Time (Fri Aug 12 2016 - 01:58:20 PDT)
Praneeth Bommisetti
- [AMBER] Error with nmode calculations (Fri Aug 05 2016 - 11:10:32 PDT)
pratibha sharma
- [AMBER] Generating topology and parameter file for a peptide (Tue Aug 23 2016 - 23:34:57 PDT)
rain
- [AMBER] the end phosphoric acid group is deformed during simulation (Tue Aug 02 2016 - 17:12:34 PDT)
Ray Luo
- Re: [AMBER] default value (inp= 0,1,2)? MMPBSA (Mon Aug 01 2016 - 12:25:42 PDT)
- Re: [AMBER] tinker_to_amber error (Mon Aug 01 2016 - 10:40:08 PDT)
- Re: [AMBER] default value (inp= 0,1,2)? MMPBSA (Mon Aug 01 2016 - 10:35:04 PDT)
Robert Molt
- Re: [AMBER] Question of Parameter Defaults (Mon Aug 15 2016 - 10:49:12 PDT)
- [AMBER] Question of Parameter Defaults (Fri Aug 12 2016 - 18:00:57 PDT)
Ross Walker
- Re: [AMBER] Issues compiling Amber with CUDA support (Sat Aug 27 2016 - 15:53:28 PDT)
- Re: [AMBER] Issues compiling Amber with CUDA support (Thu Aug 25 2016 - 04:30:46 PDT)
- Re: [AMBER] Does Scaled MD require NVT ensemble? (Fri Aug 19 2016 - 07:13:12 PDT)
- Re: [AMBER] Restarting a crushed run (Tue Aug 16 2016 - 15:53:43 PDT)
- Re: [AMBER] lipid simulation with Lipid14 FF failed (Tue Aug 16 2016 - 07:07:30 PDT)
- Re: [AMBER] Amber16 Parallel CUDA Tests (Thu Aug 11 2016 - 21:39:19 PDT)
- Re: [AMBER] not sure if this is an ERROR in installation please suggest (Thu Aug 11 2016 - 21:32:26 PDT)
- Re: [AMBER] Amber16 Parallel CUDA Tests (Thu Aug 11 2016 - 21:29:05 PDT)
- Re: [AMBER] Amber16 Parallel CUDA Tests (Thu Aug 11 2016 - 20:17:16 PDT)
- Re: [AMBER] LINMIN FAILURE on large protein minimization with GB and explicit (Thu Aug 11 2016 - 18:47:20 PDT)
- Re: [AMBER] GPU peer support disabled (Thu Aug 11 2016 - 14:01:33 PDT)
- Re: [AMBER] Amber 14.13 pmemd.cuda: Error: invalid configuration argument launching kernel kPMEReduceChargeGridBuffer (Wed Aug 10 2016 - 20:01:52 PDT)
- Re: [AMBER] Implicit solvent in pmemd.cuda (Fri Aug 05 2016 - 09:39:36 PDT)
- Re: [AMBER] which forcefield it is? (Tue Aug 02 2016 - 09:22:05 PDT)
Ruth Helena Tichauer
- [AMBER] Water flexibility in QM/MM simulation (Tue Aug 16 2016 - 09:27:14 PDT)
- Re: [AMBER] Sander bomb: how to create a larger box (Tue Aug 02 2016 - 07:14:33 PDT)
- Re: [AMBER] Sander bomb: how to create a larger box (Mon Aug 01 2016 - 05:38:12 PDT)
- Re: [AMBER] Sander bomb: how to create a larger box (Mon Aug 01 2016 - 04:42:28 PDT)
- Re: [AMBER] Sander bomb: how to create a larger box (Mon Aug 01 2016 - 03:53:51 PDT)
Saman Yousuf ali
- [AMBER] Frac in cpptraj hydrogen bond command. (Sun Aug 21 2016 - 05:25:42 PDT)
- [AMBER] minimum restraint_wt. (Sun Aug 21 2016 - 00:05:43 PDT)
- [AMBER] percentages of protein secondary structure. (Thu Aug 18 2016 - 21:17:59 PDT)
- Re: [AMBER] bellymask option. (Tue Aug 16 2016 - 07:48:26 PDT)
- [AMBER] bellymask option. (Mon Aug 15 2016 - 19:24:05 PDT)
- Re: [AMBER] simultaneous use of ibelly=1 and ntr=1 (Tue Aug 09 2016 - 12:41:00 PDT)
- [AMBER] simultaneous use of ibelly=1 and ntr=1 (Tue Aug 09 2016 - 08:54:47 PDT)
- Re: [AMBER] query regarding restraint on specific residues. (Tue Aug 09 2016 - 08:08:10 PDT)
- [AMBER] query regarding restraint on specific residues. (Tue Aug 09 2016 - 00:00:57 PDT)
- Re: [AMBER] error running production with restraint. (Sat Aug 06 2016 - 02:29:13 PDT)
- Re: [AMBER] error running production with restraint. (Fri Aug 05 2016 - 02:04:39 PDT)
- [AMBER] error running production with restraint. (Wed Aug 03 2016 - 22:16:51 PDT)
Samuel Bowerman
- Re: [AMBER] Problem with atommap function in cpptraj (v16) (Tue Aug 30 2016 - 12:39:05 PDT)
- [AMBER] Problem with atommap function in cpptraj (v16) (Tue Aug 23 2016 - 12:23:56 PDT)
- Re: [AMBER] Running tleap with old prmtop (Thu Aug 11 2016 - 10:30:18 PDT)
Sidhu, Khushwant (Dr.)
- [AMBER] HBond command (Tue Aug 02 2016 - 05:50:08 PDT)
Sivanandam M
- [AMBER] Regarding the free energy calculation (Tue Aug 16 2016 - 11:00:06 PDT)
Sivy, Shawn
- [AMBER] Issues compiling Amber with CUDA support (Wed Aug 24 2016 - 11:47:10 PDT)
Sonia Ziada
- [AMBER] File redirection commands with targeted MD (Wed Aug 31 2016 - 09:10:52 PDT)
Stephan Schott
- [AMBER] Copper +1 and membrane with LJ 12-6-4 potential (Tue Aug 23 2016 - 07:37:52 PDT)
- Re: [AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?) (Tue Aug 02 2016 - 07:00:29 PDT)
Steven Ford
- Re: [AMBER] Amber16 Parallel CUDA Tests (Fri Aug 12 2016 - 09:44:54 PDT)
- Re: [AMBER] Amber16 Parallel CUDA Tests (Thu Aug 11 2016 - 21:38:10 PDT)
- Re: [AMBER] Amber16 Parallel CUDA Tests (Thu Aug 11 2016 - 21:33:15 PDT)
- Re: [AMBER] Amber16 Parallel CUDA Tests (Thu Aug 11 2016 - 21:21:52 PDT)
- Re: [AMBER] Amber16 Parallel CUDA Tests (Thu Aug 11 2016 - 19:54:15 PDT)
Stregone
- [AMBER] Fw: Problems to calculate frequencies (Thu Aug 25 2016 - 03:14:42 PDT)
- [AMBER] Optimal force constant for AMBER (Fri Aug 12 2016 - 06:29:15 PDT)
- Re: [AMBER] QMMM MD, Simulation does not start (Mon Aug 08 2016 - 01:20:03 PDT)
- Re: [AMBER] QMMM MD, Simulation does not start (Sun Aug 07 2016 - 04:01:57 PDT)
- [AMBER] QMMM MD, Simulation does not start (Fri Aug 05 2016 - 06:29:59 PDT)
- Re: [AMBER] Amber´14 Solvent box simulation, something went wrong!! (Thu Aug 04 2016 - 02:08:37 PDT)
- [AMBER] Amber´14 Solvent box simulation, something went wrong!! (Wed Aug 03 2016 - 06:43:18 PDT)
Suguru ASAI
- Re: [AMBER] EEL become ****** in minimization (Sun Jul 31 2016 - 21:10:44 PDT)
SUNHEE CHO
- [AMBER] LINMIN FAILURE on large protein minimization with GB and explicit (Thu Aug 11 2016 - 18:25:19 PDT)
sunita guptacDgug
- Re: [AMBER] Two ion problem with mcpb.py (Fri Aug 12 2016 - 12:50:46 PDT)
Taylor Quinn
- [AMBER] Running tleap with old prmtop (Thu Aug 11 2016 - 10:13:09 PDT)
Thakur, Abhishek
- [AMBER] WHAM analysis (Fri Aug 19 2016 - 14:55:16 PDT)
- Re: [AMBER] umbrella sampling restraining both angle and distance (Fri Aug 12 2016 - 15:49:30 PDT)
- [AMBER] umbrella sampling restraining both angle and distance (Fri Aug 12 2016 - 09:50:11 PDT)
- Re: [AMBER] for what kind of post simulation analysis I need to do reweighing? (Tue Aug 09 2016 - 08:08:32 PDT)
- [AMBER] for what kind of post simulation analysis I need to do reweighing? (Tue Aug 09 2016 - 08:01:27 PDT)
- [AMBER] phi-psi distribution (Mon Aug 08 2016 - 13:54:24 PDT)
- [AMBER] reweighting scheme (Mon Aug 08 2016 - 12:02:00 PDT)
- Re: [AMBER] default value (inp= 0,1,2)? MMPBSA (Mon Aug 01 2016 - 11:42:29 PDT)
- [AMBER] default value (inp= 0,1,2)? MMPBSA (Mon Aug 01 2016 - 09:35:16 PDT)
Thomas Evangelidis
- Re: [AMBER] lowering the temperature (Wed Aug 31 2016 - 03:33:26 PDT)
- [AMBER] lowering the temperature (Tue Aug 30 2016 - 16:51:40 PDT)
- Re: [AMBER] copy charges using Python API (Mon Aug 08 2016 - 03:00:44 PDT)
- Re: [AMBER] copy charges using Python API (Sun Aug 07 2016 - 06:50:23 PDT)
- [AMBER] copy charges using Python API (Sun Aug 07 2016 - 04:28:38 PDT)
- [AMBER] gbsa parameter (Wed Aug 03 2016 - 08:54:11 PDT)
Thomas Pochapsky
- Re: [AMBER] Fwd: cpptraj issues (Tue Aug 16 2016 - 08:23:25 PDT)
- [AMBER] Fwd: cpptraj issues (Tue Aug 16 2016 - 07:20:30 PDT)
- [AMBER] Fwd: cpptraj issues (Mon Aug 15 2016 - 08:02:22 PDT)
- [AMBER] cpptraj issues (Fri Aug 12 2016 - 09:52:19 PDT)
Tom Kurtzman
- Re: [AMBER] autocorr of hydrogen bonds (Tue Aug 30 2016 - 08:07:36 PDT)
Tomek Wlodarski
- [AMBER] Parameters for modified nucleosides (Tue Aug 30 2016 - 10:34:09 PDT)
Tyler Luchko (Lists)
- Re: [AMBER] running RISM/MD on multi processors (Tue Aug 02 2016 - 14:46:02 PDT)
vadiraj kurdekar
- Re: [AMBER] SEP parameter with ff15ipq (Thu Aug 25 2016 - 21:43:22 PDT)
- [AMBER] SEP parameter with ff15ipq (Thu Aug 25 2016 - 00:08:31 PDT)
Vaibhav Dixit
- Re: [AMBER] not sure if this is an ERROR in installation please suggest (Fri Aug 12 2016 - 00:43:29 PDT)
- [AMBER] not sure if this is an ERROR in installation please suggest (Thu Aug 11 2016 - 20:44:07 PDT)
- [AMBER] does AMBER already have Pt parameters for modeling cisplatin like compounds? (Wed Aug 10 2016 - 04:49:05 PDT)
Vishal Nemaysh
- Re: [AMBER] Regarding antechamber command Error (Thu Aug 11 2016 - 23:36:29 PDT)
- Re: [AMBER] Regarding antechamber command Error (Thu Aug 11 2016 - 06:07:53 PDT)
- [AMBER] Fwd: Regarding antechamber command Error (Thu Aug 11 2016 - 00:10:40 PDT)
- [AMBER] Regarding antechamber command Error (Wed Aug 10 2016 - 08:47:05 PDT)
Vlad Cojocaru
- [AMBER] modeling flexible loops in protein-DNA complexes (Fri Aug 12 2016 - 01:43:23 PDT)
William Lees
- Re: [AMBER] Amber 14.13 pmemd.cuda: Error: invalid configuration argument launching kernel kPMEReduceChargeGridBuffer (Fri Aug 12 2016 - 06:19:05 PDT)
- [AMBER] Amber 14.13 pmemd.cuda: Error: invalid configuration argument launching kernel kPMEReduceChargeGridBuffer (Wed Aug 10 2016 - 02:02:59 PDT)
- Re: [AMBER] copy charges using Python API (Tue Aug 09 2016 - 02:07:50 PDT)
windy
- [AMBER] change the atom charge in a restart simulations (Wed Aug 31 2016 - 01:49:25 PDT)
Wong Li Zhe
- [AMBER] Simulation Time (Mon Aug 22 2016 - 22:00:03 PDT)
- [AMBER] Output Files (Mon Aug 22 2016 - 18:03:36 PDT)
- Re: [AMBER] RMSd (Wed Aug 17 2016 - 22:50:22 PDT)
- Re: [AMBER] RMSd (Wed Aug 17 2016 - 21:12:52 PDT)
- [AMBER] RMSd (Wed Aug 17 2016 - 21:08:05 PDT)
Xiaoliu Zhang
- Re: [AMBER] Problem when visualizing bonds in VMD (Fri Aug 19 2016 - 13:30:22 PDT)
- Re: [AMBER] Problem when visualizing bonds in VMD (Thu Aug 18 2016 - 14:56:00 PDT)
- [AMBER] Problem when visualizing bonds in VMD (Wed Aug 17 2016 - 12:40:22 PDT)
- [AMBER] box of polar molecules using amoeba force field (Fri Aug 05 2016 - 14:32:46 PDT)
- Re: [AMBER] Use two different force fields in Amber (Fri Aug 05 2016 - 08:30:56 PDT)
- Re: [AMBER] tinker_to_amber error (Wed Aug 03 2016 - 07:46:04 PDT)
- [AMBER] tinker_to_amber error (Mon Aug 01 2016 - 08:52:17 PDT)
- [AMBER] Use two different force fields in Amber (Mon Aug 01 2016 - 07:41:19 PDT)
Ye Mei
- [AMBER] a bug in leaprc.gaff2 file (Thu Aug 18 2016 - 02:21:16 PDT)
yunshi11 .
- [AMBER] Getting free energy (difference) from GPU simulations (Wed Aug 03 2016 - 16:18:05 PDT)
zoran matovic
- Re: [AMBER] error running production with restraint. (Fri Aug 05 2016 - 00:14:00 PDT)
- Re: [AMBER] error running production with restraint. (Thu Aug 04 2016 - 11:38:52 PDT)
- Re: [AMBER] error running production with restraint. (Thu Aug 04 2016 - 11:27:49 PDT)
乔艳
- [AMBER] the phosphoric acid group is deformed (Tue Aug 02 2016 - 16:40:30 PDT)
张姝姝
- [AMBER] errors in doing TI tutorial calculation (Mon Aug 29 2016 - 07:26:56 PDT)
- [AMBER] EEL energy of QM/MM-GBSA (Sun Jul 31 2016 - 20:11:42 PDT)

Amber Archive Aug 2016 by author