Amber Archive Apr 2017: by author

Adams, John E.
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 (Sat Apr 29 2017 - 09:43:27 PDT)
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 (Fri Apr 28 2017 - 15:49:46 PDT)
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 (Fri Apr 28 2017 - 15:24:10 PDT)
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 (Fri Apr 28 2017 - 14:59:15 PDT)
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 (Fri Apr 28 2017 - 11:03:36 PDT)
- [AMBER] tleap input file that fails following upgrade to AmberTools17 (Thu Apr 27 2017 - 08:45:51 PDT)
Adrian Roitberg
- Re: [AMBER] Stricter convergence Criterion for stretching (Tue Apr 25 2017 - 11:01:02 PDT)
- Re: [AMBER] Segmentation fault (Fri Apr 21 2017 - 06:40:34 PDT)
- Re: [AMBER] Internal dielectric constant and pmemd (Fri Apr 21 2017 - 06:26:37 PDT)
- Re: [AMBER] Internal dielectric constant and pmemd (Fri Apr 21 2017 - 06:14:52 PDT)
- Re: [AMBER] coordinate bond between them and S and FE (Mon Apr 17 2017 - 08:14:58 PDT)
- Re: [AMBER] PCA - concatenating trajectories (Mon Apr 17 2017 - 06:21:50 PDT)
- Re: [AMBER] coordinate bond between them and S and FE (Fri Apr 14 2017 - 13:48:37 PDT)
Aishani Prem
- [AMBER] Pairwise energy calculations in cpptraj (Mon Apr 24 2017 - 20:07:52 PDT)
Andreas Tosstorff
- [AMBER] Post Doc position in Munich, German required (Wed Apr 26 2017 - 09:01:44 PDT)
- Re: [AMBER] AMBER umbrella sampling (Thu Apr 13 2017 - 09:59:01 PDT)
- Re: [AMBER] Minimization fails when switching from steepest descent to conjugate gradient (Sun Apr 09 2017 - 14:40:02 PDT)
- [AMBER] Minimization fails when switching from steepest descent to conjugate gradient (Sat Apr 08 2017 - 16:08:36 PDT)
- Re: [AMBER] Acetonitrile Water Mix (Fri Apr 07 2017 - 06:32:01 PDT)
- [AMBER] How to write an frcmod file (Thu Apr 06 2017 - 01:13:23 PDT)
- Re: [AMBER] Acetonitrile Water Mix (Wed Apr 05 2017 - 09:08:53 PDT)
- Re: [AMBER] GPU performance (Wed Apr 05 2017 - 07:35:54 PDT)
- Re: [AMBER] Acetonitrile Water Mix (Wed Apr 05 2017 - 05:50:55 PDT)
- [AMBER] Acetonitrile Water Mix (Wed Apr 05 2017 - 05:35:31 PDT)
- Re: [AMBER] 3 GPUs ? (Tue Apr 04 2017 - 00:18:53 PDT)
Andrew Schaub
- Re: [AMBER] coordinate bond between them and S and FE (Fri Apr 14 2017 - 14:23:27 PDT)
Andy Watkins
- Re: [AMBER] reorientation in rmsd (Wed Apr 12 2017 - 20:18:26 PDT)
- Re: [AMBER] reorientation in rmsd (Wed Apr 12 2017 - 20:18:23 PDT)
Anna Cebrian Prats
- [AMBER] MMPBSA - error (Thu Apr 20 2017 - 08:02:45 PDT)
- [AMBER] mmpbsa- binding energy between ligand-receptor (Tue Apr 04 2017 - 06:27:06 PDT)
Aseel Bala
- [AMBER] Creating a pdb of only certain molecules from a frame (Tue Apr 04 2017 - 09:46:37 PDT)
Baker, Joseph
- Re: [AMBER] Warning message in AmberTools17 upgrade (Mon Apr 24 2017 - 11:53:37 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade (Mon Apr 24 2017 - 09:41:09 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade (Fri Apr 21 2017 - 13:53:04 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade (Fri Apr 21 2017 - 13:23:13 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade (Fri Apr 21 2017 - 12:43:43 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade (Fri Apr 21 2017 - 12:36:56 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade (Fri Apr 21 2017 - 12:30:27 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade (Fri Apr 21 2017 - 12:23:51 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade (Fri Apr 21 2017 - 12:17:52 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade (Fri Apr 21 2017 - 11:53:11 PDT)
- [AMBER] Warning message in AmberTools17 upgrade (Fri Apr 21 2017 - 11:41:19 PDT)
Ben Roberts
- Re: [AMBER] You won't believe what happens with maximum coordination limits... (Tue Apr 04 2017 - 12:53:23 PDT)
Bill Ross
- Re: [AMBER] barostat=1 error at Stampede (Thu Apr 27 2017 - 00:23:15 PDT)
- Re: [AMBER] Trouble with simple MD simulation of short peptide and Cu2+ ion (Tue Apr 25 2017 - 21:33:07 PDT)
- Re: [AMBER] Trouble with simple MD simulation of short peptide and Cu2+ ion (Tue Apr 25 2017 - 20:54:58 PDT)
- Re: [AMBER] Post MD minimization (Thu Apr 20 2017 - 02:51:25 PDT)
- Re: [AMBER] Release of AmberTools17 (Wed Apr 19 2017 - 14:08:30 PDT)
- Re: [AMBER] Adding hydrogens to a ligand (Tue Apr 18 2017 - 02:22:20 PDT)
- Re: [AMBER] How to calculate the solvation free energy using Amber? (Mon Apr 17 2017 - 01:52:51 PDT)
- Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? (Fri Apr 14 2017 - 23:48:34 PDT)
- Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? (Fri Apr 14 2017 - 23:01:41 PDT)
- Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? (Fri Apr 14 2017 - 22:22:34 PDT)
- Re: [AMBER] problem with temperature after rst (Wed Apr 12 2017 - 23:52:25 PDT)
- Re: [AMBER] problem with temperature after rst (Wed Apr 12 2017 - 23:44:36 PDT)
- Re: [AMBER] problem with temperature after rst (Wed Apr 12 2017 - 22:57:25 PDT)
- Re: [AMBER] problem with temperature after rst (Wed Apr 12 2017 - 22:52:51 PDT)
- Re: [AMBER] problem with temperature after rst (Wed Apr 12 2017 - 22:15:49 PDT)
- Re: [AMBER] reorientation in rmsd (Wed Apr 12 2017 - 11:28:35 PDT)
- Re: [AMBER] Periodic box error for restarting simulations with restraints (Tue Apr 11 2017 - 13:15:59 PDT)
- Re: [AMBER] Periodic box error for restarting simulations with restraints (Fri Apr 07 2017 - 22:13:48 PDT)
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy (Thu Apr 06 2017 - 01:57:08 PDT)
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy (Thu Apr 06 2017 - 00:41:25 PDT)
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy (Wed Apr 05 2017 - 10:35:51 PDT)
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy (Tue Apr 04 2017 - 21:17:26 PDT)
- Re: [AMBER] distance calculations - Protein-RNA (Tue Apr 04 2017 - 01:59:59 PDT)
Budhathoki, Dipesh
- Re: [AMBER] Regarding gaussian namelist error (Tue Apr 25 2017 - 20:48:12 PDT)
- [AMBER] Regarding gaussian namelist error (Tue Apr 25 2017 - 16:35:45 PDT)
Carlos Simmerling
- Re: [AMBER] Regarding REMD simulations of Proteins (Sun Apr 09 2017 - 09:22:24 PDT)
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy (Tue Apr 04 2017 - 14:19:54 PDT)
Charles Lin
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 (Wed Apr 05 2017 - 12:46:03 PDT)
Chris Moth
- [AMBER] PMEMD should halt with error exit after netcdf write failure (Thu Apr 20 2017 - 15:30:25 PDT)
- Re: [AMBER] Minimization fails when switching from steepest descent to conjugate gradient (Sun Apr 09 2017 - 14:06:06 PDT)
Chris Neale
- Re: [AMBER] PCA - concatenating trajectories (Mon Apr 17 2017 - 06:58:57 PDT)
- Re: [AMBER] Periodic box error for restarting simulations with restraints (Thu Apr 13 2017 - 13:19:14 PDT)
- Re: [AMBER] Diffusion and permeability coefficients (Thu Apr 06 2017 - 12:16:12 PDT)
- Re: [AMBER] 3 GPUs ? (Wed Apr 05 2017 - 17:04:27 PDT)
- Re: [AMBER] 3 GPUs ? (Tue Apr 04 2017 - 17:06:04 PDT)
- Re: [AMBER] 3 GPUs ? (Tue Apr 04 2017 - 13:28:43 PDT)
- [AMBER] 3 GPUs ? (Mon Apr 03 2017 - 19:43:01 PDT)
- Re: [AMBER] restarting Amber calculations gives abnormal structures (Sun Apr 02 2017 - 23:45:00 PDT)
d00b46022
- [AMBER] CPPTRAJ Cluster (Wed Apr 05 2017 - 02:26:09 PDT)
Daniel Roe
- Re: [AMBER] intra-residue water bridge with cpptraj (Wed Apr 26 2017 - 08:25:49 PDT)
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior (Tue Apr 25 2017 - 13:02:46 PDT)
- Re: [AMBER] Pairwise energy calculations in cpptraj (Tue Apr 25 2017 - 06:33:09 PDT)
- Re: [AMBER] cpptraj configure may fail in AmberTools17 (Tue Apr 25 2017 - 06:16:46 PDT)
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior (Tue Apr 25 2017 - 06:09:14 PDT)
- Re: [AMBER] AmberTools17 + intel17 = bug (Tue Apr 18 2017 - 17:34:24 PDT)
- Re: [AMBER] PCA - concatenating trajectories (Mon Apr 17 2017 - 06:25:47 PDT)
- Re: [AMBER] cpptraj creates pdb file it cannot read (Mon Apr 17 2017 - 05:40:13 PDT)
- Re: [AMBER] cpptraj creates pdb file it cannot read (Sun Apr 16 2017 - 08:17:09 PDT)
- Re: [AMBER] cpptraj creates pdb file it cannot read (Wed Apr 12 2017 - 08:05:56 PDT)
- Re: [AMBER] Creating a pdb of only certain molecules from a frame (Mon Apr 10 2017 - 11:46:20 PDT)
- Re: [AMBER] Periodic box error for restarting simulations with restraints (Fri Apr 07 2017 - 06:08:09 PDT)
- Re: [AMBER] CPPTRAJ Cluster (Wed Apr 05 2017 - 10:08:46 PDT)
- Re: [AMBER] ptraj hbonds (Wed Apr 05 2017 - 09:45:58 PDT)
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy (Wed Apr 05 2017 - 09:20:33 PDT)
- Re: [AMBER] distance calculations - Protein-RNA (Tue Apr 04 2017 - 05:17:02 PDT)
- Re: [AMBER] coordinates in restraint mast (Mon Apr 03 2017 - 10:29:24 PDT)
danil kutov
- [AMBER] How to perform good quality local optimization with Sander (Sat Apr 01 2017 - 00:48:50 PDT)
David A Case
- Re: [AMBER] problem with temperature after rst (Thu Apr 13 2017 - 04:55:54 PDT)
- Re: [AMBER] ERROR in load_lbfgs(): YS=0. (Thu Apr 13 2017 - 04:49:29 PDT)
- Re: [AMBER] Tleap error. (Thu Apr 06 2017 - 20:36:43 PDT)
- Re: [AMBER] Atom types for Baaden Hydronium Ion (Wed Apr 05 2017 - 12:17:21 PDT)
- Re: [AMBER] Binding site volume calculation (Wed Apr 05 2017 - 12:14:29 PDT)
- Re: [AMBER] Acetonitrile Water Mix (Wed Apr 05 2017 - 07:37:58 PDT)
- Re: [AMBER] How to distinguish between water molecules? (Wed Apr 05 2017 - 04:55:30 PDT)
- Re: [AMBER] Atom types for Baaden Hydronium Ion (Wed Apr 05 2017 - 04:51:49 PDT)
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy (Tue Apr 04 2017 - 05:17:39 PDT)
David Adrian Saez San Martin
- [AMBER] Using AmberTools17 and Amber14 (Fri Apr 28 2017 - 20:40:38 PDT)
David Case
- Re: [AMBER] Quenstions about Constraints in AMBER (Sun Apr 30 2017 - 17:14:40 PDT)
- Re: [AMBER] Dftb3 (Sat Apr 29 2017 - 14:33:59 PDT)
- Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. (Sat Apr 29 2017 - 05:28:00 PDT)
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 (Sat Apr 29 2017 - 05:20:13 PDT)
- Re: [AMBER] Release of AmberTools17 binary (Wed Apr 26 2017 - 12:22:25 PDT)
- Re: [AMBER] Regarding gaussian namelist error (Tue Apr 25 2017 - 17:22:08 PDT)
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior (Tue Apr 25 2017 - 10:27:45 PDT)
- Re: [AMBER] antechamber convergence problem. (Tue Apr 25 2017 - 05:07:34 PDT)
- Re: [AMBER] Query regarding energy calcuation using 3D-RISM (Mon Apr 24 2017 - 04:55:40 PDT)
- Re: [AMBER] Query regarding convergence issue of 3D-RISM (Mon Apr 24 2017 - 04:50:45 PDT)
- Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 (Sun Apr 23 2017 - 14:57:40 PDT)
- Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 (Sun Apr 23 2017 - 06:00:41 PDT)
- Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? (Sat Apr 22 2017 - 05:38:53 PDT)
- Re: [AMBER] residue-based dielectric model in MMGBSA (Sat Apr 22 2017 - 05:32:02 PDT)
- Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? (Fri Apr 21 2017 - 19:34:03 PDT)
- Re: [AMBER] Segmentation fault (Fri Apr 21 2017 - 19:17:50 PDT)
- Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 (Fri Apr 21 2017 - 18:42:49 PDT)
- Re: [AMBER] residue-based dielectric model in MMGBSA (Fri Apr 21 2017 - 18:25:25 PDT)
- Re: [AMBER] Segmentation fault (Fri Apr 21 2017 - 07:49:16 PDT)
- Re: [AMBER] Internal dielectric constant and pmemd (Fri Apr 21 2017 - 05:04:49 PDT)
- Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? (Thu Apr 20 2017 - 18:48:12 PDT)
- Re: [AMBER] Run NPT in a small periodic box (Thu Apr 20 2017 - 09:48:44 PDT)
- Re: [AMBER] Post MD minimization (Thu Apr 20 2017 - 08:07:50 PDT)
- Re: [AMBER] Release of AmberTools17 (Wed Apr 19 2017 - 12:27:36 PDT)
- Re: [AMBER] EVB with RPMD (Wed Apr 19 2017 - 08:59:58 PDT)
- Re: [AMBER] AmberTools17 + intel17 = bug (Tue Apr 18 2017 - 18:19:19 PDT)
- Re: [AMBER] pmemd.cuda on an Amber Certified High-End workstation (Tue Apr 18 2017 - 10:29:26 PDT)
- Re: [AMBER] Quasi-harmonic entropy calculation ---- Vibrational component of entropy (Tue Apr 18 2017 - 05:06:20 PDT)
- Re: [AMBER] Quasi-harmonic entropy calculation ---- Vibrational component of entropy (Tue Apr 18 2017 - 05:02:39 PDT)
- [AMBER] Release of AmberTools17 (Mon Apr 17 2017 - 18:28:04 PDT)
- Re: [AMBER] coordinate bond between them and S and FE (Mon Apr 17 2017 - 09:00:50 PDT)
- Re: [AMBER] weird asymmetries in solvent box (Mon Apr 17 2017 - 07:32:23 PDT)
- Re: [AMBER] weird asymmetries in solvent box (Mon Apr 17 2017 - 04:43:39 PDT)
- Re: [AMBER] Format error in frcmod file of HEME (Fri Apr 14 2017 - 11:41:09 PDT)
- Re: [AMBER] BCC charge for my HEME (Fri Apr 14 2017 - 11:34:28 PDT)
- Re: [AMBER] About Tutorial B3 (Thu Apr 13 2017 - 18:44:17 PDT)
- Re: [AMBER] Incorrect ligand parameterization using GAFF (Thu Apr 13 2017 - 18:40:41 PDT)
- Re: [AMBER] solvateBox for large size of RNA (Thu Apr 13 2017 - 07:20:39 PDT)
- Re: [AMBER] reorientation in rmsd (Wed Apr 12 2017 - 19:06:13 PDT)
- Re: [AMBER] antechamber problem (Wed Apr 12 2017 - 07:47:07 PDT)
- Re: [AMBER] simulation energies are exploding (Tue Apr 11 2017 - 05:12:59 PDT)
- Re: [AMBER] MMPBSA entropy calculation help (Mon Apr 10 2017 - 05:29:00 PDT)
- Re: [AMBER] Query regarding output of 3D-RISM in Amber. (Sun Apr 09 2017 - 17:26:28 PDT)
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy (Tue Apr 04 2017 - 18:44:22 PDT)
- Re: [AMBER] restarting Amber calculations gives abnormal structures (Mon Apr 03 2017 - 18:43:03 PDT)
- Re: [AMBER] placing water at specified coordinates with tleap (Mon Apr 03 2017 - 09:49:00 PDT)
- Re: [AMBER] mmpbsa - stability calculation (Mon Apr 03 2017 - 05:11:33 PDT)
- Re: [AMBER] How to perform good quality local optimization with Sander (Sat Apr 01 2017 - 06:17:22 PDT)
David Cerutti
- Re: [AMBER] Acetonitrile Water Mix (Wed Apr 05 2017 - 08:00:55 PDT)
David Poole
- Re: [AMBER] You won't believe what happens with maximum coordination limits... (Thu Apr 06 2017 - 03:22:04 PDT)
- [AMBER] You won't believe what happens with maximum coordination limits... (Tue Apr 04 2017 - 07:23:11 PDT)
Edson Katekawa
- Re: [AMBER] Membrane Protein Simulation Methodology (Thu Apr 20 2017 - 11:18:24 PDT)
Elka Firmanda
- Re: [AMBER] cpptraj creates pdb file it cannot read (Tue Apr 11 2017 - 23:00:55 PDT)
Elvis Martis
- Re: [AMBER] barostat=1 error at Stampede (Thu Apr 27 2017 - 07:05:42 PDT)
- Re: [AMBER] barostat=1 error at Stampede (Wed Apr 26 2017 - 23:53:12 PDT)
- Re: [AMBER] barostat=1 error at Stampede (Wed Apr 26 2017 - 23:51:56 PDT)
- Re: [AMBER] consult about LEaP in amber (Wed Apr 26 2017 - 03:39:01 PDT)
- Re: [AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc (Mon Apr 24 2017 - 00:24:14 PDT)
- Re: [AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc (Sat Apr 22 2017 - 05:53:17 PDT)
- Re: [AMBER] Membrane Protein Simulation Methodology (Thu Apr 20 2017 - 22:13:20 PDT)
- Re: [AMBER] HEME-CYS (Wed Apr 19 2017 - 09:50:05 PDT)
- Re: [AMBER] HEME-CYS (Wed Apr 19 2017 - 09:35:02 PDT)
- Re: [AMBER] HEME-CYS (Tue Apr 18 2017 - 21:44:33 PDT)
- Re: [AMBER] HEME-CYS (Tue Apr 18 2017 - 08:22:26 PDT)
- Re: [AMBER] HEME-CYS (Mon Apr 17 2017 - 20:31:14 PDT)
- Re: [AMBER] HEME-CYS (Mon Apr 17 2017 - 20:30:25 PDT)
- Re: [AMBER] HEME-CYS (Mon Apr 17 2017 - 10:10:21 PDT)
- Re: [AMBER] BCC charge for my HEME (Fri Apr 14 2017 - 09:42:25 PDT)
- Re: [AMBER] BCC charge for my HEME (Fri Apr 14 2017 - 08:29:23 PDT)
- Re: [AMBER] Minimization fails when switching from steepest descent to conjugate gradient (Sat Apr 08 2017 - 22:23:07 PDT)
Emilia Pecora-de-barros
- [AMBER] RES: Incorrect ligand parameterization using GAFF (Fri Apr 14 2017 - 13:50:05 PDT)
- [AMBER] RES: Incorrect ligand parameterization using GAFF (Thu Apr 13 2017 - 18:53:54 PDT)
- [AMBER] Incorrect ligand parameterization using GAFF (Thu Apr 13 2017 - 10:16:07 PDT)
Eugene Cha
- [AMBER] Trouble with simple MD simulation of short peptide and Cu2+ ion (Tue Apr 25 2017 - 20:34:27 PDT)
Fabrício Bracht
- Re: [AMBER] Diffusion and permeability coefficients (Thu Apr 06 2017 - 13:21:14 PDT)
- [AMBER] Diffusion and permeability coefficients (Thu Apr 06 2017 - 12:01:19 PDT)
Feng Pan
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file (Mon Apr 17 2017 - 10:11:22 PDT)
- Re: [AMBER] AMBER umbrella sampling (Thu Apr 13 2017 - 13:04:56 PDT)
George Giambasu
- Re: [AMBER] solvateBox for large size of RNA (Thu Apr 13 2017 - 09:59:52 PDT)
George Tzotzos
- [AMBER] Quasi-harmonic entropy calculation ---- Vibrational component of entropy (Tue Apr 18 2017 - 04:42:20 PDT)
- Re: [AMBER] PCA - concatenating trajectories (Mon Apr 17 2017 - 07:12:23 PDT)
- Re: [AMBER] PCA - concatenating trajectories (Mon Apr 17 2017 - 06:23:53 PDT)
- [AMBER] PCA - concatenating trajectories (Mon Apr 17 2017 - 06:19:03 PDT)
Gerald Monard
- Re: [AMBER] antechamber problem (Wed Apr 12 2017 - 08:00:39 PDT)
giulia palermo
- Re: [AMBER] simulation energies are exploding (Tue Apr 11 2017 - 14:44:28 PDT)
- [AMBER] simulation energies are exploding (Mon Apr 10 2017 - 17:30:28 PDT)
Goetz, Andreas
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file (Mon Apr 17 2017 - 11:21:32 PDT)
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file (Mon Apr 17 2017 - 10:15:17 PDT)
Gulsevin,Alican
- [AMBER] Membrane Protein Simulation Methodology (Mon Apr 24 2017 - 04:10:18 PDT)
- Re: [AMBER] Can't not run cpptraj (Thu Apr 20 2017 - 19:45:42 PDT)
- [AMBER] Membrane Protein Simulation Methodology (Thu Apr 20 2017 - 08:53:30 PDT)
Guqin Shi
- Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? (Sat Apr 22 2017 - 13:43:33 PDT)
- Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? (Fri Apr 21 2017 - 21:05:34 PDT)
- Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? (Fri Apr 21 2017 - 07:58:01 PDT)
- [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? (Thu Apr 20 2017 - 15:59:14 PDT)
Hadeer ELHabashy
- [AMBER] About Tutorial B3 (Thu Apr 13 2017 - 15:40:12 PDT)
Hai Nguyen
- Re: [AMBER] Using AmberTools17 and Amber14 (Fri Apr 28 2017 - 22:00:48 PDT)
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 (Fri Apr 28 2017 - 15:15:20 PDT)
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 (Fri Apr 28 2017 - 11:55:22 PDT)
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 (Fri Apr 28 2017 - 11:50:48 PDT)
- Re: [AMBER] Tutorial - 3 / MM-PBSA (Wed Apr 26 2017 - 14:26:51 PDT)
- [AMBER] Release of AmberTools17 binary (Wed Apr 26 2017 - 07:30:04 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade (Mon Apr 24 2017 - 09:54:08 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade (Fri Apr 21 2017 - 20:49:02 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade (Fri Apr 21 2017 - 12:46:30 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade (Fri Apr 21 2017 - 12:39:59 PDT)
- Re: [AMBER] Can't not run cpptraj (Thu Apr 20 2017 - 19:15:51 PDT)
- Re: [AMBER] Minor bug with updating Amber/AmberTools with Python3 (Thu Apr 20 2017 - 13:57:28 PDT)
- Re: [AMBER] How to make sure there is bond in my complex (Thu Apr 20 2017 - 12:17:09 PDT)
- Re: [AMBER] How to make sure there is bond in my complex (Thu Apr 20 2017 - 11:59:20 PDT)
- Re: [AMBER] cpptraj creates pdb file it cannot read (Wed Apr 12 2017 - 07:47:21 PDT)
- Re: [AMBER] cpptraj creates pdb file it cannot read (Tue Apr 11 2017 - 13:51:49 PDT)
- Re: [AMBER] cpptraj creates pdb file it cannot read (Tue Apr 11 2017 - 13:07:16 PDT)
- Re: [AMBER] Minimization fails when switching from steepest descent to conjugate gradient (Sat Apr 08 2017 - 22:43:42 PDT)
Hannes Loeffler
- Re: [AMBER] Restraint in Steered MD/Jarzynski method (Sun Apr 30 2017 - 09:05:15 PDT)
- Re: [AMBER] Quenstions about Constraints in AMBER (Fri Apr 28 2017 - 00:31:50 PDT)
- [AMBER] cpptraj configure may fail in AmberTools17 (Sat Apr 22 2017 - 03:38:57 PDT)
- Re: [AMBER] Adding hydrogens to a ligand (Tue Apr 18 2017 - 02:22:38 PDT)
- Re: [AMBER] RES: Incorrect ligand parameterization using GAFF (Sat Apr 15 2017 - 03:32:12 PDT)
- Re: [AMBER] Incorrect ligand parameterization using GAFF (Fri Apr 14 2017 - 01:23:26 PDT)
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file (Thu Apr 13 2017 - 09:35:02 PDT)
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file (Thu Apr 13 2017 - 08:40:22 PDT)
- Re: [AMBER] AMBER umbrella sampling (Thu Apr 13 2017 - 06:04:10 PDT)
- Re: [AMBER] using pmemd.MPI for REMD (Wed Apr 12 2017 - 10:31:25 PDT)
- Re: [AMBER] Steered MD using two reaction coordinates (Fri Apr 07 2017 - 23:28:52 PDT)
- Re: [AMBER] How to write an frcmod file (Thu Apr 06 2017 - 02:15:43 PDT)
- Re: [AMBER] How to distinguish between water molecules? (Wed Apr 05 2017 - 05:42:57 PDT)
- Re: [AMBER] How to distinguish between water molecules? (Wed Apr 05 2017 - 04:50:34 PDT)
- Re: [AMBER] How to distinguish between water molecules? (Wed Apr 05 2017 - 02:53:06 PDT)
- Re: [AMBER] You won't believe what happens with maximum coordination limits... (Tue Apr 04 2017 - 07:50:27 PDT)
hannes.loeffler.stfc.ac.uk
- Re: [AMBER] How to calculate the solvation free energy using Amber? (Mon Apr 17 2017 - 03:19:43 PDT)
Hector A. Baldoni
- Re: [AMBER] AmberTools17 + intel17 = bug (Wed Apr 19 2017 - 06:09:50 PDT)
- Re: [AMBER] AmberTools17 + intel17 = bug (Tue Apr 18 2017 - 16:30:05 PDT)
- [AMBER] AmberTools17 + intel17 = bug (Tue Apr 18 2017 - 16:02:39 PDT)
Iqbal, Muhammad Sajid
- [AMBER] Discussion questions regarding PyRED FF development (Tue Apr 18 2017 - 10:28:40 PDT)
jacob wick
- Re: [AMBER] Adding hydrogens to a ligand (Tue Apr 18 2017 - 03:27:54 PDT)
- [AMBER] Adding hydrogens to a ligand (Tue Apr 18 2017 - 01:57:34 PDT)
Jacopo Sgrignani
- [AMBER] Dftb3 (Sat Apr 29 2017 - 13:40:28 PDT)
- [AMBER] GTX 1080 error (Thu Apr 06 2017 - 13:41:57 PDT)
Jaime Rubio Martinez
- Re: [AMBER] residue-based dielectric model in MMGBSA (Mon Apr 24 2017 - 00:45:47 PDT)
James Kress
- Re: [AMBER] Internal dielectric constant and pmemd (Fri Apr 21 2017 - 11:19:43 PDT)
- Re: [AMBER] Internal dielectric constant and pmemd (Fri Apr 21 2017 - 09:55:38 PDT)
- Re: [AMBER] Internal dielectric constant and pmemd (Fri Apr 21 2017 - 09:53:13 PDT)
- Re: [AMBER] Release of AmberTools17 (Wed Apr 19 2017 - 19:11:09 PDT)
- Re: [AMBER] Release of AmberTools17 (Wed Apr 19 2017 - 13:55:22 PDT)
- Re: [AMBER] Release of AmberTools17 (Wed Apr 19 2017 - 13:52:36 PDT)
- Re: [AMBER] Release of AmberTools17 (Wed Apr 19 2017 - 11:22:54 PDT)
- Re: [AMBER] cpptraj creates pdb file it cannot read (Mon Apr 17 2017 - 13:26:03 PDT)
- Re: [AMBER] cpptraj creates pdb file it cannot read (Sun Apr 16 2017 - 11:41:41 PDT)
- Re: [AMBER] cpptraj creates pdb file it cannot read (Sat Apr 15 2017 - 14:09:56 PDT)
- Re: [AMBER] reorientation in rmsd (Wed Apr 12 2017 - 19:55:08 PDT)
- Re: [AMBER] reorientation in rmsd (Wed Apr 12 2017 - 12:08:37 PDT)
- [AMBER] reorientation in rmsd (Wed Apr 12 2017 - 10:32:31 PDT)
- Re: [AMBER] cpptraj creates pdb file it cannot read (Wed Apr 12 2017 - 07:28:47 PDT)
- Re: [AMBER] cpptraj creates pdb file it cannot read (Tue Apr 11 2017 - 14:37:10 PDT)
- Re: [AMBER] cpptraj creates pdb file it cannot read (Tue Apr 11 2017 - 14:03:17 PDT)
- Re: [AMBER] cpptraj creates pdb file it cannot read (Tue Apr 11 2017 - 13:44:09 PDT)
- [AMBER] cpptraj creates pdb file it cannot read (Tue Apr 11 2017 - 12:29:13 PDT)
- Re: [AMBER] cpptraj analysis of two different dsDNA strands. (Sun Apr 09 2017 - 08:43:57 PDT)
- [AMBER] cpptraj analysis of two different dsDNA strands. (Sat Apr 08 2017 - 11:31:57 PDT)
Jason Swails
- Re: [AMBER] Warning message in AmberTools17 upgrade (Fri Apr 21 2017 - 13:48:47 PDT)
- Re: [AMBER] Error with MMPSA.py calculation (Wed Apr 19 2017 - 17:20:59 PDT)
- Re: [AMBER] cpptraj creates pdb file it cannot read (Sun Apr 16 2017 - 19:56:34 PDT)
- Re: [AMBER] reorientation in rmsd (Thu Apr 13 2017 - 06:21:19 PDT)
- Re: [AMBER] reorientation in rmsd (Wed Apr 12 2017 - 11:41:06 PDT)
- Re: [AMBER] How to distinguish between water molecules? (Wed Apr 05 2017 - 05:53:56 PDT)
JinpengYang
- [AMBER] How to calculate the solvation free energy using Amber? (Mon Apr 17 2017 - 01:05:07 PDT)
Joanna Sarzynska
- Re: [AMBER] intra-residue water bridge with cpptraj (Fri Apr 28 2017 - 03:22:09 PDT)
- [AMBER] intra-residue water bridge with cpptraj (Wed Apr 26 2017 - 07:27:36 PDT)
Johannes Kalliauer
- [AMBER] DNA Tutorial B1 - Temperature Drop (Tue Apr 11 2017 - 02:42:42 PDT)
Jorgen Simonsen
- Re: [AMBER] problem with temperature after rst (Wed Apr 12 2017 - 23:10:51 PDT)
- Re: [AMBER] problem with temperature after rst (Wed Apr 12 2017 - 22:41:45 PDT)
- [AMBER] problem with temperature after rst (Wed Apr 12 2017 - 22:03:57 PDT)
Khatcharin Siriwong
- Re: [AMBER] Can't not run cpptraj (Thu Apr 20 2017 - 20:04:39 PDT)
- Re: [AMBER] Can't not run cpptraj (Thu Apr 20 2017 - 19:21:13 PDT)
- [AMBER] Can't not run cpptraj (Thu Apr 20 2017 - 19:13:06 PDT)
Kris Feher
- Re: [AMBER] using pmemd.MPI for REMD (Thu Apr 13 2017 - 04:01:15 PDT)
- Re: [AMBER] using pmemd.MPI for REMD (Thu Apr 13 2017 - 03:38:41 PDT)
- [AMBER] using pmemd.MPI for REMD (Wed Apr 12 2017 - 09:48:36 PDT)
kungking Hanpaibool
- [AMBER] Too many iterations in routine! in RMSD calculation (Sat Apr 29 2017 - 02:16:06 PDT)
Li, Wen
- Re: [AMBER] pmemd.cuda on an Amber Certified High-End workstation (Thu Apr 20 2017 - 12:52:43 PDT)
- [AMBER] pmemd.cuda on an Amber Certified High-End workstation (Tue Apr 18 2017 - 09:02:52 PDT)
- [AMBER] solvateBox for large size of RNA (Thu Apr 13 2017 - 07:03:15 PDT)
Lucia Fusani
- Re: [AMBER] 3D-RISM centering 0 (Wed Apr 26 2017 - 08:45:30 PDT)
- [AMBER] 3D-RISM centering 0 (Thu Apr 20 2017 - 10:05:42 PDT)
Manju Sah
- Re: [AMBER] Linkage problem in branched oligosaccharide (Sat Apr 01 2017 - 03:10:13 PDT)
Manjula Saravanan
- [AMBER] Post MD minimization (Thu Apr 20 2017 - 02:33:48 PDT)
Marcel Passon
- [AMBER] Error with 'surf' and acetonitrile-water solvent mixture (Thu Apr 27 2017 - 01:21:32 PDT)
Marcelo Andrade Chagas
- [AMBER] Tutorial - 3 / MM-PBSA (Wed Apr 26 2017 - 14:19:55 PDT)
Marcos Serrou do Amaral
- Re: [AMBER] coordinate bond between them and S and FE (Fri Apr 14 2017 - 12:24:54 PDT)
- Re: [AMBER] Format error in frcmod file of HEME (Fri Apr 14 2017 - 09:50:57 PDT)
- Re: [AMBER] Acetonitrile Water Mix (Fri Apr 07 2017 - 06:44:44 PDT)
- Re: [AMBER] Acetonitrile Water Mix (Fri Apr 07 2017 - 05:58:51 PDT)
- Re: [AMBER] Acetonitrile Water Mix (Wed Apr 05 2017 - 05:46:25 PDT)
Marek Maly
- [AMBER] Recommended LJ parameters for divalent cations used for negatively charged lipid bilayers simulations ? (Thu Apr 20 2017 - 09:02:08 PDT)
- Re: [AMBER] You won't believe what happens with maximum coordination limits... (Tue Apr 04 2017 - 14:49:21 PDT)
Markowska
- Re: [AMBER] How to distinguish between water molecules? (Wed Apr 05 2017 - 05:52:05 PDT)
- Re: [AMBER] How to distinguish between water molecules? (Wed Apr 05 2017 - 05:11:07 PDT)
- Re: [AMBER] How to distinguish between water molecules? (Wed Apr 05 2017 - 04:32:05 PDT)
- [AMBER] How to distinguish between water molecules? (Wed Apr 05 2017 - 02:11:03 PDT)
Mary Varughese
- [AMBER] MMPBSA entropy calculation help (Mon Apr 10 2017 - 04:02:21 PDT)
- [AMBER] ptraj hbonds (Wed Apr 05 2017 - 03:33:55 PDT)
- [AMBER] density plot of Na+ ions using grid (Tue Apr 04 2017 - 23:17:14 PDT)
- [AMBER] mmpbsa - stability calculation (Mon Apr 03 2017 - 00:12:32 PDT)
Maura Malinska
- Re: [AMBER] antechamber problem (Thu Apr 13 2017 - 00:25:10 PDT)
- [AMBER] antechamber problem (Wed Apr 12 2017 - 06:59:37 PDT)
Miguel Rivera
- [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. (Fri Apr 28 2017 - 15:12:18 PDT)
mish
- [AMBER] Discrepancy in delta G total and per residues decomposition results in MMPBSA.py (Wed Apr 12 2017 - 01:35:32 PDT)
MOHD HOMAIDUR RAHMAN
- Re: [AMBER] Trouble with simple MD simulation of short peptide and Cu2+ ion (Tue Apr 25 2017 - 21:29:30 PDT)
- [AMBER] Regarding REMD simulations of Proteins (Sun Apr 09 2017 - 08:35:32 PDT)
Mooers, Blaine H.M. (HSC)
- Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 (Wed Apr 26 2017 - 08:06:50 PDT)
- Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 (Sun Apr 23 2017 - 09:10:44 PDT)
- Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 (Sat Apr 22 2017 - 14:01:02 PDT)
- [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 (Fri Apr 21 2017 - 12:36:27 PDT)
Mrinda Jones
- [AMBER] residue-based dielectric model in MMGBSA (Fri Apr 21 2017 - 11:28:44 PDT)
nagakumarb.ccamp.res.in
- Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? (Sat Apr 15 2017 - 05:24:45 PDT)
- Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? (Fri Apr 14 2017 - 23:32:09 PDT)
- Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? (Fri Apr 14 2017 - 22:47:49 PDT)
- [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? (Fri Apr 14 2017 - 22:02:36 PDT)
Neville Bethel
- [AMBER] External electric fields on CUDA enabled PMEMD (Sun Apr 30 2017 - 13:14:00 PDT)
Nhai
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 (Fri Apr 28 2017 - 15:58:05 PDT)
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior (Tue Apr 25 2017 - 16:10:53 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade (Fri Apr 21 2017 - 12:27:24 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade (Fri Apr 21 2017 - 12:07:29 PDT)
- Re: [AMBER] Compilation of MPI 3D-RISM issue in amber1 4 (Thu Apr 13 2017 - 22:13:26 PDT)
- Re: [AMBER] cpptraj analysis of two different dsDNA strands. (Sun Apr 09 2017 - 01:35:49 PDT)
Niel Henriksen
- Re: [AMBER] antechamber problem (Wed Apr 12 2017 - 09:54:53 PDT)
Paul Westphaelinger
- Re: [AMBER] GTX 1080 error (Thu Apr 06 2017 - 13:49:44 PDT)
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 (Wed Apr 05 2017 - 13:03:53 PDT)
Pengfei Li
- [AMBER] Quenstions about Constraints in AMBER (Thu Apr 27 2017 - 21:05:26 PDT)
Praneeth Bommisetti
- [AMBER] Error with MMPSA.py calculation (Tue Apr 18 2017 - 14:22:16 PDT)
Rakesh Srivastava
- [AMBER] Query regarding convergence issue of 3D-RISM (Sun Apr 23 2017 - 23:28:53 PDT)
- [AMBER] Compilation of MPI 3D-RISM issue in amber1 4 (Thu Apr 13 2017 - 21:54:07 PDT)
- Re: [AMBER] Query regarding output of 3D-RISM in Amber. (Mon Apr 10 2017 - 02:10:38 PDT)
- [AMBER] Query regarding output of 3D-RISM in Amber. (Fri Apr 07 2017 - 21:48:22 PDT)
Ramin Salimi
- Re: [AMBER] Restraint in Steered MD/Jarzynski method (Sun Apr 30 2017 - 11:41:18 PDT)
- [AMBER] Restraint in Steered MD/Jarzynski method (Sat Apr 29 2017 - 10:55:20 PDT)
- [AMBER] Restraint in Steered MD/Jarzynski method (Sat Apr 29 2017 - 04:02:01 PDT)
- Re: [AMBER] Stricter convergence Criterion for stretching (Tue Apr 25 2017 - 16:18:14 PDT)
- Re: [AMBER] Stricter convergence Criterion for stretching (Tue Apr 25 2017 - 11:26:43 PDT)
- [AMBER] Stricter convergence Criterion for stretching (Tue Apr 25 2017 - 10:57:29 PDT)
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy (Wed Apr 05 2017 - 19:54:43 PDT)
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy (Wed Apr 05 2017 - 03:01:25 PDT)
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy (Tue Apr 04 2017 - 19:13:38 PDT)
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy (Tue Apr 04 2017 - 10:50:13 PDT)
- [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy (Mon Apr 03 2017 - 18:02:46 PDT)
Ray Luo
- Re: [AMBER] MMPBSA - error (Thu Apr 20 2017 - 09:06:20 PDT)
Rob Arbon
- [AMBER] EVB with RPMD (Wed Apr 19 2017 - 08:25:33 PDT)
Rohith Mohan
- [AMBER] Minor bug with updating Amber/AmberTools with Python3 (Thu Apr 20 2017 - 13:52:35 PDT)
Ross Walker
- Re: [AMBER] barostat=1 error at Stampede (Thu Apr 27 2017 - 04:33:35 PDT)
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior (Tue Apr 25 2017 - 12:32:21 PDT)
- Re: [AMBER] pmemd.cuda on an Amber Certified High-End workstation (Tue Apr 18 2017 - 10:20:31 PDT)
- Re: [AMBER] GTX 1080 error (Thu Apr 06 2017 - 14:30:04 PDT)
- Re: [AMBER] GPU performance (Wed Apr 05 2017 - 16:26:41 PDT)
- Re: [AMBER] 3 GPUs ? (Wed Apr 05 2017 - 12:41:33 PDT)
- Re: [AMBER] 3 GPUs ? (Tue Apr 04 2017 - 16:46:34 PDT)
- Re: [AMBER] 3 GPUs ? (Tue Apr 04 2017 - 08:26:57 PDT)
Sadegh Faramarzi Ganjabad
- Re: [AMBER] Periodic box error for restarting simulations with restraints (Sun Apr 16 2017 - 00:24:41 PDT)
- Re: [AMBER] Periodic box error for restarting simulations with restraints (Thu Apr 13 2017 - 13:12:21 PDT)
- Re: [AMBER] Periodic box error for restarting simulations with restraints (Tue Apr 11 2017 - 12:39:12 PDT)
- Re: [AMBER] Periodic box error for restarting simulations with restraints (Fri Apr 07 2017 - 22:05:37 PDT)
- [AMBER] Periodic box error for restarting simulations with restraints (Fri Apr 07 2017 - 00:44:28 PDT)
- [AMBER] parmed doesn't give any output or error message (Wed Apr 05 2017 - 10:55:59 PDT)
- Re: [AMBER] restarting Amber calculations gives abnormal structures (Sun Apr 02 2017 - 23:37:09 PDT)
- Re: [AMBER] restarting Amber calculations gives abnormal structures (Sun Apr 02 2017 - 23:28:02 PDT)
Samaneh Ghassabi Kondalaji
- Re: [AMBER] Internal dielectric constant and pmemd (Fri Apr 21 2017 - 14:23:48 PDT)
- Re: [AMBER] Internal dielectric constant and pmemd (Fri Apr 21 2017 - 11:04:34 PDT)
- Re: [AMBER] Internal dielectric constant and pmemd (Fri Apr 21 2017 - 06:36:17 PDT)
- Re: [AMBER] Internal dielectric constant and pmemd (Fri Apr 21 2017 - 06:21:45 PDT)
- Re: [AMBER] Internal dielectric constant and pmemd (Fri Apr 21 2017 - 06:11:47 PDT)
- [AMBER] Internal dielectric constant and pmemd (Thu Apr 20 2017 - 11:02:59 PDT)
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file (Mon Apr 17 2017 - 11:36:58 PDT)
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file (Mon Apr 17 2017 - 10:40:37 PDT)
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file (Mon Apr 17 2017 - 10:19:55 PDT)
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file (Mon Apr 17 2017 - 09:50:20 PDT)
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file (Thu Apr 13 2017 - 09:56:02 PDT)
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file (Thu Apr 13 2017 - 09:01:35 PDT)
- [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file (Thu Apr 13 2017 - 08:29:59 PDT)
- Re: [AMBER] QM/MM equilibration before SMD in vacuum (Mon Apr 10 2017 - 09:58:49 PDT)
- [AMBER] QM/MM equilibration before SMD in vacuum (Mon Apr 10 2017 - 09:04:21 PDT)
- Re: [AMBER] Atom types for Baaden Hydronium Ion (Wed Apr 05 2017 - 13:11:21 PDT)
- Re: [AMBER] Atom types for Baaden Hydronium Ion (Wed Apr 05 2017 - 09:06:39 PDT)
- [AMBER] Atom types for Baaden Hydronium Ion (Tue Apr 04 2017 - 18:51:26 PDT)
Scott Brozell
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 (Fri Apr 28 2017 - 09:21:35 PDT)
- [AMBER] Announcement: Release of DOCK 6.8 (Thu Apr 27 2017 - 13:23:57 PDT)
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior (Tue Apr 25 2017 - 10:48:19 PDT)
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior (Tue Apr 25 2017 - 08:44:50 PDT)
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior (Mon Apr 24 2017 - 13:26:21 PDT)
- Re: [AMBER] Tleap error. (Thu Apr 06 2017 - 19:26:42 PDT)
Sharon D. Morris
- [AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc (Sat Apr 22 2017 - 02:00:17 PDT)
Sidhu, Khushwant (Dr.)
- Re: [AMBER] distance calculations - Protein-RNA (Tue Apr 04 2017 - 01:50:01 PDT)
Sofia Vasilakaki
- [AMBER] GPU performance (Wed Apr 05 2017 - 07:27:35 PDT)
Sowmya Indrakumar
- Re: [AMBER] Acetonitrile Water Mix (Wed Apr 05 2017 - 07:48:34 PDT)
Suchetana Gupta
- [AMBER] Steered MD using two reaction coordinates (Fri Apr 07 2017 - 21:27:26 PDT)
sylvester kisembo
- Re: [AMBER] Segmentation fault (Fri Apr 21 2017 - 16:50:39 PDT)
- [AMBER] Segmentation fault (Fri Apr 21 2017 - 06:35:04 PDT)
Tarsis
- [AMBER] barostat=1 error at Stampede (Wed Apr 26 2017 - 13:10:05 PDT)
Thakur, Abhishek
- Re: [AMBER] How to make sure there is bond in my complex (Thu Apr 20 2017 - 12:23:09 PDT)
- Re: [AMBER] How to make sure there is bond in my complex (Thu Apr 20 2017 - 12:06:48 PDT)
- [AMBER] How to make sure there is bond in my complex (Thu Apr 20 2017 - 11:56:22 PDT)
- Re: [AMBER] HEME-CYS (Wed Apr 19 2017 - 09:42:58 PDT)
- Re: [AMBER] HEME-CYS (Wed Apr 19 2017 - 07:19:20 PDT)
- Re: [AMBER] HEME-CYS (Tue Apr 18 2017 - 09:10:04 PDT)
- Re: [AMBER] HEME-CYS (Mon Apr 17 2017 - 11:37:43 PDT)
- Re: [AMBER] HEME-CYS (Mon Apr 17 2017 - 10:56:41 PDT)
- [AMBER] HEME-CYS (Mon Apr 17 2017 - 09:45:38 PDT)
- Re: [AMBER] coordinate bond between them and S and FE (Mon Apr 17 2017 - 08:38:55 PDT)
- Re: [AMBER] coordinate bond between them and S and FE (Mon Apr 17 2017 - 07:45:31 PDT)
- Re: [AMBER] coordinate bond between them and S and FE (Fri Apr 14 2017 - 13:44:44 PDT)
- [AMBER] coordinate bond between them and S and FE (Fri Apr 14 2017 - 12:18:37 PDT)
- Re: [AMBER] Format error in frcmod file of HEME (Fri Apr 14 2017 - 11:46:25 PDT)
- [AMBER] Format error in frcmod file of HEME (Fri Apr 14 2017 - 09:42:46 PDT)
- Re: [AMBER] BCC charge for my HEME (Fri Apr 14 2017 - 09:16:23 PDT)
- [AMBER] BCC charge for my HEME (Fri Apr 14 2017 - 07:12:51 PDT)
- [AMBER] Binding site volume calculation (Wed Apr 05 2017 - 08:45:53 PDT)
Thomas Charles Pochapsky
- [AMBER] weird asymmetries in solvent box (Sat Apr 15 2017 - 05:52:11 PDT)
Thomas Cheatham
- Re: [AMBER] residue-based dielectric model in MMGBSA (Fri Apr 21 2017 - 18:32:27 PDT)
- Re: [AMBER] residue-based dielectric model in MMGBSA (Fri Apr 21 2017 - 18:26:13 PDT)
- Re: [AMBER] Internal dielectric constant and pmemd (Fri Apr 21 2017 - 13:48:22 PDT)
Thomas Evangelidis
- [AMBER] placing water at specified coordinates with tleap (Mon Apr 03 2017 - 08:14:51 PDT)
- Re: [AMBER] coordinates in restraint mast (Sun Apr 02 2017 - 09:25:48 PDT)
Thomas Exner
- [AMBER] Early-bird and bursary deadline April 30: eChemInfo Training and Innovation Course in Drug Design (Mon Apr 24 2017 - 04:09:50 PDT)
- [AMBER] eChemInfo Training and Innovation Course in Drug Design (Tue Apr 04 2017 - 02:51:20 PDT)
Thomas Pochapsky
- Re: [AMBER] weird asymmetries in solvent box (Wed Apr 19 2017 - 12:03:18 PDT)
- Re: [AMBER] weird asymmetries in solvent box (Mon Apr 17 2017 - 06:57:34 PDT)
Tyler Luchko (Lists)
- Re: [AMBER] 3D-RISM centering 0 (Thu Apr 20 2017 - 11:18:04 PDT)
- Re: [AMBER] Compilation of MPI 3D-RISM issue in amber1 4 (Thu Apr 13 2017 - 22:03:50 PDT)
Vatsal Purohit
- [AMBER] antechamber convergence problem. (Mon Apr 24 2017 - 13:32:52 PDT)
- [AMBER] Tleap error. (Thu Apr 06 2017 - 17:11:45 PDT)
Vertika Gautam
- [AMBER] Query regarding energy calcuation using 3D-RISM (Mon Apr 24 2017 - 01:50:11 PDT)
Xiaoliu Zhang
- [AMBER] Run NPT in a small periodic box (Thu Apr 20 2017 - 07:44:37 PDT)
吴萌
- Re: [AMBER] AMBER umbrella sampling (Fri Apr 14 2017 - 20:02:07 PDT)
- [AMBER] AMBER umbrella sampling (Thu Apr 13 2017 - 02:27:20 PDT)
张壮壮
- [AMBER] consult about LEaP in amber (Tue Apr 25 2017 - 20:49:48 PDT)
杨满意
- Re: [AMBER] ERROR in load_lbfgs(): YS=0. (Thu Apr 13 2017 - 19:20:45 PDT)
- [AMBER] ERROR in load_lbfgs(): YS=0. (Wed Apr 12 2017 - 20:46:26 PDT)
白正亚
- [AMBER] problem about amber install of MMPBSA.py.mpi (Tue Apr 11 2017 - 00:38:27 PDT)

Amber Archive Apr 2017 by author