Amber Archive Dec 2015: by author

Abhilash J
- Re: [AMBER] MD study of transition of protein from one conformation to another (Mon Dec 28 2015 - 20:58:55 PST)
- [AMBER] MD study of transition of protein from one conformation to another (Mon Dec 28 2015 - 09:40:28 PST)
Adrian Roitberg
- Re: [AMBER] pH-REMD GPU runs (Wed Dec 02 2015 - 06:01:16 PST)
Anasuya Dighe
- [AMBER] Irregular ligand positioning in simulations (Mon Dec 14 2015 - 22:58:43 PST)
Andrea Spitaleri
- Re: [AMBER] kinetic (Fri Dec 04 2015 - 06:24:20 PST)
Andrew Bostick
- [AMBER] average structure (Thu Dec 17 2015 - 14:35:59 PST)
- [AMBER] WARNING: There is a bond of 420.000806 angstroms between: ------- .R<LIG 546>.A<O2 28> and .R<LIG 546>.A<H2 31> (Fri Dec 11 2015 - 07:30:16 PST)
- [AMBER] per-residue or pairwise per-residue basis in decomposing the free energy contributions to the binding free energy (Sun Dec 06 2015 - 10:45:18 PST)
- [AMBER] per-residue or pairwise per-residue basis in decomposing the free energy contributions to the binding free energy (Sat Dec 05 2015 - 11:20:19 PST)
anu chandra
- Re: [AMBER] High PB deltaG values from MMPBSA.py calculation (Sat Dec 05 2015 - 03:46:40 PST)
- Re: [AMBER] High PB deltaG values from MMPBSA.py calculation (Thu Dec 03 2015 - 02:28:58 PST)
- Re: [AMBER] High PB deltaG values from MMPBSA.py calculation (Wed Dec 02 2015 - 06:48:05 PST)
- [AMBER] High PB deltaG values from MMPBSA.py calculation (Wed Dec 02 2015 - 05:59:48 PST)
Arjun Sharma
- [AMBER] pH-REMD GPU runs (Wed Dec 02 2015 - 05:53:22 PST)
Arnoult, Eric [JRDUS]
- Re: [AMBER] Charmm-gui conversion (Wed Dec 09 2015 - 12:31:09 PST)
- Re: [AMBER] Charmm-gui conversion (Wed Dec 09 2015 - 10:26:54 PST)
Atila Petrosian
- Re: [AMBER] mmgbsa_CalcError (Tue Dec 01 2015 - 10:59:15 PST)
- [AMBER] mmgbsa_CalcError (Tue Dec 01 2015 - 04:13:48 PST)
Ayesha Kanwal
- [AMBER] confusion in xleap for ligand and comlex (Mon Dec 14 2015 - 23:50:07 PST)
- Re: [AMBER] xleap terminal terminate (Fri Dec 04 2015 - 00:36:07 PST)
- [AMBER] xleap terminal terminate (Thu Dec 03 2015 - 04:33:08 PST)
Beale, John
- [AMBER] Principal Component Analysis (Wed Dec 02 2015 - 02:23:57 PST)
bharat lakhani
- [AMBER] different dielectric constant value for polar non-polar hydrophobic residue in MMGBSA (Tue Dec 29 2015 - 21:47:05 PST)
Bill
- Re: [AMBER] bond connections (Sun Dec 06 2015 - 01:24:34 PST)
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) (Fri Dec 04 2015 - 01:02:05 PST)
- Re: [AMBER] bond connections (Wed Dec 02 2015 - 23:51:04 PST)
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) (Tue Dec 01 2015 - 02:13:33 PST)
Bill Ross
- Re: [AMBER] Warning regarding "triangular bond" (Wed Dec 16 2015 - 11:45:48 PST)
- Re: [AMBER] Time Step (Sun Dec 13 2015 - 23:10:05 PST)
- Re: [AMBER] Problems regarding using ZAFF (Sun Dec 13 2015 - 23:01:56 PST)
- Re: [AMBER] ligand is not opening in the binding site of protein (Fri Dec 11 2015 - 00:36:03 PST)
- Re: [AMBER] Charmm-gui conversion (Fri Dec 11 2015 - 00:05:29 PST)
- Re: [AMBER] Charmm-gui conversion (Thu Dec 10 2015 - 12:31:36 PST)
- Re: [AMBER] Charmm-gui conversion (Wed Dec 09 2015 - 12:48:44 PST)
- Re: [AMBER] Charmm-gui conversion (Wed Dec 09 2015 - 12:07:49 PST)
Brian Radak
- Re: [AMBER] mbar (Tue Dec 15 2015 - 07:35:36 PST)
- Re: [AMBER] Charmm-gui conversion (Thu Dec 10 2015 - 13:12:26 PST)
- Re: [AMBER] Charmm-gui conversion (Wed Dec 09 2015 - 12:55:29 PST)
- Re: [AMBER] Charmm-gui conversion (Wed Dec 09 2015 - 08:10:06 PST)
- Re: [AMBER] bond connections (Thu Dec 03 2015 - 10:16:56 PST)
Carlos Simmerling
- Re: [AMBER] TIP3 simulated annealing, 200ps*50 loops = 10ns ==> Minimization of lower energy structures (Sun Dec 20 2015 - 06:44:15 PST)
- Re: [AMBER] TIP3 simulated annealing, 200ps*50 loops = 10ns ==> Minimization of lower energy structures (Sun Dec 20 2015 - 05:04:31 PST)
- Re: [AMBER] Ligand's parameterization (Wed Dec 16 2015 - 06:20:13 PST)
- Re: [AMBER] Irregular ligand positioning in simulations (Tue Dec 15 2015 - 03:08:32 PST)
- Re: [AMBER] WARNING: There is a bond of 420.000806 angstroms between: ------- .R<LIG 546>.A<O2 28> and .R<LIG 546>.A<H2 31> (Fri Dec 11 2015 - 07:48:59 PST)
- Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond (Thu Dec 10 2015 - 12:08:08 PST)
- Re: [AMBER] rmsd as order parameter in umbrella sampling (Mon Dec 07 2015 - 03:18:25 PST)
- Re: [AMBER] Amber calculated structure(PDB) visualization in pymol vs chimera (Wed Dec 02 2015 - 11:56:23 PST)
Charles Lin
- Re: [AMBER] pmemd.cuda with CoM restraints (Thu Dec 03 2015 - 22:30:04 PST)
- Re: [AMBER] pmemd.cuda with CoM restraints (Thu Dec 03 2015 - 09:22:33 PST)
Christina Bergonzo
- Re: [AMBER] External forces (Tue Dec 08 2015 - 07:26:42 PST)
Claire Coderch Boué
- [AMBER] Termodinamic Integration setup error (Thu Dec 17 2015 - 01:46:17 PST)
conor parks
- [AMBER] charge fitting procedure in amber (Mon Dec 14 2015 - 13:27:21 PST)
Daniel Roe
- Re: [AMBER] How to calculate the interplanar angle between 2 Trp residues? (Mon Dec 21 2015 - 08:38:44 PST)
- Re: [AMBER] How to have special residues in trajectory file using cpptraj (Thu Dec 17 2015 - 07:23:29 PST)
- Re: [AMBER] HBOND_water mediated (Tue Dec 15 2015 - 09:01:24 PST)
- Re: [AMBER] MMPBSA.py.MPI compling issue (Tue Dec 15 2015 - 08:51:57 PST)
- Re: [AMBER] Irregular ligand positioning in simulations (Tue Dec 15 2015 - 08:38:36 PST)
- Re: [AMBER] problem in plotting secondary structure graph (Tue Dec 15 2015 - 08:12:41 PST)
- Re: [AMBER] gnu plot of cpptraj Secstruct (Fri Dec 11 2015 - 07:55:28 PST)
- Re: [AMBER] FW: FW: How to use "divergence" command (Wed Dec 09 2015 - 08:51:15 PST)
- Re: [AMBER] problem with hist command in cpptraj in AmberTools15 (Tue Dec 08 2015 - 14:03:47 PST)
- Re: [AMBER] problem with hist command in cpptraj in AmberTools15 (Tue Dec 08 2015 - 13:00:53 PST)
- Re: [AMBER] standard deviation of Hbond lengths and angles (Mon Dec 07 2015 - 08:04:07 PST)
- Re: [AMBER] cpptraj: grid and gist (Mon Dec 07 2015 - 07:39:02 PST)
- Re: [AMBER] problem with "closest" waters being wrapped (Thu Dec 03 2015 - 13:20:04 PST)
- Re: [AMBER] Amber calculated structure(PDB) visualization in pymol vs chimera (Wed Dec 02 2015 - 12:06:07 PST)
- Re: [AMBER] Principal Component Analysis (Wed Dec 02 2015 - 10:00:49 PST)
David A Case
- Re: [AMBER] Error in running AMBER 12 GPU simulations (Thu Dec 31 2015 - 08:22:59 PST)
- Re: [AMBER] different dielectric constant value for polar non-polar hydrophobic residue in MMGBSA (Wed Dec 30 2015 - 05:30:30 PST)
- Re: [AMBER] Group specification (Tue Dec 29 2015 - 17:43:05 PST)
- Re: [AMBER] MD study of transition of protein from one conformation to another (Mon Dec 28 2015 - 12:42:40 PST)
- Re: [AMBER] ig=-1 for multi production runs (Mon Dec 21 2015 - 05:20:50 PST)
- Re: [AMBER] pmemd issue (Mon Dec 21 2015 - 05:18:42 PST)
- Re: [AMBER] bug or not bug ???? (Sun Dec 20 2015 - 08:42:40 PST)
- Re: [AMBER] Water model (Fri Dec 18 2015 - 08:17:38 PST)
- Re: [AMBER] Warning regarding "triangular bond" (Wed Dec 16 2015 - 04:57:44 PST)
- Re: [AMBER] confusion in xleap for ligand and comlex (Tue Dec 15 2015 - 04:53:20 PST)
- Re: [AMBER] restraints on group of atoms (Mon Dec 14 2015 - 05:06:57 PST)
- Re: [AMBER] [Amber] Imaginary Frequencies from nmode() (Sat Dec 12 2015 - 13:32:03 PST)
- Re: [AMBER] Amber 14, sander.MPI, NaN (Sat Dec 12 2015 - 07:42:14 PST)
- Re: [AMBER] Charmm-gui conversion (Thu Dec 10 2015 - 13:34:08 PST)
- Re: [AMBER] free energy of solvation of small molecules (Mon Dec 07 2015 - 07:06:33 PST)
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) (Fri Dec 04 2015 - 05:13:37 PST)
- Re: [AMBER] Question Regarding Input File Preparation (Fri Dec 04 2015 - 05:10:24 PST)
- Re: [AMBER] Simulation of the docked complex with phosphorylated tyrosine (Thu Dec 03 2015 - 05:33:30 PST)
- Re: [AMBER] AMBER 12 XLEAP options were disabled (Thu Dec 03 2015 - 05:28:32 PST)
- Re: [AMBER] bond connections (Thu Dec 03 2015 - 05:26:15 PST)
- Re: [AMBER] kinetic (Wed Dec 02 2015 - 06:06:13 PST)
- Re: [AMBER] How does the collision frequency gamma_ln value affect the temperature in Langevin dynamics (Wed Dec 02 2015 - 06:03:08 PST)
Dhananjay
- [AMBER] restraints on group of atoms (Mon Dec 14 2015 - 01:47:47 PST)
Fabian Glaser
- Re: [AMBER] free energy of solvation of small molecules (Mon Dec 07 2015 - 13:07:03 PST)
- Re: [AMBER] free energy of solvation of small molecules (Fri Dec 04 2015 - 07:06:22 PST)
- Re: [AMBER] free energy of solvation of small molecules (Fri Dec 04 2015 - 04:09:29 PST)
Fabian gmail
- Re: [AMBER] ig=-1 for multi production runs (Mon Dec 21 2015 - 05:36:04 PST)
- [AMBER] ig=-1 for multi production runs (Mon Dec 21 2015 - 04:31:01 PST)
- Re: [AMBER] free energy of solvation of small molecules (Sun Dec 13 2015 - 06:10:25 PST)
- Re: [AMBER] free energy of solvation of small molecules (Mon Dec 07 2015 - 06:58:51 PST)
- Re: [AMBER] free energy of solvation of small molecules (Thu Dec 03 2015 - 04:15:17 PST)
- Re: [AMBER] free energy of solvation of small molecules (Wed Dec 02 2015 - 06:55:43 PST)
- Re: [AMBER] free energy of solvation of small molecules (Wed Dec 02 2015 - 06:49:20 PST)
- Re: [AMBER] free energy of solvation of small molecules (Wed Dec 02 2015 - 04:41:31 PST)
George Tzotzos
- Re: [AMBER] cpptraj average structure warning (Thu Dec 17 2015 - 02:22:12 PST)
- [AMBER] cpptraj average structure warning (Thu Dec 17 2015 - 01:05:26 PST)
- Re: [AMBER] gnu plot of cpptraj Secstruct (Fri Dec 11 2015 - 11:32:42 PST)
- Re: [AMBER] gnu plot of cpptraj Secstruct (Fri Dec 11 2015 - 07:58:36 PST)
- Re: [AMBER] gnu plot of cpptraj Secstruct (Fri Dec 11 2015 - 06:01:54 PST)
- Re: [AMBER] gnu plot of cpptraj Secstruct (Fri Dec 11 2015 - 04:22:28 PST)
- [AMBER] gnu plot of cpptraj Secstruct (Thu Dec 10 2015 - 13:42:20 PST)
- Re: [AMBER] OSX 10.11.1: Amber installation problem (Thu Dec 10 2015 - 02:16:14 PST)
- [AMBER] OSX 10.11.1: Amber installation problem (Wed Dec 09 2015 - 10:19:47 PST)
Guqin Shi
- Re: [AMBER] [Amber] Imaginary Frequencies from nmode() (Tue Dec 15 2015 - 13:51:27 PST)
- [AMBER] [Amber] Imaginary Frequencies from nmode() (Tue Dec 08 2015 - 13:19:53 PST)
- Re: [AMBER] [Amber] nmode() results with imaginary frequencies (Sun Dec 06 2015 - 11:13:28 PST)
- Re: [AMBER] [Amber] nmode() results with imaginary frequencies (Wed Dec 02 2015 - 06:15:58 PST)
- [AMBER] [Amber] nmode() results with imaginary frequencies (Tue Dec 01 2015 - 15:18:17 PST)
Gustavo Seabra
- Re: [AMBER] weird output of SMD simulation combined with Constant pH (Mon Dec 07 2015 - 17:34:47 PST)
- Re: [AMBER] weird output of SMD simulation combined with Constant pH (Mon Dec 07 2015 - 11:38:49 PST)
Hadeer ELHabashy
- [AMBER] standard deviation of Hbond lengths and angles (Sun Dec 06 2015 - 07:20:12 PST)
Hai Nguyen
- Re: [AMBER] average structure (Thu Dec 17 2015 - 14:43:59 PST)
- Re: [AMBER] standard deviation of Hbond lengths and angles (Mon Dec 07 2015 - 12:24:16 PST)
Hannes Loeffler
- Re: [AMBER] Termodinamic Integration setup error (Thu Dec 17 2015 - 01:59:01 PST)
- Re: [AMBER] mbar (Tue Dec 15 2015 - 09:02:41 PST)
- Re: [AMBER] mbar (Tue Dec 15 2015 - 08:14:07 PST)
- Re: [AMBER] mbar (Tue Dec 15 2015 - 07:17:05 PST)
- Re: [AMBER] mbar (Tue Dec 15 2015 - 05:46:51 PST)
- Re: [AMBER] free energy of solvation of small molecules (Mon Dec 14 2015 - 01:35:43 PST)
- Re: [AMBER] free energy of solvation of small molecules (Fri Dec 04 2015 - 06:21:23 PST)
- Re: [AMBER] free energy of solvation of small molecules (Fri Dec 04 2015 - 01:44:40 PST)
- Re: [AMBER] free energy of solvation of small molecules (Thu Dec 03 2015 - 03:46:45 PST)
- Re: [AMBER] free energy of solvation of small molecules (Thu Dec 03 2015 - 03:35:12 PST)
Havva Mehralitabar
- [AMBER] Group specification (Mon Dec 28 2015 - 12:52:51 PST)
Jack Shepherd
- [AMBER] External forces (Mon Dec 07 2015 - 09:29:07 PST)
Jason Swails
- Re: [AMBER] which chain to select for MD simulation. (Wed Dec 30 2015 - 17:55:44 PST)
- Re: [AMBER] MMPBSA error (Wed Dec 23 2015 - 10:09:59 PST)
- Re: [AMBER] GPU support (Mon Dec 21 2015 - 08:53:38 PST)
- Re: [AMBER] ig=-1 for multi production runs (Mon Dec 21 2015 - 06:38:43 PST)
- Re: [AMBER] ig=-1 for multi production runs (Mon Dec 21 2015 - 05:09:40 PST)
- Re: [AMBER] pmemd issue (Mon Dec 21 2015 - 05:03:42 PST)
- Re: [AMBER] Confusion on "No Pressure" (Thu Dec 17 2015 - 09:27:41 PST)
- Re: [AMBER] Time Step (Mon Dec 14 2015 - 09:05:29 PST)
- Re: [AMBER] problem in adding ACE and NME to CSX. (Sun Dec 13 2015 - 08:28:16 PST)
- Re: [AMBER] gnu plot of cpptraj Secstruct (Fri Dec 11 2015 - 05:43:30 PST)
- Re: [AMBER] Charmm-gui conversion (Fri Dec 11 2015 - 05:40:43 PST)
- Re: [AMBER] Charmm-gui conversion (Fri Dec 11 2015 - 04:07:01 PST)
- Re: [AMBER] OSX 10.11.1: Amber installation problem (Wed Dec 09 2015 - 12:34:25 PST)
- Re: [AMBER] FW: FW: How to use "divergence" command (Wed Dec 09 2015 - 05:28:22 PST)
- Re: [AMBER] Problem with GPU equilibration step [ cudaMalloc GpuBuffer::Allocate failed out of memory] (Wed Dec 09 2015 - 04:46:00 PST)
- Re: [AMBER] xparmed.py (Tue Dec 08 2015 - 12:07:38 PST)
- Re: [AMBER] xparmed.py (Tue Dec 08 2015 - 07:55:02 PST)
- Re: [AMBER] cpptraj: grid and gist (Tue Dec 08 2015 - 05:28:50 PST)
- Re: [AMBER] weird output of SMD simulation combined with Constant pH (Mon Dec 07 2015 - 18:55:31 PST)
- Re: [AMBER] weird output of SMD simulation combined with Constant pH (Mon Dec 07 2015 - 12:14:30 PST)
- Re: [AMBER] weird output of SMD simulation combined with Constant pH (Mon Dec 07 2015 - 06:29:41 PST)
- Re: [AMBER] bond connections (Sun Dec 06 2015 - 16:54:45 PST)
- Re: [AMBER] per-residue or pairwise per-residue basis in decomposing the free energy contributions to the binding free energy (Sun Dec 06 2015 - 13:38:32 PST)
- Re: [AMBER] bond connections (Sun Dec 06 2015 - 06:07:45 PST)
- Re: [AMBER] per-residue or pairwise per-residue basis in decomposing the free energy contributions to the binding free energy (Sat Dec 05 2015 - 12:06:57 PST)
- Re: [AMBER] bond connections (Sat Dec 05 2015 - 12:05:47 PST)
- Re: [AMBER] bond connections (Thu Dec 03 2015 - 20:39:04 PST)
- Re: [AMBER] Question Regarding Input File Preparation (Fri Dec 04 2015 - 04:29:44 PST)
- Re: [AMBER] xleap terminal terminate (Fri Dec 04 2015 - 04:11:48 PST)
- Re: [AMBER] bond connections (Thu Dec 03 2015 - 12:59:30 PST)
- Re: [AMBER] bond connections (Thu Dec 03 2015 - 10:05:15 PST)
- Re: [AMBER] xleap terminal terminate (Thu Dec 03 2015 - 04:42:50 PST)
- Re: [AMBER] bond connections (Thu Dec 03 2015 - 04:41:11 PST)
- Re: [AMBER] AMBER 12 XLEAP options were disabled (Thu Dec 03 2015 - 04:36:01 PST)
- Re: [AMBER] High PB deltaG values from MMPBSA.py calculation (Wed Dec 02 2015 - 06:25:20 PST)
- Re: [AMBER] pH-REMD GPU runs (Wed Dec 02 2015 - 06:23:26 PST)
- Re: [AMBER] Principal Component Analysis (Wed Dec 02 2015 - 05:50:24 PST)
- Re: [AMBER] free energy of solvation of small molecules (Wed Dec 02 2015 - 05:42:10 PST)
- Re: [AMBER] kinetic (Wed Dec 02 2015 - 05:34:35 PST)
- Re: [AMBER] mac hangs when compile ambertools15 on El capitan (Wed Dec 02 2015 - 04:40:26 PST)
- Re: [AMBER] [Amber] nmode() results with imaginary frequencies (Tue Dec 01 2015 - 19:05:55 PST)
- Re: [AMBER] Can I use the Nose-Hoover thermostat in Amber (Tue Dec 01 2015 - 19:02:59 PST)
- Re: [AMBER] mmgbsa_CalcError (Tue Dec 01 2015 - 11:08:10 PST)
- Re: [AMBER] malloc error during MM-PBSA calculation on AMBER14 ... mmpbsa_py_energy: malloc.c:2372: sysmalloc (Tue Dec 01 2015 - 08:50:04 PST)
- Re: [AMBER] mmgbsa_CalcError (Tue Dec 01 2015 - 05:19:25 PST)
- Re: [AMBER] Docking before MD of scratch ligands OR not (Tue Dec 01 2015 - 05:13:12 PST)
- Re: [AMBER] Utilizing two different nodes simultaneously for one job (Tue Dec 01 2015 - 05:11:15 PST)
- Re: [AMBER] mac hangs when compile ambertools15 on El capitan (Tue Dec 01 2015 - 05:07:45 PST)
- Re: [AMBER] Not matching test AMBER14 with CUDA (Tue Dec 01 2015 - 04:55:29 PST)
jfliu
- [AMBER] Water model (Thu Dec 17 2015 - 05:07:40 PST)
- [AMBER] Can I use the Nose-Hoover thermostat in Amber (Tue Dec 01 2015 - 18:12:54 PST)
- [AMBER] How does the collision frequency gamma_ln value affect the temperature in Langevin dynamics (Tue Dec 01 2015 - 18:07:17 PST)
Jim William Snyder Jr
- [AMBER] QM/MM Implementation Details (Thu Dec 03 2015 - 10:38:35 PST)
Johannes Loeffler
- Re: [AMBER] mbar (Tue Dec 15 2015 - 07:24:02 PST)
- Re: [AMBER] mbar (Tue Dec 15 2015 - 06:42:18 PST)
- [AMBER] mbar (Tue Dec 15 2015 - 05:36:06 PST)
Johannes Löffler
- Re: [AMBER] mbar (Tue Dec 15 2015 - 08:42:25 PST)
Jonathan Sheehan
- Re: [AMBER] bond connections (Sun Dec 06 2015 - 00:41:34 PST)
Josh Berryman
- Re: [AMBER] External forces (Tue Dec 08 2015 - 02:12:00 PST)
Kalenkiewicz, Andrew (NIH/NICHD) [F]
- Re: [AMBER] Problem with initial complex structure for TI (Mon Dec 14 2015 - 13:37:56 PST)
- [AMBER] Problem with initial complex structure for TI (Fri Dec 11 2015 - 15:17:11 PST)
- Re: [AMBER] problem with "closest" waters being wrapped (Thu Dec 03 2015 - 14:34:59 PST)
- [AMBER] problem with "closest" waters being wrapped (Thu Dec 03 2015 - 13:17:57 PST)
Karl Kirschner
- Re: [AMBER] Ligand's parameterization (Thu Dec 17 2015 - 04:02:27 PST)
- Re: [AMBER] charge fitting procedure in amber (Tue Dec 15 2015 - 02:16:13 PST)
- Re: [AMBER] charge fitting procedure in amber (Tue Dec 15 2015 - 00:16:51 PST)
- Re: [AMBER] RED vIII for Amber (Sun Dec 13 2015 - 23:42:54 PST)
- Re: [AMBER] Add charges to new molecule with out Gaussian package (Sat Dec 05 2015 - 06:42:07 PST)
Kenneth Huang
- Re: [AMBER] How to have special residues in trajectory file using cpptraj (Thu Dec 17 2015 - 06:39:14 PST)
- [AMBER] MMPBSA bad atom type error persisting (Mon Dec 07 2015 - 10:40:13 PST)
- Re: [AMBER] How to run two single-card jobs on the node with two GPU cards (Mon Nov 30 2015 - 22:34:36 PST)
Lachele Foley
- Re: [AMBER] gnu plot of cpptraj Secstruct (Fri Dec 11 2015 - 11:28:53 PST)
- Re: [AMBER] gnu plot of cpptraj Secstruct (Thu Dec 10 2015 - 20:55:47 PST)
Lara rajam
- [AMBER] MMPBSA error (Wed Dec 23 2015 - 10:05:05 PST)
- Re: [AMBER] HBOND_water mediated (Thu Dec 17 2015 - 06:49:00 PST)
- [AMBER] HBOND_water mediated (Mon Dec 14 2015 - 07:16:58 PST)
Mahendra B Thapa
- [AMBER] Finding PDF of individual dihedral angles (Mon Dec 21 2015 - 09:27:37 PST)
- Re: [AMBER] FW: FW: How to use "divergence" command (Wed Dec 09 2015 - 05:08:30 PST)
Mahmoud A. A. Ibrahim
- [AMBER] pmemd issue (Mon Dec 21 2015 - 02:04:08 PST)
Marc van der Kamp
- Re: [AMBER] problem with "closest" waters being wrapped (Thu Dec 03 2015 - 14:45:40 PST)
- Re: [AMBER] pmemd.cuda with CoM restraints (Thu Dec 03 2015 - 09:25:00 PST)
Marc Zhang
- [AMBER] MMPBSA.py.MPI compling issue (Mon Dec 14 2015 - 13:22:14 PST)
Mary Dutta
- Re: [AMBER] xleap terminal terminate (Fri Dec 04 2015 - 02:22:17 PST)
Mathy Froeyen
- Re: [AMBER] Ligand's parameterization (Wed Dec 16 2015 - 06:47:50 PST)
Mijiddorj Batsaikhan
- [AMBER] malloc error during MM-PBSA calculation on AMBER14 ... mmpbsa_py_energy: malloc.c:2372: sysmalloc (Tue Dec 01 2015 - 08:44:19 PST)
- Re: [AMBER] Not matching test AMBER14 with CUDA (Mon Nov 30 2015 - 20:20:13 PST)
Min Li
- [AMBER] bug or not bug ???? (Tue Dec 01 2015 - 19:54:38 PST)
mohammad r
- Re: [AMBER] Charmm-gui conversion (Fri Dec 11 2015 - 07:30:06 PST)
- Re: [AMBER] Charmm-gui conversion (Thu Dec 10 2015 - 21:06:04 PST)
- Re: [AMBER] Charmm-gui conversion (Thu Dec 10 2015 - 13:28:46 PST)
- Re: [AMBER] Charmm-gui conversion (Thu Dec 10 2015 - 13:13:25 PST)
- Re: [AMBER] Charmm-gui conversion (Thu Dec 10 2015 - 12:57:17 PST)
- Re: [AMBER] Charmm-gui conversion (Thu Dec 10 2015 - 12:25:11 PST)
- Re: [AMBER] Charmm-gui conversion (Wed Dec 09 2015 - 12:31:01 PST)
- Re: [AMBER] Charmm-gui conversion (Wed Dec 09 2015 - 11:58:29 PST)
- [AMBER] Charmm-gui conversion (Wed Dec 09 2015 - 08:02:20 PST)
- Re: [AMBER] bond connections (Mon Dec 07 2015 - 00:08:15 PST)
- Re: [AMBER] bond connections (Sun Dec 06 2015 - 14:53:43 PST)
- Re: [AMBER] bond connections (Sun Dec 06 2015 - 00:59:33 PST)
- Re: [AMBER] bond connections (Thu Dec 03 2015 - 11:27:51 PST)
- Re: [AMBER] bond connections (Thu Dec 03 2015 - 04:26:05 PST)
- [AMBER] bond connections (Wed Dec 02 2015 - 23:02:03 PST)
Morrow,John Kenneth
- [AMBER] Is triplicate analysis required for pmemd.MPI and ig=-1? (Thu Dec 17 2015 - 14:25:51 PST)
muhammad tahir ayub
- [AMBER] ligand is not opening in the binding site of protein (Fri Dec 11 2015 - 00:22:36 PST)
- [AMBER] Docking before MD of scratch ligands OR not (Mon Nov 30 2015 - 23:49:57 PST)
- [AMBER] Utilizing two different nodes simultaneously for one job (Mon Nov 30 2015 - 22:35:26 PST)
Nash, Anthony
- Re: [AMBER] RED vIII for Amber (Sun Dec 20 2015 - 09:23:28 PST)
- Re: [AMBER] RED vIII for Amber (Sun Dec 13 2015 - 23:50:56 PST)
- [AMBER] RED vIII for Amber (Sun Dec 13 2015 - 13:41:19 PST)
Nathalie Willems
- Re: [AMBER] xparmed.py (Tue Dec 08 2015 - 08:12:21 PST)
- Re: [AMBER] xparmed.py (Tue Dec 08 2015 - 07:23:19 PST)
Nikolay N. Kuzmich
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) (Fri Dec 04 2015 - 00:51:21 PST)
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) (Tue Dec 01 2015 - 01:27:53 PST)
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) (Tue Dec 01 2015 - 01:08:49 PST)
Osman, Roman
- Re: [AMBER] problem with hist command in cpptraj in AmberTools15 (Tue Dec 08 2015 - 16:35:56 PST)
- Re: [AMBER] problem with hist command in cpptraj in AmberTools15 (Tue Dec 08 2015 - 13:22:19 PST)
- [AMBER] problem with hist command in cpptraj in AmberTools15 (Tue Dec 08 2015 - 12:59:46 PST)
Pallavi Mohanty
- Re: [AMBER] Simulation of the docked complex with phosphorylated tyrosine (Fri Dec 04 2015 - 01:27:35 PST)
- [AMBER] Simulation of the docked complex with phosphorylated tyrosine (Thu Dec 03 2015 - 03:53:38 PST)
Pengfei Li
- Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond (Fri Dec 11 2015 - 19:59:11 PST)
Ray Luo, Ph.D.
- Re: [AMBER] High PB deltaG values from MMPBSA.py calculation (Thu Dec 03 2015 - 10:26:51 PST)
- Re: [AMBER] High PB deltaG values from MMPBSA.py calculation (Wed Dec 02 2015 - 16:09:14 PST)
Robert Molt
- [AMBER] Confusion on "No Pressure" (Thu Dec 17 2015 - 08:38:13 PST)
Ross Walker
- Re: [AMBER] GPU support (Mon Dec 21 2015 - 08:31:07 PST)
- Re: [AMBER] Is triplicate analysis required for pmemd.MPI and ig=-1? (Thu Dec 17 2015 - 14:56:01 PST)
- Re: [AMBER] average structure (Thu Dec 17 2015 - 14:44:04 PST)
Rupak Pal
- Re: [AMBER] GPU support (Tue Dec 22 2015 - 01:03:46 PST)
- [AMBER] GPU support (Sun Dec 20 2015 - 22:51:10 PST)
Saman Yousuf ali
- [AMBER] which chain to select for MD simulation. (Wed Dec 30 2015 - 11:58:24 PST)
- [AMBER] problem in adding ACE and NME to CSX. (Sun Dec 13 2015 - 04:58:06 PST)
Sehrish Naz
- [AMBER] problem in plotting secondary structure graph (Mon Dec 14 2015 - 23:19:32 PST)
shahab shariati
- [AMBER] How to have special residues in trajectory file using cpptraj (Thu Dec 17 2015 - 06:14:43 PST)
Soong Jiaxin
- [AMBER] Problem in interpreting snapshot_statistics.out after per-residue decomposition analysis (Wed Dec 30 2015 - 19:36:54 PST)
Srinivasaraghavan Kannan
- [AMBER] rmsd as order parameter in umbrella sampling (Sun Dec 06 2015 - 19:09:46 PST)
Starovoytov, Oleg
- [AMBER] Amber 14, sander.MPI, NaN (Tue Dec 08 2015 - 12:38:07 PST)
Stephen Wang
- [AMBER] How to run two single-card jobs on the node with two GPU cards (Mon Nov 30 2015 - 22:25:57 PST)
Steven M. Graham
- Re: [AMBER] RED vIII for Amber (Sun Dec 20 2015 - 15:40:56 PST)
Steven Ramsey
- Re: [AMBER] cpptraj: grid and gist (Mon Dec 07 2015 - 08:34:29 PST)
Thomas Cheatham
- Re: [AMBER] problem with "closest" waters being wrapped (Thu Dec 03 2015 - 14:53:25 PST)
Thomas Fox
- Re: [AMBER] cpptraj grid command (Mon Dec 14 2015 - 08:24:46 PST)
- Re: [AMBER] cpptraj: grid and gist (Tue Dec 08 2015 - 08:50:15 PST)
- Re: [AMBER] cpptraj: grid and gist (Tue Dec 08 2015 - 05:15:38 PST)
- [AMBER] cpptraj: grid and gist (Mon Dec 07 2015 - 02:22:19 PST)
Trang Nguyen
- [AMBER] Ligand's parameterization (Wed Dec 16 2015 - 06:07:55 PST)
V. Kumar
- Re: [AMBER] TIP3 simulated annealing, 200ps*50 loops = 10ns ==> Minimization of lower energy structures (Sun Dec 20 2015 - 07:23:18 PST)
- Re: [AMBER] TIP3 simulated annealing, 200ps*50 loops = 10ns ==> Minimization of lower energy structures (Sun Dec 20 2015 - 05:27:03 PST)
- [AMBER] TIP3 simulated annealing, 200ps*50 loops = 10ns ==> Minimization of lower energy structures (Sun Dec 20 2015 - 04:23:27 PST)
- [AMBER] Minimization after simulated annealing (0° C) ans CSH script need to be combined (Wed Dec 16 2015 - 09:14:26 PST)
- Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond (Sat Dec 12 2015 - 05:58:42 PST)
- Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond (Thu Dec 10 2015 - 12:34:16 PST)
- Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond (Thu Dec 10 2015 - 08:05:43 PST)
- Re: [AMBER] Add charges to new molecule with out Gaussian package (Sat Dec 05 2015 - 12:01:09 PST)
- [AMBER] Add charges to new molecule with out Gaussian package (Sat Dec 05 2015 - 06:08:41 PST)
- Re: [AMBER] AMBER 12 XLEAP options were disabled (Thu Dec 03 2015 - 06:14:02 PST)
- [AMBER] AMBER 12 XLEAP options were disabled (Thu Dec 03 2015 - 03:36:58 PST)
- Re: [AMBER] Amber calculated structure(PDB) visualization in pymol vs chimera (Wed Dec 02 2015 - 12:42:01 PST)
- Re: [AMBER] Amber calculated structure(PDB) visualization in pymol vs chimera (Wed Dec 02 2015 - 12:17:32 PST)
- [AMBER] Amber calculated structure(PDB) visualization in pymol vs chimera (Wed Dec 02 2015 - 11:38:00 PST)
- Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond (Mon Nov 30 2015 - 23:54:06 PST)
- Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond (Mon Nov 30 2015 - 23:52:56 PST)
wliu
- [AMBER] TI/MBAR energy re-calculating with imin5 (Wed Dec 23 2015 - 01:16:12 PST)
Wong Li Zhe
- [AMBER] Time Step (Mon Dec 14 2015 - 16:21:37 PST)
- [AMBER] Time Step (Sun Dec 13 2015 - 23:01:18 PST)
Xiong Jiawei
- [AMBER] Warning regarding "triangular bond" (Tue Dec 15 2015 - 23:30:52 PST)
Yew Mun Yip
- [AMBER] How to calculate the interplanar angle between 2 Trp residues? (Sun Dec 20 2015 - 01:12:00 PST)
Yogeeshwar Ajjugal
- [AMBER] Error in running AMBER 12 GPU simulations (Thu Dec 31 2015 - 05:35:30 PST)
- Re: [AMBER] Problem with GPU equilibration step [ cudaMalloc GpuBuffer::Allocate failed out of memory] (Wed Dec 09 2015 - 22:04:51 PST)
- [AMBER] Problem with GPU equilibration step [ cudaMalloc GpuBuffer::Allocate failed out of memory] (Tue Dec 08 2015 - 21:42:25 PST)
Yong Yao
- Re: [AMBER] mac hangs when compile ambertools15 on El capitan (Tue Dec 01 2015 - 20:10:45 PST)
- Re: [AMBER] mac hangs when compile ambertools15 on El capitan (Mon Nov 30 2015 - 20:54:28 PST)
- [AMBER] mac hangs when compile ambertools15 on El capitan (Mon Nov 30 2015 - 19:13:31 PST)
zhonghe xu
- [AMBER] weird output of SMD simulation combined with Constant pH (Mon Dec 07 2015 - 06:25:27 PST)
Ziba Bahadori
- [AMBER] kinetic (Wed Dec 02 2015 - 04:14:32 PST)
Ziheng Wang
- [AMBER] Question Regarding Input File Preparation (Thu Dec 03 2015 - 18:35:49 PST)
Åke Sandgren
- Re: [AMBER] bug or not bug ???? (Sat Dec 19 2015 - 05:24:05 PST)
东不拉
- [AMBER] A problem about using AMBER (Sun Dec 27 2015 - 21:34:01 PST)
達南杰
- Re: [AMBER] pmemd.cuda with CoM restraints (Thu Dec 03 2015 - 20:09:24 PST)
- [AMBER] pmemd.cuda with CoM restraints (Thu Dec 03 2015 - 06:56:20 PST)

Amber Archive Dec 2015 by author