Amber Archive Feb 2016: by author

A kS
- Re: [AMBER] Question about AmberTools14/15 installation (Tue Feb 09 2016 - 21:33:12 PST)
- Re: [AMBER] Question about AmberTools14/15 installation (Tue Feb 09 2016 - 11:10:03 PST)
- [AMBER] Question about AmberTools14/15 installation (Mon Feb 08 2016 - 00:15:28 PST)
- Re: [AMBER] Regaridng FIle preparation in AMBERTOOLS14 (Tue Feb 02 2016 - 01:32:11 PST)
- [AMBER] Question about mask command (Tue Feb 02 2016 - 01:28:24 PST)
abdennour braka
- [AMBER] REMD tutorial (Thu Feb 04 2016 - 09:51:23 PST)
Abelak, Kavin
- Re: [AMBER] charge derivation (Fri Feb 26 2016 - 02:52:37 PST)
- Re: [AMBER] charge derivation (Fri Feb 26 2016 - 02:41:11 PST)
- Re: [AMBER] charge derivation (Tue Feb 23 2016 - 07:48:51 PST)
- [AMBER] charge derivation (Fri Feb 19 2016 - 07:48:18 PST)
Adrian Roitberg
- Re: [AMBER] Paradynamics with Amber (Mon Feb 22 2016 - 08:24:01 PST)
- Re: [AMBER] Technical problem running pH-REMD (Wed Feb 17 2016 - 06:34:26 PST)
- Re: [AMBER] Z-constraint PMF method (Mon Feb 08 2016 - 06:38:30 PST)
Alan
- [AMBER] Getting and keeping ACPYPE updated (Tue Feb 09 2016 - 03:33:03 PST)
Amy Rice
- [AMBER] parmed/chamber problem recognizing atom types (Tue Feb 16 2016 - 10:02:42 PST)
Andrea Spitaleri
- [AMBER] Post-doctoral position in Computational Physics (Tue Feb 23 2016 - 02:08:26 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 01:52:01 PST)
ankita mehta
- Re: [AMBER] Dear all (Tue Feb 16 2016 - 21:21:25 PST)
- Re: [AMBER] Dear all (Tue Feb 16 2016 - 02:43:57 PST)
- Re: [AMBER] Dear all (Fri Feb 12 2016 - 04:18:58 PST)
- Re: [AMBER] Dear all (Fri Feb 12 2016 - 04:10:13 PST)
- Re: [AMBER] Dear all (Fri Feb 12 2016 - 03:40:22 PST)
- [AMBER] Dear all (Fri Feb 12 2016 - 03:03:33 PST)
- Re: [AMBER] Dear All (Tue Feb 02 2016 - 04:29:56 PST)
- [AMBER] Dear All (Tue Feb 02 2016 - 03:18:52 PST)
Anna Cebrian Prats
- Re: [AMBER] External library for leap (Mon Feb 29 2016 - 01:39:28 PST)
- [AMBER] External library for leap (Fri Feb 26 2016 - 05:14:28 PST)
- Re: [AMBER] Minimization error using Sander (Thu Feb 25 2016 - 06:24:54 PST)
- [AMBER] Minimization error using Sander (Thu Feb 25 2016 - 02:17:15 PST)
anu chandra
- Re: [AMBER] Regarding caution message in the out file with pmemd.cuda.MPI (Mon Feb 29 2016 - 06:33:09 PST)
- [AMBER] Regarding caution message in the out file with pmemd.cuda.MPI (Fri Feb 26 2016 - 03:28:45 PST)
- [AMBER] Gaussian error with MCPB ion modeling calculation (Fri Feb 26 2016 - 03:20:22 PST)
- [AMBER] Normalizing histogram with CPPTRAJ (Wed Feb 10 2016 - 09:05:25 PST)
Arati Paudyal
- Re: [AMBER] How to separate a protein complex to its components (Sun Feb 28 2016 - 04:56:21 PST)
- Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop (Thu Feb 11 2016 - 04:47:00 PST)
- Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop (Wed Feb 10 2016 - 15:42:47 PST)
- Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop (Wed Feb 10 2016 - 07:53:40 PST)
- Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop (Wed Feb 10 2016 - 07:26:28 PST)
- [AMBER] MMPB (GB) SA cpptraj failed with prmtop (Wed Feb 10 2016 - 06:39:53 PST)
Aronica, Pietro
- [AMBER] Quasi-harmonic Calculations (Thu Feb 11 2016 - 07:34:56 PST)
Atila Petrosian
- [AMBER] standard deviation of rmsd values (Tue Feb 02 2016 - 23:39:04 PST)
Ayesha Kanwal
- [AMBER] Need Amber entropy calculated values (Mon Feb 29 2016 - 06:48:41 PST)
- [AMBER] want script for plotting graph on entropy (Mon Feb 22 2016 - 03:40:15 PST)
- [AMBER] how to check protonation state (Tue Feb 16 2016 - 12:46:13 PST)
- Re: [AMBER] want to ask you about PCA plotting (Tue Feb 16 2016 - 12:42:08 PST)
- [AMBER] want to ask you about PCA plotting (Tue Feb 16 2016 - 01:58:58 PST)
Balaji Selvam
- [AMBER] CPPtraj & ParmEd - delete atoms (Mon Feb 22 2016 - 10:41:20 PST)
- [AMBER] membrane potential (Thu Feb 18 2016 - 17:22:04 PST)
Batuhan Kav
- Re: [AMBER] gzip -9 heat.mdcrd Error (Sat Feb 27 2016 - 06:54:50 PST)
- [AMBER] charmmlipid2amber.py (Mon Feb 22 2016 - 04:44:57 PST)
- Re: [AMBER] Error: Bad > topology file. (Thu Feb 11 2016 - 12:24:54 PST)
- [AMBER] Error: Bad > topology file. (Thu Feb 11 2016 - 11:56:50 PST)
- [AMBER] Zero pressure with pmemd.cuda (Fri Feb 05 2016 - 08:10:57 PST)
Bill Ross
- Re: [AMBER] Regarding trajectory analysis using CPPTRAJ (Fri Feb 26 2016 - 02:44:32 PST)
- Re: [AMBER] Minimization error using Sander (Thu Feb 25 2016 - 03:27:55 PST)
- Re: [AMBER] How to transfer amino acid sequence to Xleap. (Wed Feb 24 2016 - 11:28:57 PST)
- Re: [AMBER] How to transfer amino acid sequence to Xleap. (Wed Feb 24 2016 - 03:13:24 PST)
- Re: [AMBER] How to transfer amino acid sequence to Xleap. (Wed Feb 24 2016 - 03:00:41 PST)
- Re: [AMBER] Typing {} in Xleap (Wed Feb 24 2016 - 02:50:00 PST)
- Re: [AMBER] Typing {} in Xleap (Wed Feb 24 2016 - 02:10:33 PST)
- Re: [AMBER] parameter file for isoaspartate acid (Mon Feb 22 2016 - 02:40:32 PST)
- Re: [AMBER] parameter file for isoaspartate acid (Mon Feb 22 2016 - 01:18:57 PST)
- Re: [AMBER] unable to generate Mercury parameter file (Tue Feb 16 2016 - 22:14:09 PST)
- Re: [AMBER] Li & Mertz ion parameters (Sat Feb 13 2016 - 13:34:35 PST)
- Re: [AMBER] broken iodine bond problem in NEWPDB.PDB file. (Sat Feb 13 2016 - 11:44:11 PST)
- Re: [AMBER] Dear all (Fri Feb 12 2016 - 04:40:26 PST)
- Re: [AMBER] Dear all (Fri Feb 12 2016 - 04:12:50 PST)
- Re: [AMBER] Dear all (Fri Feb 12 2016 - 03:49:43 PST)
- Re: [AMBER] Dear all (Fri Feb 12 2016 - 03:36:18 PST)
- Re: [AMBER] minimization error : segmentation fault (AMBER Digest, Vol 1483, Issue 1) (Thu Feb 11 2016 - 22:10:47 PST)
- Re: [AMBER] minimization error : segmentation fault (AMBER Digest, Vol 1483, Issue 1) (Thu Feb 11 2016 - 22:09:30 PST)
- Re: [AMBER] minimization error : segmentation fault (AMBER Digest, Vol 1483, Issue 1) (Thu Feb 11 2016 - 21:19:43 PST)
- Re: [AMBER] Is there a way to compare trajectories? (Thu Feb 11 2016 - 01:19:49 PST)
- Re: [AMBER] minimization error : segmentation fault (Wed Feb 10 2016 - 23:39:50 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 02:58:55 PST)
BLEY Michael
- [AMBER] Maximum input value for the isothermal compressibility in AMBER (Thu Feb 25 2016 - 05:25:55 PST)
Carlos Romero
- [AMBER] interpret results (Thu Feb 11 2016 - 09:27:08 PST)
- [AMBER] amber14 update (Mon Feb 01 2016 - 16:50:14 PST)
Carlos Simmerling
- Re: [AMBER] Pdb file to Mol2 (Mon Feb 29 2016 - 05:30:32 PST)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Sun Feb 28 2016 - 06:20:38 PST)
- Re: [AMBER] How to analyze mutational free energy difference? (Sat Feb 27 2016 - 10:55:21 PST)
- Re: [AMBER] How to analyze mutational free energy difference? (Sat Feb 27 2016 - 09:32:00 PST)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Sat Feb 27 2016 - 05:17:51 PST)
- Re: [AMBER] How to analyze mutational free energy difference? (Sat Feb 27 2016 - 05:13:31 PST)
- Re: [AMBER] How to analyze mutational free energy difference? (Sat Feb 27 2016 - 04:48:38 PST)
- Re: [AMBER] How to analyze mutational free energy difference? (Sat Feb 27 2016 - 04:39:14 PST)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Sat Feb 27 2016 - 04:34:40 PST)
- Re: [AMBER] tMD with ligand (Tue Feb 23 2016 - 06:14:45 PST)
- Re: [AMBER] tMD with ligand (Tue Feb 23 2016 - 04:19:03 PST)
- Re: [AMBER] tMD with ligand (Tue Feb 23 2016 - 03:14:36 PST)
- Re: [AMBER] how to check protonation state (Tue Feb 16 2016 - 13:25:01 PST)
- Re: [AMBER] average 3D structure with condition (Mon Feb 15 2016 - 08:54:26 PST)
- Re: [AMBER] Restarting a heating simulation (Thu Feb 11 2016 - 05:14:29 PST)
- Re: [AMBER] Is there a way to compare trajectories? (Thu Feb 11 2016 - 03:15:39 PST)
- Re: [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide (Wed Feb 10 2016 - 04:52:14 PST)
- Re: [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide (Tue Feb 09 2016 - 06:55:11 PST)
- Re: [AMBER] Size of solvent box, RDF (Fri Feb 05 2016 - 10:42:01 PST)
- Re: [AMBER] Size of solvent box, RDF (Fri Feb 05 2016 - 04:10:05 PST)
- Re: [AMBER] Size of solvent box (Wed Feb 03 2016 - 10:38:24 PST)
- Re: [AMBER] Dihedral angles restraints from x-ray to NMR (Wed Feb 03 2016 - 04:32:51 PST)
- Re: [AMBER] Dear All (Tue Feb 02 2016 - 04:43:48 PST)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Tue Feb 02 2016 - 04:26:46 PST)
Casalini Tommaso
- Re: [AMBER] Problem with HIS/HIE residue and ff14SB force field (Fri Feb 26 2016 - 02:45:10 PST)
- Re: [AMBER] Problem with HIS/HIE residue and ff14SB force field (Fri Feb 26 2016 - 02:38:59 PST)
- [AMBER] Problem with HIS/HIE residue and ff14SB force field (Fri Feb 26 2016 - 02:20:02 PST)
Dan Morris
- [AMBER] Ligand Molecules Being Rejected in SHIFTS 5.0.1 (Mon Feb 22 2016 - 12:01:11 PST)
Daniel Roe
- Re: [AMBER] reading Amber trajectory files with chamber topology file (Mon Feb 29 2016 - 08:17:35 PST)
- Re: [AMBER] reading Amber trajectory files with chamber topology file (Mon Feb 29 2016 - 07:42:01 PST)
- Re: [AMBER] Pdb file to Mol2 (Mon Feb 29 2016 - 07:34:20 PST)
- Re: [AMBER] Bounds command with GIst (Mon Feb 29 2016 - 07:32:29 PST)
- Re: [AMBER] How to separate a protein complex to its components (Sun Feb 28 2016 - 05:57:07 PST)
- Re: [AMBER] draw vector along axis of an alpha helix (Sat Feb 27 2016 - 12:57:38 PST)
- Re: [AMBER] Pdb file to Mol2 (Fri Feb 26 2016 - 08:08:00 PST)
- Re: [AMBER] Pdb file to Mol2 (Fri Feb 26 2016 - 07:47:03 PST)
- Re: [AMBER] AMBER Digest, Vol 1497, Issue 1 (Fri Feb 26 2016 - 07:26:28 PST)
- Re: [AMBER] External library for leap (Fri Feb 26 2016 - 07:24:10 PST)
- Re: [AMBER] Duration parmchk (Fri Feb 26 2016 - 07:21:30 PST)
- Re: [AMBER] Pdb file to Mol2 (Fri Feb 26 2016 - 07:20:25 PST)
- Re: [AMBER] Regarding trajectory analysis using CPPTRAJ (Fri Feb 26 2016 - 07:18:20 PST)
- Re: [AMBER] error in running rmsf command cpptraj (Wed Feb 24 2016 - 07:19:57 PST)
- Re: [AMBER] Query: extracting protons from trajectory/coordinate file (Wed Feb 24 2016 - 07:18:27 PST)
- Re: [AMBER] No exe file in Amberhome (Tue Feb 23 2016 - 09:05:04 PST)
- Re: [AMBER] No exe file in Amberhome (Tue Feb 23 2016 - 08:07:06 PST)
- Re: [AMBER] cpptraj command for pi-stacking or hydrophobic interactions. (Tue Feb 23 2016 - 08:05:51 PST)
- Re: [AMBER] velocity auto correlation function (Tue Feb 23 2016 - 07:57:52 PST)
- Re: [AMBER] Defining Units in nastruct (Tue Feb 23 2016 - 07:49:49 PST)
- Re: [AMBER] CPPtraj & ParmEd - delete atoms (Mon Feb 22 2016 - 10:53:16 PST)
- Re: [AMBER] calculate ligand RMSD for MD simulations; nofit or not? (Mon Feb 22 2016 - 09:15:47 PST)
- Re: [AMBER] lmod & xmin in sander (Sun Feb 21 2016 - 06:59:58 PST)
- Re: [AMBER] Covariance Matrix in CPPTRAJ (Sun Feb 21 2016 - 06:53:42 PST)
- Re: [AMBER] Covariance Matrix in CPPTRAJ (Sat Feb 20 2016 - 15:40:59 PST)
- Re: [AMBER] A question about cpptraj autoimage (Thu Feb 18 2016 - 19:09:23 PST)
- Re: [AMBER] Technical problem running pH-REMD (Wed Feb 17 2016 - 07:57:09 PST)
- Re: [AMBER] Technical problem running pH-REMD (Wed Feb 17 2016 - 07:25:10 PST)
- Re: [AMBER] Technical problem running pH-REMD (Wed Feb 17 2016 - 07:23:50 PST)
- Re: [AMBER] Fwd: PC square fluctuations (Tue Feb 16 2016 - 07:31:36 PST)
- Re: [AMBER] want to ask you about PCA plotting (Tue Feb 16 2016 - 07:26:47 PST)
- Re: [AMBER] average 3D structure with condition (Mon Feb 15 2016 - 13:22:37 PST)
- Re: [AMBER] average 3D structure with condition (Mon Feb 15 2016 - 08:59:35 PST)
- Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered (Sat Feb 13 2016 - 08:18:28 PST)
- Re: [AMBER] Is there a way to compare trajectories? (Fri Feb 12 2016 - 02:48:00 PST)
- Re: [AMBER] cpptraj nativecontacts. (Thu Feb 11 2016 - 15:48:24 PST)
- Re: [AMBER] cpptraj nativecontacts. (Thu Feb 11 2016 - 15:10:21 PST)
- Re: [AMBER] Error: Bad > topology file. (Thu Feb 11 2016 - 12:07:50 PST)
- Re: [AMBER] Quasi-harmonic Calculations (Thu Feb 11 2016 - 09:20:48 PST)
- Re: [AMBER] Is there a way to compare trajectories? (Thu Feb 11 2016 - 07:20:04 PST)
- Re: [AMBER] Regarding MMGBSA calculation (Thu Feb 11 2016 - 07:22:49 PST)
- Re: [AMBER] Normalizing histogram with CPPTRAJ (Wed Feb 10 2016 - 09:25:40 PST)
- Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop (Wed Feb 10 2016 - 08:00:40 PST)
- Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop (Wed Feb 10 2016 - 07:37:15 PST)
- Re: [AMBER] accelerated MD - frequency of conformational change (Fri Feb 05 2016 - 10:00:58 PST)
- Re: [AMBER] REMD tutorial (Thu Feb 04 2016 - 10:51:28 PST)
- Re: [AMBER] Question about mask command (Wed Feb 03 2016 - 08:17:53 PST)
- Re: [AMBER] standard deviation of rmsd values (Wed Feb 03 2016 - 05:50:43 PST)
- Re: [AMBER] Question about mask command (Tue Feb 02 2016 - 07:27:52 PST)
David A Case
- Re: [AMBER] problem running MD for diphosphoric acid anion (Mon Feb 29 2016 - 04:43:19 PST)
- Re: [AMBER] Problem with HIS/HIE residue and ff14SB force field (Fri Feb 26 2016 - 05:31:36 PST)
- Re: [AMBER] error in sqm.out file (Fri Feb 26 2016 - 05:26:47 PST)
- Re: [AMBER] Maximum input value for the isothermal compressibility in AMBER (Thu Feb 25 2016 - 06:06:39 PST)
- Re: [AMBER] Minimization error using Sander (Thu Feb 25 2016 - 05:16:49 PST)
- Re: [AMBER] How to transfer amino acid sequence to Xleap. (Wed Feb 24 2016 - 10:54:06 PST)
- Re: [AMBER] How to transfer amino acid sequence to Xleap. (Wed Feb 24 2016 - 04:56:35 PST)
- Re: [AMBER] Query regarding extracting protons from coordinate/trajectory file (Wed Feb 24 2016 - 04:53:50 PST)
- Re: [AMBER] No exe file in Amberhome (Tue Feb 23 2016 - 09:03:17 PST)
- Re: [AMBER] Ligand Molecules Being Rejected in SHIFTS 5.0.1 (Tue Feb 23 2016 - 05:03:58 PST)
- Re: [AMBER] No exe file in Amberhome (Tue Feb 23 2016 - 04:52:50 PST)
- Re: [AMBER] No exe file in Amberhome (Mon Feb 22 2016 - 13:03:33 PST)
- Re: [AMBER] Paradynamics with Amber (Mon Feb 22 2016 - 12:06:26 PST)
- Re: [AMBER] No exe file in Amberhome (Mon Feb 22 2016 - 11:53:02 PST)
- Re: [AMBER] calculate ligand RMSD for MD simulations; nofit or not? (Mon Feb 22 2016 - 09:21:32 PST)
- Re: [AMBER] Paradynamics with Amber (Mon Feb 22 2016 - 08:51:20 PST)
- Re: [AMBER] Paradynamics with Amber (Mon Feb 22 2016 - 07:30:58 PST)
- Re: [AMBER] want script for plotting graph on entropy (Mon Feb 22 2016 - 05:00:38 PST)
- Re: [AMBER] parameter file for isoaspartate acid (Mon Feb 22 2016 - 04:57:11 PST)
- Re: [AMBER] Fwd: Error with disulphide bonds in tleap (Mon Feb 22 2016 - 04:50:17 PST)
- Re: [AMBER] lmod & xmin in sander (Mon Feb 22 2016 - 04:47:37 PST)
- Re: [AMBER] charge derivation (Fri Feb 19 2016 - 09:24:49 PST)
- Re: [AMBER] Dear all (Wed Feb 17 2016 - 06:58:56 PST)
- Re: [AMBER] unable to generate Mercury parameter file (Wed Feb 17 2016 - 06:53:31 PST)
- Re: [AMBER] Getting and keeping ACPYPE updated (Tue Feb 16 2016 - 11:01:46 PST)
- Re: [AMBER] Reg: problem in generating prmtop and crd files by using ff12SB of magnesium ions (Tue Feb 16 2016 - 10:22:57 PST)
- Re: [AMBER] Dear all (Tue Feb 16 2016 - 04:54:27 PST)
- Re: [AMBER] Unable to run QM/MM with RNA and sodium ion (Thu Feb 11 2016 - 14:33:38 PST)
- Re: [AMBER] Restarting a heating simulation (Thu Feb 11 2016 - 04:50:39 PST)
- Re: [AMBER] Regarding MMGBSA calculation (Thu Feb 11 2016 - 04:45:22 PST)
- Re: [AMBER] Gist Installation in Amber12 (Thu Feb 11 2016 - 04:17:03 PST)
- Re: [AMBER] error in minimization whole system (Sun Feb 07 2016 - 05:24:44 PST)
- Re: [AMBER] Regarding MMGBSA calculation (Sat Feb 06 2016 - 05:24:34 PST)
- Re: [AMBER] Regarding MMGBSA calculation (Fri Feb 05 2016 - 05:05:07 PST)
- Re: [AMBER] MMPBSA ImportError (Thu Feb 04 2016 - 14:50:28 PST)
- Re: [AMBER] Problems with when using DFTB halorg .skf files in sqm (Thu Feb 04 2016 - 11:01:32 PST)
- Re: [AMBER] MMPBSA ImportError (Wed Feb 03 2016 - 12:16:57 PST)
- Re: [AMBER] Dihedral angles restraints from x-ray to NMR (Wed Feb 03 2016 - 04:49:47 PST)
- Re: [AMBER] Dear All (Tue Feb 02 2016 - 04:59:43 PST)
- Re: [AMBER] Regaridng FIle preparation in AMBERTOOLS14 (Tue Feb 02 2016 - 04:57:21 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 05:08:48 PST)
David Cerutti
- Re: [AMBER] EPtot, Angle, Bond, Dihed (Mon Feb 29 2016 - 19:11:19 PST)
- Re: [AMBER] charge derivation (Fri Feb 26 2016 - 07:41:10 PST)
- Re: [AMBER] Fwd: Thermodynamic Integration (Wed Feb 24 2016 - 23:45:09 PST)
- Re: [AMBER] Dihedral parameters (Tue Feb 23 2016 - 08:42:22 PST)
- Re: [AMBER] charge derivation (Tue Feb 23 2016 - 08:04:56 PST)
David Poole
- Re: [AMBER] Paramfit, negative bond parameters (Fri Feb 12 2016 - 12:25:22 PST)
- [AMBER] Paramfit, negative bond parameters (Thu Feb 11 2016 - 15:53:41 PST)
Dickson, Callum J
- Re: [AMBER] membrane potential (Fri Feb 19 2016 - 10:04:06 PST)
- Re: [AMBER] Z-constraint PMF method (Mon Feb 08 2016 - 06:36:22 PST)
Dr. Anselm Horn
- Re: [AMBER] Is there a way to compare trajectories? (Thu Feb 11 2016 - 01:27:03 PST)
- Re: [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide (Wed Feb 10 2016 - 06:31:13 PST)
Ebert Maximilian
- Re: [AMBER] No exe file in Amberhome (Mon Feb 22 2016 - 11:11:26 PST)
Eiros Zamora, Juan
- Re: [AMBER] Downloading of Ambertools15 (Fri Feb 12 2016 - 01:40:20 PST)
Elisa Pieri
- [AMBER] waters inside cavity (Fri Feb 26 2016 - 07:00:54 PST)
- Re: [AMBER] R: R: Fwd: cpinutil.py problem (Fri Feb 26 2016 - 01:59:02 PST)
- [AMBER] R: R: Fwd: cpinutil.py problem (Wed Feb 24 2016 - 22:33:45 PST)
- [AMBER] R: Fwd: cpinutil.py problem (Wed Feb 24 2016 - 10:18:12 PST)
- Re: [AMBER] Fwd: cpinutil.py problem (Wed Feb 24 2016 - 07:14:25 PST)
- Re: [AMBER] Fwd: cpinutil.py problem (Wed Feb 24 2016 - 05:15:03 PST)
- [AMBER] Fwd: cpinutil.py problem (Tue Feb 23 2016 - 07:39:38 PST)
- Re: [AMBER] Technical problem running pH-REMD (Wed Feb 17 2016 - 07:35:16 PST)
- Re: [AMBER] Technical problem running pH-REMD (Wed Feb 17 2016 - 06:53:37 PST)
- [AMBER] Technical problem running pH-REMD (Wed Feb 17 2016 - 06:22:06 PST)
- Re: [AMBER] Restarting a heating simulation (Thu Feb 11 2016 - 05:05:21 PST)
- [AMBER] Restarting a heating simulation (Thu Feb 11 2016 - 02:43:50 PST)
Emilio Angelina
- Re: [AMBER] draw vector along axis of an alpha helix (Sat Feb 27 2016 - 13:50:14 PST)
- [AMBER] draw vector along axis of an alpha helix (Sat Feb 27 2016 - 07:50:28 PST)
Emilio Lence
- Re: [AMBER] Problem with saving parameters for a complex having Heme group (Mon Feb 08 2016 - 08:46:43 PST)
Falko Jähnert
- Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors (Thu Feb 11 2016 - 13:40:10 PST)
- Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors (Thu Feb 11 2016 - 05:37:32 PST)
- [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors (Thu Feb 11 2016 - 04:36:50 PST)
Fatemeh Sadat Alavi
- [AMBER] error in minimization whole system (Sun Feb 07 2016 - 04:26:32 PST)
- Re: [AMBER] Wrong or no center in RdPar (Sat Feb 06 2016 - 01:05:38 PST)
- [AMBER] Wrong or no center in RdPar. (Sun Jan 31 2016 - 22:25:38 PST)
FyD
- Re: [AMBER] charge derivation (Fri Feb 26 2016 - 02:57:57 PST)
- Re: [AMBER] parameter file for graphene oxide (Fri Feb 26 2016 - 01:28:00 PST)
- Re: [AMBER] charge derivation (Fri Feb 26 2016 - 01:10:17 PST)
Gary Zhang
- Re: [AMBER] Segmentation fault when converting charmm to amber toppar using chamber (Tue Feb 02 2016 - 06:53:12 PST)
- [AMBER] Segmentation fault when converting charmm to amber toppar using chamber (Mon Feb 01 2016 - 13:09:27 PST)
George Tzotzos
- Re: [AMBER] summary.ETOT analysis and MMPBSA.py (Sun Feb 14 2016 - 07:09:02 PST)
- Re: [AMBER] cpptraj nativecontacts. (Thu Feb 11 2016 - 15:38:34 PST)
- [AMBER] cpptraj nativecontacts. (Thu Feb 11 2016 - 13:49:58 PST)
Gerald Monard
- [AMBER] Ph.D. position, Nancy, France (Thu Feb 25 2016 - 00:39:31 PST)
- Re: [AMBER] Paradynamics with Amber (Mon Feb 22 2016 - 07:54:27 PST)
- Re: [AMBER] Paradynamics with Amber (Mon Feb 22 2016 - 07:28:26 PST)
Gustavo Seabra
- Re: [AMBER] No exe file in Amberhome (Wed Feb 24 2016 - 03:35:06 PST)
- Re: [AMBER] Relabeling Atoms after a Run Trajectory (Fri Feb 19 2016 - 09:57:22 PST)
- Re: [AMBER] Dear all (Fri Feb 12 2016 - 06:21:49 PST)
- Re: [AMBER] Problems with when using DFTB halorg .skf files in sqm (Thu Feb 04 2016 - 05:28:07 PST)
Hai Nguyen
- Re: [AMBER] the angle between two axis (Thu Feb 25 2016 - 23:27:10 PST)
- Re: [AMBER] 回复：Re: Nucleic acid builder (Tue Feb 23 2016 - 19:46:52 PST)
- Re: [AMBER] 回复：Re: Nucleic acid builder (Tue Feb 23 2016 - 19:00:18 PST)
- Re: [AMBER] No exe file in Amberhome (Mon Feb 22 2016 - 23:54:23 PST)
- Re: [AMBER] PDB to distance in AMBER (Wed Feb 10 2016 - 07:51:54 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 11:32:26 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 09:09:55 PST)
Hannes Loeffler
- Re: [AMBER] Preparing needed input files for TI (Mon Feb 29 2016 - 04:00:53 PST)
- Re: [AMBER] Problem with HIS/HIE residue and ff14SB force field (Fri Feb 26 2016 - 02:53:35 PST)
- Re: [AMBER] Problem with HIS/HIE residue and ff14SB force field (Fri Feb 26 2016 - 02:34:02 PST)
- Re: [AMBER] antechamber run for FAD (Fri Feb 19 2016 - 02:59:02 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 02:13:11 PST)
Indrajit Deb
- Re: [AMBER] MMGBSA error (Thu Feb 25 2016 - 17:06:42 PST)
- Re: [AMBER] MMGBSA error (Thu Feb 25 2016 - 16:27:29 PST)
- [AMBER] MMGBSA error (Thu Feb 25 2016 - 09:24:38 PST)
Ivanov, Maxim
- [AMBER] more extra points needed (Mon Feb 29 2016 - 09:15:17 PST)
Jason Swails
- Re: [AMBER] more extra points needed (Mon Feb 29 2016 - 20:34:44 PST)
- Re: [AMBER] Need Amber entropy calculated values (Mon Feb 29 2016 - 20:25:25 PST)
- Re: [AMBER] EPtot, Angle, Bond, Dihed (Mon Feb 29 2016 - 20:20:29 PST)
- Re: [AMBER] MMGBSA error (Thu Feb 25 2016 - 17:01:38 PST)
- Re: [AMBER] R: R: Fwd: cpinutil.py problem (Thu Feb 25 2016 - 15:56:35 PST)
- Re: [AMBER] R: Fwd: cpinutil.py problem (Wed Feb 24 2016 - 18:28:37 PST)
- Re: [AMBER] Fwd: cpinutil.py problem (Wed Feb 24 2016 - 09:31:40 PST)
- Re: [AMBER] No exe file in Amberhome (Wed Feb 24 2016 - 09:24:54 PST)
- Re: [AMBER] Fwd: cpinutil.py problem (Tue Feb 23 2016 - 18:45:46 PST)
- Re: [AMBER] Covariance Matrix in CPPTRAJ (Sat Feb 20 2016 - 17:27:56 PST)
- Re: [AMBER] cationic-pi interactions (Fri Feb 19 2016 - 20:37:02 PST)
- Re: [AMBER] Energy decomposition error (Fri Feb 19 2016 - 20:34:44 PST)
- Re: [AMBER] parmed/chamber problem recognizing atom types (Tue Feb 16 2016 - 18:35:45 PST)
- Re: [AMBER] MMPBSA.py.MPI won't recognise mpy4pi (Sun Feb 14 2016 - 16:13:20 PST)
- Re: [AMBER] summary.ETOT analysis and MMPBSA.py (Sun Feb 14 2016 - 06:15:24 PST)
- Re: [AMBER] summary.ETOT analysis (Sun Feb 14 2016 - 04:14:39 PST)
- Re: [AMBER] MMPBSA.py.MPI won't recognise mpy4pi (Fri Feb 12 2016 - 17:03:12 PST)
- Re: [AMBER] Li & Mertz ion parameters (Fri Feb 12 2016 - 14:38:35 PST)
- Re: [AMBER] Dear all (Fri Feb 12 2016 - 05:57:48 PST)
- Re: [AMBER] Error: Bad > topology file. (Thu Feb 11 2016 - 12:48:51 PST)
- Re: [AMBER] Quasi-harmonic Calculations (Thu Feb 11 2016 - 08:42:57 PST)
- Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors (Thu Feb 11 2016 - 08:04:12 PST)
- Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors (Thu Feb 11 2016 - 05:03:19 PST)
- Re: [AMBER] Restarting a heating simulation (Thu Feb 11 2016 - 05:00:24 PST)
- Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop (Thu Feb 11 2016 - 04:50:09 PST)
- Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop (Wed Feb 10 2016 - 18:15:44 PST)
- Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop (Wed Feb 10 2016 - 09:00:58 PST)
- Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop (Wed Feb 10 2016 - 07:12:59 PST)
- Re: [AMBER] problem with energy minimization (sander) (Wed Feb 10 2016 - 05:49:07 PST)
- Re: [AMBER] problem with energy minimization (sander) (Wed Feb 10 2016 - 04:44:28 PST)
- Re: [AMBER] Question about AmberTools14/15 installation (Tue Feb 09 2016 - 11:18:41 PST)
- Re: [AMBER] Is the Force Constant in the Parm**.dat file derived from a mass-weighted Hessian (Tue Feb 09 2016 - 04:39:37 PST)
- Re: [AMBER] Error atommask selectElemMask (Mon Feb 08 2016 - 05:42:07 PST)
- Re: [AMBER] Question about AmberTools14/15 installation (Mon Feb 08 2016 - 05:15:05 PST)
- Re: [AMBER] aMD Secondary Structure (Sun Feb 07 2016 - 12:54:34 PST)
- Re: [AMBER] Z-constraint PMF method (Sun Feb 07 2016 - 12:50:03 PST)
- Re: [AMBER] MMPBSA ImportError (Sat Feb 06 2016 - 18:53:24 PST)
- Re: [AMBER] Size of solvent box, RDF (Fri Feb 05 2016 - 18:52:18 PST)
- Re: [AMBER] MMPBSA ImportError (Fri Feb 05 2016 - 18:49:18 PST)
- Re: [AMBER] MMPBSA ImportError (Fri Feb 05 2016 - 18:45:13 PST)
- Re: [AMBER] Size of solvent box, RDF (Fri Feb 05 2016 - 10:36:16 PST)
- Re: [AMBER] Zero pressure with pmemd.cuda (Fri Feb 05 2016 - 10:27:14 PST)
- Re: [AMBER] MMPBSA ImportError (Fri Feb 05 2016 - 05:13:47 PST)
- Re: [AMBER] Regarding MMGBSA calculation (Fri Feb 05 2016 - 04:58:33 PST)
- Re: [AMBER] MMPBSA ImportError (Thu Feb 04 2016 - 19:22:55 PST)
- Re: [AMBER] Size of solvent box (Wed Feb 03 2016 - 10:31:23 PST)
- Re: [AMBER] standard deviation of rmsd values (Wed Feb 03 2016 - 05:49:31 PST)
- Re: [AMBER] MMPBSA ImportError (Wed Feb 03 2016 - 05:41:21 PST)
- Re: [AMBER] MMPBSA ImportError (Wed Feb 03 2016 - 04:49:51 PST)
- Re: [AMBER] Dear All (Tue Feb 02 2016 - 04:20:11 PST)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Tue Feb 02 2016 - 04:13:22 PST)
- Re: [AMBER] Segmentation fault when converting charmm to amber toppar using chamber (Mon Feb 01 2016 - 15:08:07 PST)
- Re: [AMBER] Value of ntrx=7 (Mon Feb 01 2016 - 12:58:35 PST)
- Re: [AMBER] Value of ntrx=7 (Mon Feb 01 2016 - 11:55:43 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 11:53:43 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 08:27:51 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 06:36:39 PST)
- Re: [AMBER] Wrong or no center in RdPar. (Mon Feb 01 2016 - 06:08:54 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 06:05:48 PST)
JEAN MARC BILLOD
- Re: [AMBER] Amber/tutorial/advanced/tutorial16/ (Tue Feb 02 2016 - 06:52:24 PST)
Jean-Marc Billod
- Re: [AMBER] tMD with ligand (Tue Feb 23 2016 - 05:32:49 PST)
- Re: [AMBER] tMD with ligand (Tue Feb 23 2016 - 03:26:46 PST)
- [AMBER] tMD with ligand (Tue Feb 23 2016 - 01:45:45 PST)
Jean-Patrick Francoia
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 12:46:13 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 11:27:13 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 06:52:42 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 06:32:41 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 05:57:41 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 02:17:42 PST)
- [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 01:48:31 PST)
Jesmita Dhar
- [AMBER] error in sqm.out file (Fri Feb 26 2016 - 00:15:31 PST)
- Re: [AMBER] parameter file for graphene oxide (Thu Feb 25 2016 - 01:36:57 PST)
- Re: [AMBER] parameter file for isoaspartate acid (Tue Feb 23 2016 - 03:36:02 PST)
- [AMBER] parameter file for graphene oxide (Tue Feb 23 2016 - 03:34:23 PST)
- Re: [AMBER] parameter file for isoaspartate acid (Mon Feb 22 2016 - 03:58:13 PST)
- Re: [AMBER] parameter file for isoaspartate acid (Mon Feb 22 2016 - 03:15:50 PST)
- Re: [AMBER] parameter file for isoaspartate acid (Mon Feb 22 2016 - 02:15:23 PST)
- [AMBER] parameter file for isoaspartate acid (Mon Feb 22 2016 - 01:15:20 PST)
Joel Lapin
- Re: [AMBER] draw vector along axis of an alpha helix (Sat Feb 27 2016 - 12:53:39 PST)
- Re: [AMBER] Covariance Matrix in CPPTRAJ (Sat Feb 20 2016 - 19:57:12 PST)
- Re: [AMBER] Covariance Matrix in CPPTRAJ (Sat Feb 20 2016 - 17:33:16 PST)
- Re: [AMBER] Covariance Matrix in CPPTRAJ (Sat Feb 20 2016 - 16:29:57 PST)
- [AMBER] Covariance Matrix in CPPTRAJ (Sat Feb 20 2016 - 15:10:46 PST)
Jose luis Borioni
- [AMBER] cationic-pi interactions (Wed Feb 17 2016 - 19:56:48 PST)
Joseph Baker
- Re: [AMBER] MMPBSA ImportError (Fri Feb 05 2016 - 17:57:00 PST)
- Re: [AMBER] MMPBSA ImportError (Fri Feb 05 2016 - 03:51:13 PST)
- Re: [AMBER] MMPBSA ImportError (Thu Feb 04 2016 - 15:06:02 PST)
- Re: [AMBER] MMPBSA ImportError (Thu Feb 04 2016 - 13:54:11 PST)
- Re: [AMBER] MMPBSA ImportError (Tue Feb 02 2016 - 21:02:11 PST)
- [AMBER] MMPBSA ImportError (Tue Feb 02 2016 - 18:25:51 PST)
Josh Berryman
- Re: [AMBER] MMPBSA ImportError (Wed Feb 03 2016 - 05:33:45 PST)
- Re: [AMBER] free energy calculation of folding (Wed Feb 03 2016 - 04:06:21 PST)
- Re: [AMBER] 3DRISM: erratic values for partial molar volume (Mon Feb 01 2016 - 05:16:01 PST)
Jungho Yang
- [AMBER] Dihedral parameters (Tue Feb 23 2016 - 07:54:36 PST)
Jérémie KNOOPS [531802]
- Re: [AMBER] lmod & xmin in sander (Tue Feb 23 2016 - 06:11:36 PST)
- [AMBER] lmod & xmin in sander (Sun Feb 21 2016 - 06:09:47 PST)
Kalenkiewicz, Andrew (NIH/NICHD) [F]
- [AMBER] [AMBER} nonpolar term for MMPBSA decomp showing up as 0 (Tue Feb 16 2016 - 11:55:29 PST)
Karl Kirschner
- Re: [AMBER] parameter file for graphene oxide (Thu Feb 25 2016 - 01:54:23 PST)
- Re: [AMBER] citrulline parameters (Wed Feb 10 2016 - 06:36:11 PST)
Karolina Markowska
- Re: [AMBER] Is there a way to compare trajectories? (Fri Feb 12 2016 - 02:41:05 PST)
- Re: [AMBER] Is there a way to compare trajectories? (Fri Feb 12 2016 - 00:25:39 PST)
- Re: [AMBER] Is there a way to compare trajectories? (Thu Feb 11 2016 - 03:27:46 PST)
- Re: [AMBER] Is there a way to compare trajectories? (Thu Feb 11 2016 - 01:44:52 PST)
- [AMBER] Is there a way to compare trajectories? (Thu Feb 11 2016 - 01:07:01 PST)
kaushik chakraborty
- [AMBER] Unable to run QM/MM with RNA and sodium ion (Thu Feb 11 2016 - 08:57:39 PST)
Krantzman, Kristin D
- Re: [AMBER] Size of solvent box, RDF (Fri Feb 05 2016 - 14:31:26 PST)
- Re: [AMBER] Size of solvent box, RDF (Fri Feb 05 2016 - 09:44:27 PST)
- Re: [AMBER] Size of solvent box, RDF (Thu Feb 04 2016 - 10:42:50 PST)
- [AMBER] Size of solvent box (Wed Feb 03 2016 - 09:27:20 PST)
- Re: [AMBER] Value of ntrx=7 (Mon Feb 01 2016 - 12:02:09 PST)
- [AMBER] Value of ntrx=7 (Mon Feb 01 2016 - 11:50:21 PST)
Lorenzo Gontrani
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Sat Feb 27 2016 - 01:14:11 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 03:26:39 PST)
Madhura De
- [AMBER] Query: extracting protons from trajectory/coordinate file (Wed Feb 24 2016 - 03:52:00 PST)
- [AMBER] Query regarding extracting protons from coordinate/trajectory file (Wed Feb 24 2016 - 00:42:16 PST)
mahdie hadi
- Re: [AMBER] Preparing needed input files for TI (Mon Feb 29 2016 - 07:11:31 PST)
Mahdieh Hadi
- Re: [AMBER] Pdb file to Mol2 (Mon Feb 29 2016 - 07:19:44 PST)
- Re: [AMBER] Pdb file to Mol2 (Mon Feb 29 2016 - 06:31:44 PST)
- Re: [AMBER] Pdb file to Mol2 (Mon Feb 29 2016 - 05:13:48 PST)
- [AMBER] Preparing needed input files for TI (Mon Feb 29 2016 - 03:26:02 PST)
- [AMBER] How to separate a protein complex to its components (Sat Feb 27 2016 - 23:39:00 PST)
- [AMBER] gzip -9 heat.mdcrd Error (Sat Feb 27 2016 - 06:27:03 PST)
- Re: [AMBER] How to analyze mutational free energy difference? (Sat Feb 27 2016 - 05:02:28 PST)
- Re: [AMBER] How to analyze mutational free energy difference? (Sat Feb 27 2016 - 04:46:20 PST)
- Re: [AMBER] Pdb file to Mol2 (Fri Feb 26 2016 - 07:56:09 PST)
- Re: [AMBER] Pdb file to Mol2 (Fri Feb 26 2016 - 07:30:34 PST)
- [AMBER] Pdb file to Mol2 (Fri Feb 26 2016 - 04:03:47 PST)
- Re: [AMBER] Question regarding protein-Dna binding free energy (Thu Feb 25 2016 - 06:56:48 PST)
- [AMBER] Question regarding protein-Dna binding free energy (Thu Feb 25 2016 - 06:25:54 PST)
- Re: [AMBER] How to transfer amino acid sequence to Xleap. (Wed Feb 24 2016 - 10:59:32 PST)
- Re: [AMBER] How to transfer amino acid sequence to Xleap. (Wed Feb 24 2016 - 07:36:20 PST)
- Re: [AMBER] How to transfer amino acid sequence to Xleap. (Wed Feb 24 2016 - 03:32:15 PST)
- Re: [AMBER] How to transfer amino acid sequence to Xleap. (Wed Feb 24 2016 - 03:23:10 PST)
- Re: [AMBER] How to transfer amino acid sequence to Xleap. (Wed Feb 24 2016 - 03:07:12 PST)
- Re: [AMBER] How to transfer amino acid sequence to Xleap. (Wed Feb 24 2016 - 02:54:20 PST)
- Re: [AMBER] Typing {} in Xleap (Wed Feb 24 2016 - 02:32:47 PST)
- Re: [AMBER] No exe file in Amberhome (Wed Feb 24 2016 - 02:27:26 PST)
- Re: [AMBER] Typing {} in Xleap (Wed Feb 24 2016 - 02:18:16 PST)
- Re: [AMBER] No exe file in Amberhome (Wed Feb 24 2016 - 02:13:18 PST)
- [AMBER] Typing {} in Xleap (Wed Feb 24 2016 - 01:48:28 PST)
- Re: [AMBER] No exe file in Amberhome (Tue Feb 23 2016 - 05:25:35 PST)
- Re: [AMBER] No exe file in Amberhome (Tue Feb 23 2016 - 01:18:27 PST)
- Re: [AMBER] No exe file in Amberhome (Mon Feb 22 2016 - 23:51:04 PST)
- Re: [AMBER] No exe file in Amberhome (Mon Feb 22 2016 - 12:37:52 PST)
- [AMBER] No exe file in Amberhome (Mon Feb 22 2016 - 10:53:15 PST)
Marc van der Kamp
- Re: [AMBER] Downloading of Ambertools15 (Fri Feb 12 2016 - 02:16:07 PST)
- Re: [AMBER] Is there a way to compare trajectories? (Fri Feb 12 2016 - 01:20:51 PST)
- Re: [AMBER] Problems with when using DFTB halorg .skf files in sqm (Thu Feb 04 2016 - 06:08:00 PST)
- [AMBER] Problems with when using DFTB halorg .skf files in sqm (Thu Feb 04 2016 - 04:37:42 PST)
Marc Zhang
- Re: [AMBER] calculate ligand RMSD for MD simulations; nofit or not? (Mon Feb 22 2016 - 12:03:30 PST)
- [AMBER] calculate ligand RMSD for MD simulations; nofit or not? (Mon Feb 22 2016 - 07:52:23 PST)
Marcelo Andrade Chagas
- Re: [AMBER] How to separate a protein complex to its components (Sun Feb 28 2016 - 04:05:03 PST)
- Re: [AMBER] Pdb file to Mol2 (Fri Feb 26 2016 - 04:24:22 PST)
- Re: [AMBER] Pdb file to Mol2 (Fri Feb 26 2016 - 04:18:35 PST)
- Re: [AMBER] Fwd: cpinutil.py problem (Wed Feb 24 2016 - 07:05:12 PST)
- Re: [AMBER] No exe file in Amberhome (Wed Feb 24 2016 - 03:33:51 PST)
- Re: [AMBER] Fwd: cpinutil.py problem (Tue Feb 23 2016 - 19:26:41 PST)
- Re: [AMBER] No exe file in Amberhome (Tue Feb 23 2016 - 08:44:08 PST)
- Re: [AMBER] No exe file in Amberhome (Mon Feb 22 2016 - 15:22:59 PST)
Marie Brut
- Re: [AMBER] citrulline parameters (Wed Feb 10 2016 - 12:06:11 PST)
- [AMBER] citrulline parameters (Wed Feb 10 2016 - 06:13:46 PST)
maryam azimzadehirani
- Re: [AMBER] the angle between two axis (Fri Feb 26 2016 - 00:26:48 PST)
- [AMBER] the angle between two axis (Thu Feb 25 2016 - 23:20:57 PST)
- Re: [AMBER] Fwd: Error with disulphide bonds in tleap (Mon Feb 22 2016 - 22:11:52 PST)
- [AMBER] Fwd: Error with disulphide bonds in tleap (Mon Feb 22 2016 - 01:10:54 PST)
Maryam Hamzehee
- Re: [AMBER] problem with energy minimization (sander) (Wed Feb 10 2016 - 05:13:27 PST)
- [AMBER] problem with energy minimization (sander) (Wed Feb 10 2016 - 04:26:06 PST)
Michael Shokhen
- Re: [AMBER] average 3D structure with condition (Mon Feb 15 2016 - 14:43:38 PST)
- Re: [AMBER] average 3D structure with condition (Mon Feb 15 2016 - 10:51:41 PST)
- [AMBER] average 3D structure with condition (Mon Feb 15 2016 - 08:42:05 PST)
- Re: [AMBER] summary.ETOT analysis and MMPBSA.py (Sun Feb 14 2016 - 05:10:58 PST)
- [AMBER] summary.ETOT analysis (Sun Feb 14 2016 - 01:47:03 PST)
Mijiddorj Batsaikhan
- Re: [AMBER] How to analyze mutational free energy difference? (Sat Feb 27 2016 - 10:48:48 PST)
- [AMBER] How to analyze mutational free energy difference? (Fri Feb 26 2016 - 23:34:20 PST)
mmaestre
- Re: [AMBER] the angle between two axis (Fri Feb 26 2016 - 00:01:29 PST)
Mohammed Khaled Tumbi
- Re: [AMBER] Is there a way to compare trajectories? (Thu Feb 11 2016 - 03:30:50 PST)
- Re: [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide (Wed Feb 10 2016 - 04:12:04 PST)
- [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide (Tue Feb 09 2016 - 07:05:26 PST)
- [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide (Tue Feb 09 2016 - 06:44:18 PST)
Mongam Riba
- [AMBER] manually addition of parameters in frcmod file (Tue Feb 23 2016 - 22:22:55 PST)
- Re: [AMBER] Downloading of Ambertools15 (Fri Feb 12 2016 - 01:44:33 PST)
- [AMBER] Downloading of Ambertools15 (Fri Feb 12 2016 - 01:23:22 PST)
- [AMBER] Gist Installation in Amber12 (Wed Feb 10 2016 - 22:39:15 PST)
Nash, Anthony
- Re: [AMBER] Is the Force Constant in the Parm**.dat file derived from a mass-weighted Hessian (Tue Feb 09 2016 - 05:34:52 PST)
necmettin pirinccioglu
- Re: [AMBER] problem running MD for diphosphoric acid anion (Sun Feb 28 2016 - 23:56:44 PST)
- Re: [AMBER] AMBER Digest, Vol 1497, Issue 1 (Fri Feb 26 2016 - 05:21:53 PST)
- [AMBER] problem running MD for diphosphoric acid anion (Thu Feb 25 2016 - 00:48:45 PST)
neha chaudhary
- [AMBER] Regarding minimization in AMBER (Fri Feb 12 2016 - 22:26:18 PST)
- Re: [AMBER] Regarding MMGBSA calculation (Thu Feb 11 2016 - 02:45:44 PST)
- Re: [AMBER] Regarding MMGBSA calculation (Fri Feb 05 2016 - 23:20:28 PST)
- [AMBER] Regarding MMGBSA calculation (Thu Feb 04 2016 - 23:48:24 PST)
Nhai
- Re: [AMBER] Inquiry regarding amber installation (Mon Feb 29 2016 - 23:25:04 PST)
- Re: [AMBER] Fwd: Thermodynamic Integration (Wed Feb 24 2016 - 22:58:50 PST)
nhai.wn
- Re: [AMBER] Nucleic acid builder (Tue Feb 23 2016 - 18:15:08 PST)
nida baig
- [AMBER] Fw: Hg parameterization (Mon Feb 15 2016 - 08:43:35 PST)
Niel Henriksen
- Re: [AMBER] waters inside cavity (Fri Feb 26 2016 - 09:59:11 PST)
Novosielski, Ryan
- Re: [AMBER] Question about AmberTools14/15 installation (Mon Feb 08 2016 - 07:41:10 PST)
Ofir Tal
- [AMBER] Steered MD of membrane proteins (Mon Feb 08 2016 - 01:14:04 PST)
Osman, Roman
- Re: [AMBER] Is there a way to compare trajectories? (Thu Feb 11 2016 - 07:40:50 PST)
Pengfei Li
- Re: [AMBER] Gaussian error with MCPB ion modeling calculation (Fri Feb 26 2016 - 08:56:15 PST)
- Re: [AMBER] KeyError - MCPB.py (Mon Feb 22 2016 - 17:20:06 PST)
- Re: [AMBER] KeyError - MCPB.py (Mon Feb 22 2016 - 07:44:36 PST)
- Re: [AMBER] KeyError - MCPB.py (Mon Feb 22 2016 - 07:26:57 PST)
- Re: [AMBER] KeyError - MCPB.py (Mon Feb 22 2016 - 07:10:16 PST)
- Re: [AMBER] Hg parameterization (Mon Feb 15 2016 - 12:48:33 PST)
- Re: [AMBER] Li & Mertz ion parameters (Sat Feb 13 2016 - 13:29:31 PST)
- Re: [AMBER] Help to choose best-fit ion model (Wed Feb 03 2016 - 08:37:06 PST)
- Re: [AMBER] Help to choose best-fit ion model (Wed Feb 03 2016 - 08:17:48 PST)
peter.schmidtke.discngine.servier.com
- [AMBER] Bounds command with GIst (Mon Feb 29 2016 - 02:35:04 PST)
Prayagraj Fandilolu
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Sat Feb 27 2016 - 23:53:20 PST)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Sat Feb 27 2016 - 05:00:30 PST)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Sat Feb 27 2016 - 01:40:09 PST)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Sat Feb 27 2016 - 01:07:48 PST)
- [AMBER] SP3 Nitrogen planarity issue with ff14SB (Mon Feb 01 2016 - 20:15:17 PST)
Rajeswari A.
- Re: [AMBER] How to analyze mutational free energy difference? (Mon Feb 29 2016 - 04:22:16 PST)
- Re: [AMBER] How to analyze mutational free energy difference? (Sat Feb 27 2016 - 09:11:47 PST)
- Re: [AMBER] Fwd: PC square fluctuations (Wed Feb 17 2016 - 03:01:15 PST)
- [AMBER] Fwd: PC square fluctuations (Mon Feb 15 2016 - 01:02:24 PST)
Ray Luo, Ph.D.
- Re: [AMBER] [AMBER} nonpolar term for MMPBSA decomp showing up as 0 (Tue Feb 16 2016 - 14:04:45 PST)
Renato Freitas
- [AMBER] Energy decomposition error (Fri Feb 19 2016 - 13:17:20 PST)
Robert Molt
- Re: [AMBER] 回复：Re: Nucleic acid builder (Tue Feb 23 2016 - 18:42:27 PST)
- [AMBER] Defining Units in nastruct (Sun Feb 21 2016 - 15:45:16 PST)
- Re: [AMBER] Relabeling Atoms after a Run Trajectory (Fri Feb 19 2016 - 07:03:20 PST)
- [AMBER] Relabeling Atoms after a Run Trajectory (Fri Feb 19 2016 - 06:54:59 PST)
Robin Betz
- Re: [AMBER] Paramfit, negative bond parameters (Thu Feb 11 2016 - 16:37:48 PST)
Ross Walker
- Re: [AMBER] Regarding caution message in the out file with pmemd.cuda.MPI (Fri Feb 26 2016 - 14:36:27 PST)
- Re: [AMBER] problem running MD for diphosphoric acid anion (Thu Feb 25 2016 - 01:00:15 PST)
- Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered (Tue Feb 16 2016 - 06:33:02 PST)
- Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered (Sat Feb 13 2016 - 10:13:19 PST)
- Re: [AMBER] Regarding minimization in AMBER (Fri Feb 12 2016 - 22:47:31 PST)
- Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered (Fri Feb 12 2016 - 17:03:44 PST)
- Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered (Fri Feb 12 2016 - 14:36:23 PST)
- Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered (Fri Feb 12 2016 - 11:16:46 PST)
- Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors (Thu Feb 11 2016 - 07:29:26 PST)
- Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors (Thu Feb 11 2016 - 07:31:54 PST)
- Re: [AMBER] MMPBSA ImportError (Sun Feb 07 2016 - 09:36:08 PST)
- Re: [AMBER] MMPBSA ImportError (Sat Feb 06 2016 - 09:31:12 PST)
- Re: [AMBER] MMPBSA ImportError (Sat Feb 06 2016 - 09:29:57 PST)
- Re: [AMBER] MMPBSA ImportError (Fri Feb 05 2016 - 16:46:19 PST)
- Re: [AMBER] Zero pressure with pmemd.cuda (Fri Feb 05 2016 - 09:03:06 PST)
Ruixing Wang
- Re: [AMBER] Wrong or no center in RdPar. (Mon Feb 01 2016 - 17:54:51 PST)
Ruth Helena Tichauer
- Re: [AMBER] Error atommask selectElemMask (Mon Feb 08 2016 - 05:44:48 PST)
- [AMBER] Error atommask selectElemMask (Mon Feb 08 2016 - 05:36:38 PST)
Ryan Novosielski
- Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered (Tue Feb 16 2016 - 06:20:49 PST)
Saman Yousuf ali
- [AMBER] error in running rmsf command cpptraj (Wed Feb 24 2016 - 06:01:16 PST)
- [AMBER] cpptraj command for pi-stacking or hydrophobic interactions. (Mon Feb 22 2016 - 20:34:58 PST)
- Re: [AMBER] broken iodine bond problem in NEWPDB.PDB file. (Fri Feb 12 2016 - 23:04:20 PST)
- [AMBER] broken iodine bond problem in NEWPDB.PDB file. (Fri Feb 12 2016 - 22:30:41 PST)
- Re: [AMBER] minimization error : segmentation fault (AMBER Digest, Vol 1483, Issue 1) (Thu Feb 11 2016 - 21:41:51 PST)
- Re: [AMBER] minimization error : segmentation fault (AMBER Digest, Vol 1483, Issue 1) (Thu Feb 11 2016 - 21:14:54 PST)
- [AMBER] minimization error : segmentation fault (Wed Feb 10 2016 - 23:34:09 PST)
Sarah Anderson
- Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered (Mon Feb 15 2016 - 09:04:13 PST)
- Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered (Fri Feb 12 2016 - 16:58:34 PST)
- Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered (Fri Feb 12 2016 - 14:24:10 PST)
- [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered (Fri Feb 12 2016 - 10:42:09 PST)
Scott Le Grand
- Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered (Sat Feb 13 2016 - 08:41:04 PST)
Sehrish Naz Aijaz
- [AMBER] unable to generate Mercury parameter file (Tue Feb 16 2016 - 21:06:51 PST)
Sivanandam M
- [AMBER] Regarding trajectory analysis using CPPTRAJ (Fri Feb 26 2016 - 02:38:17 PST)
- [AMBER] Regaridng FIle preparation in AMBERTOOLS14 (Tue Feb 02 2016 - 01:24:26 PST)
Starovoytov, Oleg
- [AMBER] EPtot, Angle, Bond, Dihed (Mon Feb 29 2016 - 18:02:26 PST)
Stefano Sarao S215563
- [AMBER] Duration parmchk (Fri Feb 26 2016 - 04:41:54 PST)
Taylor, Cooper
- Re: [AMBER] KeyError - MCPB.py (Mon Feb 22 2016 - 07:17:38 PST)
- [AMBER] KeyError - MCPB.py (Sun Feb 21 2016 - 18:58:44 PST)
Thomas Cheatham
- Re: [AMBER] EPtot, Angle, Bond, Dihed (Mon Feb 29 2016 - 20:34:38 PST)
- Re: [AMBER] Pdb file to Mol2 (Mon Feb 29 2016 - 09:59:07 PST)
- Re: [AMBER] Relabeling Atoms after a Run Trajectory (Fri Feb 19 2016 - 07:01:02 PST)
Thomas Collier
- [AMBER] Is the Force Constant in the Parm**.dat file derived from a mass-weighted Hessian (Tue Feb 09 2016 - 03:56:15 PST)
Tyler Luchko (Lists)
- Re: [AMBER] 3DRISM: erratic values for partial molar volume (Wed Feb 03 2016 - 11:30:39 PST)
Ulf Ryde
- Re: [AMBER] Paradynamics with Amber (Fri Feb 26 2016 - 08:07:06 PST)
- [AMBER] Paradynamics with Amber (Mon Feb 22 2016 - 06:56:43 PST)
Vasantha Kumar
- Re: [AMBER] PDB to distance in AMBER (Mon Feb 15 2016 - 02:30:34 PST)
- [AMBER] PDB to distance in AMBER (Wed Feb 10 2016 - 07:39:57 PST)
- Re: [AMBER] Dihedral angles restraints from x-ray to NMR (Wed Feb 03 2016 - 05:00:09 PST)
- [AMBER] Dihedral angles restraints from x-ray to NMR (Wed Feb 03 2016 - 02:52:59 PST)
- Re: [AMBER] Replacement for xmgrace (Mon Feb 01 2016 - 02:51:52 PST)
Vertika Gautam
- [AMBER] Fwd: Thermodynamic Integration (Wed Feb 24 2016 - 22:49:25 PST)
- [AMBER] Thermodynamic Integration (Wed Feb 24 2016 - 22:44:05 PST)
- [AMBER] velocity auto correlation function (Sun Feb 21 2016 - 21:27:16 PST)
Vlad Cojocaru
- Re: [AMBER] Question regarding protein-Dna binding free energy (Thu Feb 25 2016 - 07:15:32 PST)
- Re: [AMBER] Question regarding protein-Dna binding free energy (Thu Feb 25 2016 - 06:52:15 PST)
- [AMBER] Li & Mertz ion parameters (Fri Feb 12 2016 - 09:51:06 PST)
Weinzierl, Robert O J
- [AMBER] aMD Secondary Structure (Sun Feb 07 2016 - 03:12:57 PST)
- [AMBER] accelerated MD - frequency of conformational change (Fri Feb 05 2016 - 09:54:33 PST)
Wesley Michael Botello-Smith
- Re: [AMBER] MMPBSA.py.MPI won't recognise mpy4pi (Sun Feb 14 2016 - 14:58:37 PST)
- [AMBER] MMPBSA.py.MPI won't recognise mpy4pi (Fri Feb 12 2016 - 16:45:14 PST)
yhzahsc
- [AMBER] 回复：Re: Nucleic acid builder (Tue Feb 23 2016 - 18:40:45 PST)
- [AMBER] Nucleic acid builder (Tue Feb 23 2016 - 18:04:39 PST)
yhzahsc
- Re: [AMBER] 回复：Re: Nucleic acid builder (Tue Feb 23 2016 - 20:08:49 PST)
- Re: [AMBER] 回复：Re: Nucleic acid builder (Tue Feb 23 2016 - 19:41:27 PST)
- Re: [AMBER] 回复：Re: Nucleic acid builder (Tue Feb 23 2016 - 19:39:59 PST)
Yogeeshwar Ajjugal
- Re: [AMBER] Reg: problem in generating prmtop and crd files by using ff12SB of magnesium ions (Tue Feb 16 2016 - 21:10:53 PST)
- [AMBER] Reg: problem in generating prmtop and crd files by using ff12SB of magnesium ions (Tue Feb 16 2016 - 04:35:32 PST)
zoran matovic
- Re: [AMBER] Z-constraint PMF method (Mon Feb 08 2016 - 07:01:47 PST)
- Re: [AMBER] Z-constraint PMF method (Sun Feb 07 2016 - 13:07:50 PST)
- Re: [AMBER] MMPBSA ImportError (Sun Feb 07 2016 - 10:40:44 PST)
- Re: [AMBER] Z-constraint PMF method (Sun Feb 07 2016 - 10:28:20 PST)
- Re: [AMBER] MMPBSA ImportError (Sat Feb 06 2016 - 10:10:28 PST)
- [AMBER] Z-constraint PMF method (Sat Feb 06 2016 - 05:32:26 PST)
- Re: [AMBER] Amber/tutorial/advanced/tutorial16/ (Tue Feb 02 2016 - 09:09:04 PST)
- Re: [AMBER] Amber/tutorial/advanced/tutorial16/ (Tue Feb 02 2016 - 07:44:56 PST)
- [AMBER] Amber/tutorial/advanced/tutorial16/ (Tue Feb 02 2016 - 06:10:42 PST)
Карлов Дмитрий
- [AMBER] delta G computation (MMPBSA.py) (Mon Feb 15 2016 - 04:29:11 PST)
肖立
- [AMBER] A question about cpptraj autoimage (Thu Feb 18 2016 - 17:02:17 PST)
홍종희
- [AMBER] antechamber run for FAD (Fri Feb 19 2016 - 02:12:20 PST)

Amber Archive Feb 2016 by author