Amber Archive Jun 2015: by author

abdennour braka
- [AMBER] proxy configuration (Thu Jun 04 2015 - 02:48:45 PDT)
Aditya Padhi
- Re: [AMBER] GPI-anchor protein cleavage (Wed Jun 17 2015 - 07:18:58 PDT)
- Re: [AMBER] GPI-anchor protein cleavage (Tue Jun 16 2015 - 17:36:11 PDT)
- [AMBER] GPI-anchor protein cleavage (Tue Jun 16 2015 - 11:49:04 PDT)
Albert
- Re: [AMBER] cuda7 not supported? (Tue Jun 30 2015 - 02:30:26 PDT)
- [AMBER] cuda7 not supported? (Mon Jun 29 2015 - 10:34:15 PDT)
- Re: [AMBER] accuracy of FEW free energy calculation (Sun Jun 21 2015 - 00:10:37 PDT)
- Re: [AMBER] accuracy of FEW free energy calculation (Sat Jun 20 2015 - 12:07:42 PDT)
- Re: [AMBER] accuracy of FEW free energy calculation (Fri Jun 19 2015 - 22:08:42 PDT)
- [AMBER] accuracy of FEW free energy calculation (Fri Jun 19 2015 - 13:44:15 PDT)
- Re: [AMBER] what's the default radius? (Tue Jun 16 2015 - 02:26:01 PDT)
- [AMBER] what's the default radius? (Mon Jun 15 2015 - 23:06:31 PDT)
- Re: [AMBER] conserved water in MMPBSA (Fri Jun 12 2015 - 07:16:56 PDT)
- [AMBER] conserved water in MMPBSA (Fri Jun 12 2015 - 06:03:15 PDT)
Aleksandra Skoric
- Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER (Thu Jun 04 2015 - 03:47:14 PDT)
- Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER (Wed Jun 03 2015 - 02:36:02 PDT)
Alessandro Contini
- Re: [AMBER] conserved water in MMPBSA (Fri Jun 12 2015 - 06:15:56 PDT)
Amanda Li
- [AMBER] Bad Frames in Corrupted Trajectories (Wed Jun 03 2015 - 12:22:55 PDT)
Angela de Manzanos
- [AMBER] Imaging & centering (Tue Jun 02 2015 - 09:33:58 PDT)
Antonios Kolocouris
- [AMBER] ΑΠ: Regarding dihedral scanning (Fri Jun 05 2015 - 02:51:35 PDT)
anu chandra
- [AMBER] united atom force field (Mon Jun 22 2015 - 07:26:54 PDT)
- Re: [AMBER] Help - setting up parallel machine (Fri Jun 12 2015 - 02:31:16 PDT)
- Re: [AMBER] Few queries about membrane protein simulations (Fri Jun 12 2015 - 02:26:51 PDT)
- [AMBER] Help - setting up parallel machine (Thu Jun 11 2015 - 03:39:26 PDT)
- [AMBER] Few queries about membrane protein simulations (Mon Jun 08 2015 - 07:45:18 PDT)
Arthur Roberts
- [AMBER] Is there a way to do simultaneous Cartesian position and distance restraints in amber? (Mon Jun 22 2015 - 09:53:42 PDT)
Arun Srikanth
- Re: [AMBER] A possible bug in t leap when creating topology file ? (Thu Jun 25 2015 - 11:41:28 PDT)
- Re: [AMBER] A possible bug in t leap when creating topology file ? (Thu Jun 25 2015 - 11:22:11 PDT)
- Re: [AMBER] A possible bug in t leap when creating topology file ? (Thu Jun 25 2015 - 08:21:30 PDT)
- [AMBER] A possible bug in t leap when creating topology file ? (Wed Jun 24 2015 - 20:59:57 PDT)
- Re: [AMBER] generating topology without loading Frcmod file (Wed Jun 24 2015 - 16:01:50 PDT)
- Re: [AMBER] generating topology without loading Frcmod file (Wed Jun 24 2015 - 15:13:00 PDT)
- Re: [AMBER] generating topology without loading Frcmod file (Wed Jun 24 2015 - 13:45:40 PDT)
- [AMBER] generating topology without loading Frcmod file (Wed Jun 24 2015 - 10:07:08 PDT)
Asmita Gupta
- [AMBER] folding RNA using SGLD (Tue Jun 30 2015 - 07:11:21 PDT)
Azade Yazdan Yar
- [AMBER] solid surface interacting with organic (Fri Jun 19 2015 - 03:12:55 PDT)
Baker, Lewis Robert
- [AMBER] tinker_to_amber doesn't like AMOEBA reference frames for chloride (Thu Jun 11 2015 - 10:30:02 PDT)
barbara rossi
- [AMBER] force-momentum based SGLD algorithm (Wed Jun 03 2015 - 02:22:16 PDT)
Benjamin D Madej
- Re: [AMBER] Lipid 14 force field (Fri Jun 26 2015 - 10:48:26 PDT)
bharat lakhani
- Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory (Wed Jun 24 2015 - 20:52:03 PDT)
- Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory (Wed Jun 24 2015 - 19:58:20 PDT)
- Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory (Wed Jun 24 2015 - 18:38:04 PDT)
- Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory (Wed Jun 24 2015 - 13:35:03 PDT)
- [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory (Wed Jun 24 2015 - 10:56:18 PDT)
- Re: [AMBER] Per residue rmsd (Mon Jun 22 2015 - 09:59:05 PDT)
- [AMBER] Free Energy Landscape for cMD Help (Wed Jun 17 2015 - 19:17:04 PDT)
- [AMBER] Free Energy Landscape for cMD (Wed Jun 17 2015 - 12:53:05 PDT)
Bill Ross
- Re: [AMBER] relaxation in t/xleap (Sat Jun 27 2015 - 16:15:14 PDT)
- Re: [AMBER] problem (Wed Jun 17 2015 - 09:01:25 PDT)
- Re: [AMBER] problem with extraction of potential energy for the ligand (Wed Jun 10 2015 - 13:32:50 PDT)
- Re: [AMBER] problem with extraction of potential energy for the ligand (Wed Jun 10 2015 - 07:29:48 PDT)
- Re: [AMBER] problem with extraction of potential energy for the ligand (Sun Jun 07 2015 - 14:20:28 PDT)
Brian Radak
- Re: [AMBER] Recover the water model and periodic box from built parm files (Mon Jun 22 2015 - 13:34:03 PDT)
- Re: [AMBER] Use of OPLS-AA/M force field in AMBER via CHAMBER (Mon Jun 22 2015 - 13:30:52 PDT)
- Re: [AMBER] Recover the water model and periodic box from built parm files (Mon Jun 22 2015 - 08:44:06 PDT)
- Re: [AMBER] problems with relative TI calculations (Thu Jun 18 2015 - 09:01:48 PDT)
Brittany Boykin
- [AMBER] QM-MM Equilibration Step (Thu Jun 18 2015 - 10:06:34 PDT)
- [AMBER] QM-MM Equilibration of the System (Mon Jun 15 2015 - 09:11:25 PDT)
- [AMBER] Dimer Rotations (Fri Jun 12 2015 - 14:56:03 PDT)
- [AMBER] Steered Molecular Dynamics (Wed Jun 10 2015 - 09:35:53 PDT)
Carlos Simmerling
- Re: [AMBER] MMGBSA on Protein-DNA/RNA complex (Tue Jun 23 2015 - 04:49:57 PDT)
- Re: [AMBER] energy difference between GBSA and PBSA (Thu Jun 18 2015 - 05:36:37 PDT)
- Re: [AMBER] energy difference between GBSA and PBSA (Thu Jun 18 2015 - 05:05:11 PDT)
- Re: [AMBER] what's the default radius? (Tue Jun 16 2015 - 02:23:30 PDT)
Chinh Su Tran To
- Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? (Thu Jun 04 2015 - 22:43:57 PDT)
- Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? (Thu Jun 04 2015 - 18:59:16 PDT)
- Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? (Thu Jun 04 2015 - 03:58:08 PDT)
- [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? (Thu Jun 04 2015 - 01:13:55 PDT)
Chris
- [AMBER] energy difference between GBSA and PBSA (Thu Jun 18 2015 - 02:32:58 PDT)
- [AMBER] error in ante-MMPBSA.py (Tue Jun 16 2015 - 21:41:25 PDT)
- [AMBER] Charges for H-atoms in GLYCAM? (Wed Jun 10 2015 - 10:32:57 PDT)
Chris
- Re: [AMBER] energy difference between GBSA and PBSA (Thu Jun 18 2015 - 05:30:15 PDT)
D.J. Pattinson
- [AMBER] Quasi harmonic bad eigenvalue error (Sat Jun 20 2015 - 07:28:45 PDT)
Damian G. Allis, Ph.D.
- [AMBER] Generating RESP Charges For Tightly-Bound Complexes - Charges from the complexes or the fragments? (Sat Jun 27 2015 - 19:08:43 PDT)
Daniel Bork
- [AMBER] acpype fails to run on provided tests (Mon Jun 29 2015 - 13:27:14 PDT)
Daniel Roe
- Re: [AMBER] Rms fitting to a reference structure with a differnt number atoms to top file (Tue Jun 30 2015 - 13:15:56 PDT)
- Re: [AMBER] PCA Calculations (Tue Jun 30 2015 - 08:44:44 PDT)
- Re: [AMBER] cuda7 not supported? (Mon Jun 29 2015 - 14:27:42 PDT)
- Re: [AMBER] Error during action on loaded multiple trajectory in cpptraj 15 (Mon Jun 29 2015 - 14:24:32 PDT)
- Re: [AMBER] lifetime (Sun Jun 28 2015 - 15:48:46 PDT)
- Re: [AMBER] Hydrogen bond bridges (Sat Jun 27 2015 - 06:36:10 PDT)
- Re: [AMBER] Hydrogen bond bridges (Fri Jun 26 2015 - 10:25:33 PDT)
- Re: [AMBER] Hydrogen bond bridges (Thu Jun 25 2015 - 07:48:44 PDT)
- Re: [AMBER] Problem in Radial command (Thu Jun 25 2015 - 07:46:12 PDT)
- Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory (Thu Jun 25 2015 - 07:28:55 PDT)
- Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory (Wed Jun 24 2015 - 20:02:32 PDT)
- Re: [AMBER] hbond (Wed Jun 24 2015 - 14:50:47 PDT)
- Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory (Wed Jun 24 2015 - 14:01:19 PDT)
- Re: [AMBER] hbond lifetime cpptraj (Wed Jun 24 2015 - 14:00:06 PDT)
- Re: [AMBER] hbond lifetime cpptraj (Wed Jun 24 2015 - 13:17:36 PDT)
- Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory (Wed Jun 24 2015 - 12:56:23 PDT)
- Re: [AMBER] Hydrogen bond bridges (Wed Jun 24 2015 - 12:50:48 PDT)
- Re: [AMBER] Error during action on loaded multiple trajectory in cpptraj 15 (Wed Jun 24 2015 - 12:32:43 PDT)
- Re: [AMBER] parmwrite in cpptraj: AmberTools13 vs. 15 (Tue Jun 23 2015 - 08:47:39 PDT)
- Re: [AMBER] Per residue rmsd (Tue Jun 23 2015 - 07:55:01 PDT)
- Re: [AMBER] parmwrite in cpptraj: AmberTools13 vs. 15 (Tue Jun 23 2015 - 07:42:43 PDT)
- Re: [AMBER] Required time for a typical MD run (Mon Jun 22 2015 - 14:32:31 PDT)
- Re: [AMBER] how to export pdb in 'cluster' with 'autoimage' (Mon Jun 22 2015 - 09:09:18 PDT)
- Re: [AMBER] Regarding hydrogen bond time correlation function in cpptraj (Sat Jun 20 2015 - 09:53:08 PDT)
- Re: [AMBER] combine multiple trajectory (Thu Jun 18 2015 - 08:25:54 PDT)
- Re: [AMBER] Spreading water molecules over the simulation time (Thu Jun 18 2015 - 08:18:17 PDT)
- Re: [AMBER] Free Energy Landscape for cMD Help (Thu Jun 18 2015 - 08:16:07 PDT)
- Re: [AMBER] help in radial command (Wed Jun 17 2015 - 07:34:15 PDT)
- Re: [AMBER] problem (Wed Jun 17 2015 - 07:27:10 PDT)
- Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized (Wed Jun 17 2015 - 07:24:35 PDT)
- Re: [AMBER] tcorr and order parameters (Mon Jun 15 2015 - 20:27:00 PDT)
- Re: [AMBER] Population analysis (Mon Jun 15 2015 - 08:21:29 PDT)
- Re: [AMBER] modifying cpptraj (Fri Jun 12 2015 - 13:19:46 PDT)
- Re: [AMBER] Regarding dihedral scanning (Fri Jun 12 2015 - 12:48:31 PDT)
- Re: [AMBER] Problem with stripped combined mdcrd files (Thu Jun 11 2015 - 21:17:43 PDT)
- Re: [AMBER] Problem with stripped combined mdcrd files (Thu Jun 11 2015 - 20:49:21 PDT)
- Re: [AMBER] write PCA mode trajectory with cpptraj (Fri Jun 05 2015 - 13:10:06 PDT)
- Re: [AMBER] Regarding dihedral scanning (Fri Jun 05 2015 - 13:03:16 PDT)
- Re: [AMBER] cpptraj crosscorr command (Thu Jun 04 2015 - 11:00:56 PDT)
- Re: [AMBER] cpptraj crosscorr command (Thu Jun 04 2015 - 09:00:39 PDT)
- Re: [AMBER] Regarding dihedral scanning (Thu Jun 04 2015 - 08:30:26 PDT)
- Re: [AMBER] Abrupt RMSD change during DNA simulation for a short interval of time (Thu Jun 04 2015 - 08:20:22 PDT)
- Re: [AMBER] Bad Frames in Corrupted Trajectories (Wed Jun 03 2015 - 12:40:59 PDT)
- Re: [AMBER] Imaging & centering (Tue Jun 02 2015 - 10:05:27 PDT)
- Re: [AMBER] How to generate Phi_Psi by cpptraj ? (Mon Jun 01 2015 - 16:40:40 PDT)
David A Case
- Re: [AMBER] error in parallel run (Tue Jun 30 2015 - 11:02:39 PDT)
- Re: [AMBER] Output format in sander (Tue Jun 30 2015 - 11:00:19 PDT)
- Re: [AMBER] simulation phosphorylated complex of protein (Tue Jun 30 2015 - 09:11:52 PDT)
- Re: [AMBER] RESP: charges on equivalent atoms (Tue Jun 30 2015 - 04:50:46 PDT)
- Re: [AMBER] Installation Question - Missing file? (Tue Jun 30 2015 - 04:43:49 PDT)
- Re: [AMBER] Experimental values about some orgnaic solvent BOX (Mon Jun 29 2015 - 04:41:16 PDT)
- Re: [AMBER] Generating RESP Charges For Tightly-Bound Complexes - Charges from the complexes or the fragments? (Sun Jun 28 2015 - 05:09:52 PDT)
- Re: [AMBER] Defining the box dimensions while making the top and crd files (Fri Jun 26 2015 - 18:59:55 PDT)
- Re: [AMBER] Regarding calculation of viscosity of system (Fri Jun 26 2015 - 08:38:25 PDT)
- Re: [AMBER] Defining the box dimensions while making the top and crd files (Thu Jun 25 2015 - 07:14:17 PDT)
- Re: [AMBER] A possible bug in t leap when creating topology file ? (Thu Jun 25 2015 - 05:22:39 PDT)
- Re: [AMBER] relaxation in t/xleap (Thu Jun 25 2015 - 05:14:31 PDT)
- Re: [AMBER] relaxation in t/xleap (Wed Jun 24 2015 - 18:07:53 PDT)
- Re: [AMBER] Question About RESP/AmberTools14 (Tue Jun 23 2015 - 05:16:39 PDT)
- Re: [AMBER] Required time for a typical MD run (Mon Jun 22 2015 - 17:53:44 PDT)
- Re: [AMBER] Is there a way to do simultaneous Cartesian position and distance restraints in amber? (Mon Jun 22 2015 - 10:29:55 PDT)
- Re: [AMBER] Recover the water model and periodic box from built parm files (Mon Jun 22 2015 - 10:17:26 PDT)
- Re: [AMBER] Load "library" of custom residues (Sun Jun 21 2015 - 10:14:20 PDT)
- Re: [AMBER] resp: errors in reading the electrostatic potential (Sun Jun 21 2015 - 08:40:54 PDT)
- Re: [AMBER] Load "library" of custom residues (Sun Jun 21 2015 - 08:26:37 PDT)
- Re: [AMBER] ERROR while running XLEAP (Fri Jun 19 2015 - 06:59:54 PDT)
- Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized (Wed Jun 17 2015 - 12:27:04 PDT)
- Re: [AMBER] savepdb command not working in xleap (Wed Jun 17 2015 - 09:27:21 PDT)
- Re: [AMBER] Error: unspecified launch failure launching kernel kNLSkinTest (Wed Jun 17 2015 - 07:27:33 PDT)
- Re: [AMBER] NMR restraints with pmemd.cuda problem (Wed Jun 17 2015 - 07:23:42 PDT)
- Re: [AMBER] Freezing atoms in space during a simulation (Tue Jun 16 2015 - 13:19:00 PDT)
- Re: [AMBER] A problem in using tLeap (Mon Jun 15 2015 - 16:19:38 PDT)
- Re: [AMBER] distance restrain (Fri Jun 12 2015 - 05:54:00 PDT)
- Re: [AMBER] tinker_to_amber doesn't like AMOEBA reference frames for chloride (Thu Jun 11 2015 - 11:08:18 PDT)
- Re: [AMBER] tinker_to_amber doesn't like AMOEBA reference frames for chloride (Thu Jun 11 2015 - 11:05:58 PDT)
- Re: [AMBER] Antechamber on regular nucleotides (Thu Jun 11 2015 - 07:08:42 PDT)
- Re: [AMBER] Help - setting up parallel machine (Thu Jun 11 2015 - 07:00:55 PDT)
- Re: [AMBER] Help - setting up parallel machine (Thu Jun 11 2015 - 05:17:33 PDT)
- Re: [AMBER] Charges for H-atoms in GLYCAM? (Wed Jun 10 2015 - 11:20:39 PDT)
- Re: [AMBER] Regarding creating Mg2+ ions topology and parameter file (Mon Jun 08 2015 - 04:49:30 PDT)
- Re: [AMBER] Torsion restraints with pmemd.amoeba (Thu Jun 04 2015 - 09:12:53 PDT)
- Re: [AMBER] Density for a protein ligand complex run (Wed Jun 03 2015 - 06:14:39 PDT)
- Re: [AMBER] Density for a protein ligand complex run (Tue Jun 02 2015 - 12:41:53 PDT)
- Re: [AMBER] Bug or feature of tleap (Mon Jun 01 2015 - 18:00:39 PDT)
- Re: [AMBER] How to Simulate Monoclinic crystal packing arrangement. (Mon Jun 01 2015 - 04:54:20 PDT)
de Manzanos Guinot, Angela
- Re: [AMBER] Imaging & centering (Tue Jun 02 2015 - 10:11:44 PDT)
Debodyuti Dutta
- [AMBER] Ligand entry and exit path (Mon Jun 22 2015 - 08:26:41 PDT)
- [AMBER] MMPBSA sasopt problem (Thu Jun 11 2015 - 23:40:31 PDT)
DEBOSTUTI GHOSHDASTIDAR
- Re: [AMBER] Hydrogen bond bridges (Mon Jun 29 2015 - 10:16:48 PDT)
- Re: [AMBER] Hydrogen bond bridges (Fri Jun 26 2015 - 21:45:16 PDT)
- Re: [AMBER] Hydrogen bond bridges (Thu Jun 25 2015 - 21:48:05 PDT)
- Re: [AMBER] Hydrogen bond bridges (Wed Jun 24 2015 - 23:38:43 PDT)
- Re: [AMBER] Hydrogen bond bridges (Wed Jun 24 2015 - 23:35:01 PDT)
- [AMBER] Hydrogen bond bridges (Wed Jun 24 2015 - 06:52:23 PDT)
Eduardo Almeida Costa
- Re: [AMBER] Only -mpi option creates the python modules. Is this right? (Tue Jun 02 2015 - 08:06:21 PDT)
- [AMBER] Only -mpi option creates the python modules. Is this right? (Tue Jun 02 2015 - 07:26:47 PDT)
Elvis Martis
- Re: [AMBER] Amber14 compatibility with GTX-760 GPU card (Sat Jun 27 2015 - 12:35:28 PDT)
- [AMBER] Amber14 compatibilty with GTX-760 GPU card (Fri Jun 26 2015 - 20:46:37 PDT)
erik.laurini.di3.units.it
- Re: [AMBER] error in MD simulation (Fri Jun 26 2015 - 05:15:40 PDT)
- [AMBER] error in MD simulation (Thu Jun 25 2015 - 07:17:56 PDT)
filip fratev
- Re: [AMBER] accuracy of FEW free energy calculation (Fri Jun 19 2015 - 15:25:54 PDT)
Gard Nelson
- Re: [AMBER] modifying cpptraj (Fri Jun 12 2015 - 14:16:03 PDT)
- [AMBER] modifying cpptraj (Fri Jun 12 2015 - 10:16:32 PDT)
- [AMBER] cpptraj matrix dist modifications (Thu Jun 11 2015 - 11:59:19 PDT)
- Re: [AMBER] cpptraj crosscorr command (Thu Jun 04 2015 - 11:22:05 PDT)
- Re: [AMBER] cpptraj crosscorr command (Thu Jun 04 2015 - 10:44:38 PDT)
- [AMBER] cpptraj crosscorr command (Wed Jun 03 2015 - 16:53:25 PDT)
George Green
- Re: [AMBER] Rms fitting to a reference structure with a differnt number atoms to top file (Tue Jun 30 2015 - 12:54:53 PDT)
- [AMBER] Rms fitting to a reference structure with a differnt number atoms to top file (Tue Jun 30 2015 - 12:42:12 PDT)
George Tzotzos
- [AMBER] MMPBSA: Generalised Born Warning (Mon Jun 15 2015 - 06:13:47 PDT)
- Re: [AMBER] conserved water in MMPBSA (Fri Jun 12 2015 - 06:31:38 PDT)
- Re: [AMBER] GPU machines in the UK. (Tue Jun 02 2015 - 10:01:19 PDT)
Gerald Monard
- Re: [AMBER] parmwrite in cpptraj: AmberTools13 vs. 15 (Tue Jun 23 2015 - 09:00:00 PDT)
- Re: [AMBER] parmwrite in cpptraj: AmberTools13 vs. 15 (Tue Jun 23 2015 - 07:59:49 PDT)
- Re: [AMBER] MMPBSA_API: AmberTools13 vs. 15 (Tue Jun 23 2015 - 07:46:42 PDT)
- [AMBER] MMPBSA_API: AmberTools13 vs. 15 (Tue Jun 23 2015 - 06:49:27 PDT)
- [AMBER] parmwrite in cpptraj: AmberTools13 vs. 15 (Tue Jun 23 2015 - 05:15:21 PDT)
- Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized (Wed Jun 17 2015 - 13:20:37 PDT)
- Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized (Wed Jun 17 2015 - 11:28:10 PDT)
- Re: [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' (Mon Jun 15 2015 - 02:40:23 PDT)
- Re: [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' (Sun Jun 14 2015 - 13:40:29 PDT)
- Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? (Thu Jun 04 2015 - 05:04:59 PDT)
- Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? (Thu Jun 04 2015 - 02:52:32 PDT)
Gould, Ian R
- Re: [AMBER] GPU machines in the UK. (Tue Jun 02 2015 - 09:05:31 PDT)
Gustavo Seabra
- Re: [AMBER] QM-MM Equilibration Step (Thu Jun 18 2015 - 11:06:23 PDT)
- Re: [AMBER] Freezing atoms in space during a simulation (Tue Jun 16 2015 - 13:38:19 PDT)
- Re: [AMBER] QM-MM Equilibration of the System (Mon Jun 15 2015 - 09:26:31 PDT)
Hadeer ELHabashy
- Re: [AMBER] Align 1000 frames into one .crd file (Fri Jun 26 2015 - 06:48:49 PDT)
- [AMBER] Align 1000 frames into one .crd file (Fri Jun 26 2015 - 04:17:46 PDT)
Hai Nguyen
- Re: [AMBER] combine multiple trajectory (Wed Jun 17 2015 - 13:45:28 PDT)
- Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized (Wed Jun 17 2015 - 13:23:26 PDT)
- Re: [AMBER] The respective references suggested by the developers of Amber and HADDOCK (Tue Jun 16 2015 - 20:15:46 PDT)
- Re: [AMBER] [cpptraj] Changing frames in a trajectory file (Tue Jun 16 2015 - 12:27:44 PDT)
- Re: [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' (Mon Jun 15 2015 - 01:55:59 PDT)
- Re: [AMBER] Problem with stripped combined mdcrd files (Thu Jun 11 2015 - 20:39:02 PDT)
- Re: [AMBER] Problem with stripped combined mdcrd files (Thu Jun 11 2015 - 20:14:36 PDT)
- Re: [AMBER] How to generate Phi_Psi by cpptraj ? (Mon Jun 01 2015 - 14:03:28 PDT)
Hannes Loeffler
- Re: [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' (Mon Jun 15 2015 - 01:57:04 PDT)
- Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER (Wed Jun 03 2015 - 01:40:39 PDT)
- Re: [AMBER] How can I do a thermodynamic integration using Simpson's rules ? (Tue Jun 02 2015 - 06:18:43 PDT)
- Re: [AMBER] How can I do a thermodynamic integration using Simpson's rules ? (Tue Jun 02 2015 - 02:43:52 PDT)
hannes.loeffler.stfc.ac.uk
- Re: [AMBER] problems with relative TI calculations (Thu Jun 18 2015 - 09:18:34 PDT)
- [AMBER] problems with relative TI calculations (Thu Jun 18 2015 - 02:35:42 PDT)
- Re: [AMBER] Antechamber on regular nucleotides (Thu Jun 11 2015 - 23:38:48 PDT)
- Re: [AMBER] Error unknown flag: –O (Sat Jun 06 2015 - 02:02:05 PDT)
Harmeet Kaur
- [AMBER] error encountered on extending production simulation on Amber14 (Sat Jun 13 2015 - 01:30:01 PDT)
Harshala Haldankar
- [AMBER] Problem generating peptide (Tue Jun 16 2015 - 04:38:50 PDT)
Hector A. Baldoni
- [AMBER] built-in scc-dftb method amber15 (Mon Jun 29 2015 - 05:22:55 PDT)
- Re: [AMBER] Amber14 compatibilty with GTX-760 GPU card (Fri Jun 26 2015 - 20:57:51 PDT)
- [AMBER] Halogen at the dftb level (Fri Jun 26 2015 - 12:42:54 PDT)
- [AMBER] 2nd mail: subroutine qm_write_pdb (Wed Jun 17 2015 - 06:47:41 PDT)
- [AMBER] subroutine qm_write_pdb (Wed Jun 17 2015 - 06:30:25 PDT)
- Re: [AMBER] Density for a protein ligand complex run (Sun Jun 07 2015 - 16:37:59 PDT)
- Re: [AMBER] Density for a protein ligand complex run (Wed Jun 03 2015 - 05:58:49 PDT)
- Re: [AMBER] Density for a protein ligand complex run (Tue Jun 02 2015 - 07:14:37 PDT)
Huang
- Re: [AMBER] AMBER Digest, Vol 1220, Issue 1 (Mon Jun 15 2015 - 21:45:01 PDT)
Iceriver Forever
- [AMBER] using AMBER 14sb force-field in CHARMM program (Sun Jun 21 2015 - 09:21:50 PDT)
Indrajit Deb
- Re: [AMBER] how to convert pdb to rst file ? (Fri Jun 05 2015 - 10:21:36 PDT)
- Re: [AMBER] how to convert pdb to rst file ? (Fri Jun 05 2015 - 09:35:38 PDT)
- Re: [AMBER] how to convert pdb to rst file ? (Fri Jun 05 2015 - 09:34:01 PDT)
- [AMBER] how to convert pdb to rst file ? (Fri Jun 05 2015 - 08:26:47 PDT)
Iqbal, Muhammad Sajid
- [AMBER] Defining the box dimensions while making the top and crd files (Fri Jun 26 2015 - 11:48:46 PDT)
- [AMBER] Defining the box dimensions while making the top and crd files (Wed Jun 24 2015 - 17:02:03 PDT)
ivan.gladich.marge.uochb.cas.cz
- Re: [AMBER] Question About RESP/AmberTools14 (Wed Jun 24 2015 - 03:05:08 PDT)
- Re: [AMBER] Question About RESP/AmberTools14 (Tue Jun 23 2015 - 23:12:39 PDT)
- [AMBER] Question About RESP/AmberTools14 (Mon Jun 22 2015 - 22:49:54 PDT)
jacob wick
- [AMBER] Restraining distance between molecules initially (Wed Jun 10 2015 - 23:40:55 PDT)
- Re: [AMBER] Abrupt RMSD change during DNA simulation for a short interval of time (Fri Jun 05 2015 - 01:08:00 PDT)
- Re: [AMBER] Abrupt RMSD change during DNA simulation for a short interval of time (Thu Jun 04 2015 - 06:59:23 PDT)
- [AMBER] Abrupt RMSD change during DNA simulation for a short interval of time (Thu Jun 04 2015 - 06:38:17 PDT)
James Maier
- Re: [AMBER] How to generate Phi_Psi by cpptraj ? (Mon Jun 01 2015 - 12:44:35 PDT)
Jason Swails
- Re: [AMBER] Compile Failure (Tue Jun 30 2015 - 20:20:21 PDT)
- Re: [AMBER] Explicit Solvent Constant pH MD (Tue Jun 30 2015 - 20:11:43 PDT)
- Re: [AMBER] Compile Failure (Tue Jun 30 2015 - 19:40:34 PDT)
- Re: [AMBER] folding RNA using SGLD (Tue Jun 30 2015 - 08:30:40 PDT)
- Re: [AMBER] Post processing of trajectory with sander (Tue Jun 30 2015 - 08:26:01 PDT)
- Re: [AMBER] cuda7 not supported? (Tue Jun 30 2015 - 06:31:05 PDT)
- Re: [AMBER] acpype fails to run on provided tests (Mon Jun 29 2015 - 21:16:57 PDT)
- Re: [AMBER] Normal mode calculation was failed with MMPBSA.py (Mon Jun 29 2015 - 21:05:13 PDT)
- Re: [AMBER] Installation Question - Missing file? (Mon Jun 29 2015 - 21:01:40 PDT)
- Re: [AMBER] Running amber forcefield in NAMD (Mon Jun 29 2015 - 05:12:52 PDT)
- Re: [AMBER] lifetime analysis (Mon Jun 29 2015 - 05:08:38 PDT)
- Re: [AMBER] Align 1000 frames into one .crd file (Fri Jun 26 2015 - 05:40:35 PDT)
- Re: [AMBER] error in MD simulation (Fri Jun 26 2015 - 05:25:40 PDT)
- Re: [AMBER] error in MD simulation (Thu Jun 25 2015 - 07:47:59 PDT)
- Re: [AMBER] Defining the box dimensions while making the top and crd files (Thu Jun 25 2015 - 06:39:03 PDT)
- Re: [AMBER] generating topology without loading Frcmod file (Wed Jun 24 2015 - 14:26:16 PDT)
- Re: [AMBER] generating topology without loading Frcmod file (Wed Jun 24 2015 - 10:19:01 PDT)
- Re: [AMBER] MMGBSA on Protein-DNA/RNA complex (Wed Jun 24 2015 - 07:46:02 PDT)
- Re: [AMBER] MMGBSA on Protein-DNA/RNA complex (Wed Jun 24 2015 - 05:27:32 PDT)
- Re: [AMBER] MMPBSA_API: AmberTools13 vs. 15 (Tue Jun 23 2015 - 07:52:07 PDT)
- Re: [AMBER] MMPBSA_API: AmberTools13 vs. 15 (Tue Jun 23 2015 - 07:32:56 PDT)
- Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex (Tue Jun 23 2015 - 05:37:10 PDT)
- Re: [AMBER] Required time for a typical MD run (Mon Jun 22 2015 - 17:22:55 PDT)
- Re: [AMBER] Recover the water model and periodic box from built parm files (Mon Jun 22 2015 - 13:52:46 PDT)
- Re: [AMBER] Recover the water model and periodic box from built parm files (Mon Jun 22 2015 - 07:12:59 PDT)
- Re: [AMBER] accuracy of FEW free energy calculation (Sun Jun 21 2015 - 10:00:55 PDT)
- Re: [AMBER] accuracy of FEW free energy calculation (Sun Jun 21 2015 - 09:30:01 PDT)
- Re: [AMBER] accuracy of FEW free energy calculation (Sat Jun 20 2015 - 18:56:36 PDT)
- Re: [AMBER] standard and non-standard residues (Sat Jun 20 2015 - 09:39:44 PDT)
- Re: [AMBER] Quasi harmonic bad eigenvalue error (Sat Jun 20 2015 - 09:33:36 PDT)
- Re: [AMBER] accuracy of FEW free energy calculation (Sat Jun 20 2015 - 09:29:10 PDT)
- Re: [AMBER] RESP charge derivation (Fri Jun 19 2015 - 19:47:18 PDT)
- Re: [AMBER] RESP charge derivation (Fri Jun 19 2015 - 12:31:37 PDT)
- Re: [AMBER] solid surface interacting with organic (Fri Jun 19 2015 - 09:59:38 PDT)
- Re: [AMBER] Energy contribution of phosphorylated residues (Fri Jun 19 2015 - 09:26:52 PDT)
- Re: [AMBER] About OH conformation in protonated Asp/Glu (ASH/GLH) (Fri Jun 19 2015 - 09:09:36 PDT)
- Re: [AMBER] Recover .lib from .prmtop and .inpcrd (Thu Jun 18 2015 - 09:18:59 PDT)
- Re: [AMBER] Connect atoms in a pdb created with nab (Thu Jun 18 2015 - 07:05:16 PDT)
- Re: [AMBER] Connect atoms in a pdb created with nab (Thu Jun 18 2015 - 06:47:29 PDT)
- Re: [AMBER] Get energy information (Thu Jun 18 2015 - 06:42:01 PDT)
- Re: [AMBER] Free Energy Landscape for cMD Help (Wed Jun 17 2015 - 21:26:18 PDT)
- Re: [AMBER] Spreading water molecules over the simulation time (Wed Jun 17 2015 - 21:19:57 PDT)
- Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized (Wed Jun 17 2015 - 21:18:49 PDT)
- Re: [AMBER] error in ante-MMPBSA.py (Tue Jun 16 2015 - 22:21:46 PDT)
- Re: [AMBER] GPI-anchor protein cleavage (Tue Jun 16 2015 - 19:11:34 PDT)
- Re: [AMBER] GPI-anchor protein cleavage (Tue Jun 16 2015 - 17:06:20 PDT)
- Re: [AMBER] AMBER Digest, Vol 1220, Issue 1 (Mon Jun 15 2015 - 22:51:44 PDT)
- Re: [AMBER] Converting Gromacs topology files to Amber format (Mon Jun 15 2015 - 07:37:34 PDT)
- Re: [AMBER] Population analysis (Mon Jun 15 2015 - 06:25:08 PDT)
- Re: [AMBER] MMPBSA: Generalised Born Warning (Mon Jun 15 2015 - 06:22:25 PDT)
- Re: [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' (Mon Jun 15 2015 - 06:18:31 PDT)
- Re: [AMBER] Issue Lennard jones interaction (Sat Jun 13 2015 - 04:02:20 PDT)
- Re: [AMBER] error encountered on extending production simulation on Amber14 (Sat Jun 13 2015 - 03:49:20 PDT)
- Re: [AMBER] Pairwise Interaction Energy between two urea pairs (Fri Jun 12 2015 - 05:42:12 PDT)
- Re: [AMBER] MMPBSA sasopt problem (Fri Jun 12 2015 - 02:32:22 PDT)
- Re: [AMBER] Help - setting up parallel machine (Fri Jun 12 2015 - 02:32:50 PDT)
- Re: [AMBER] distance restrain (Fri Jun 12 2015 - 02:24:44 PDT)
- Re: [AMBER] Pairwise Interaction Energy between two urea pairs (Fri Jun 12 2015 - 02:20:57 PDT)
- Re: [AMBER] problem with extraction of potential energy for the ligand (Wed Jun 10 2015 - 11:16:33 PDT)
- Re: [AMBER] basic question - sanity check (Wed Jun 10 2015 - 11:09:52 PDT)
- Re: [AMBER] basic question - sanity check (Wed Jun 10 2015 - 11:07:42 PDT)
- Re: [AMBER] Parmed.py_ImportError: No module named ParmedTools.logos (Wed Jun 10 2015 - 09:22:39 PDT)
- Re: [AMBER] Centre of Mass or geometry issue (Tue Jun 09 2015 - 04:36:59 PDT)
- Re: [AMBER] Few queries about membrane protein simulations (Mon Jun 08 2015 - 09:04:11 PDT)
- Re: [AMBER] Error while running leap for a protein containing Co2+ (Mon Jun 08 2015 - 07:30:36 PDT)
- Re: [AMBER] Leap : problem with copying and combining DNA items (Mon Jun 08 2015 - 05:19:12 PDT)
- Re: [AMBER] How to avoid protein drift? (Sun Jun 07 2015 - 09:36:51 PDT)
- Re: [AMBER] Converting Gromacs topology files to Amber format (Sun Jun 07 2015 - 09:25:52 PDT)
- Re: [AMBER] Converting Gromacs topology files to Amber format (Sun Jun 07 2015 - 09:22:02 PDT)
- Re: [AMBER] Density for a protein ligand complex run (Fri Jun 05 2015 - 11:31:59 PDT)
- Re: [AMBER] how to convert pdb to rst file ? (Fri Jun 05 2015 - 09:54:24 PDT)
- Re: [AMBER] how to convert pdb to rst file ? (Fri Jun 05 2015 - 08:49:44 PDT)
- Re: [AMBER] ΑΠ: Regarding dihedral scanning (Fri Jun 05 2015 - 04:39:03 PDT)
- Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? (Thu Jun 04 2015 - 20:32:16 PDT)
- Re: [AMBER] Abrupt RMSD change during DNA simulation for a short interval of time (Thu Jun 04 2015 - 09:17:44 PDT)
- Re: [AMBER] Abrupt RMSD change during DNA simulation for a short interval of time (Thu Jun 04 2015 - 06:51:00 PDT)
- [AMBER] Converting Gromacs topology files to Amber format (Thu Jun 04 2015 - 06:33:09 PDT)
- Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? (Thu Jun 04 2015 - 05:51:11 PDT)
- Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? (Thu Jun 04 2015 - 05:15:12 PDT)
- Re: [AMBER] proxy configuration (Thu Jun 04 2015 - 05:09:12 PDT)
- Re: [AMBER] Density for a protein ligand complex run (Wed Jun 03 2015 - 06:01:23 PDT)
- Re: [AMBER] Imaging & centering (Tue Jun 02 2015 - 09:49:42 PDT)
- Re: [AMBER] torsions in parm10.dat (Tue Jun 02 2015 - 08:05:04 PDT)
- Re: [AMBER] Only -mpi option creates the python modules. Is this right? (Tue Jun 02 2015 - 07:58:42 PDT)
- Re: [AMBER] Bug or feature of tleap (Mon Jun 01 2015 - 18:06:27 PDT)
- Re: [AMBER] How to generate Phi_Psi by cpptraj ? (Mon Jun 01 2015 - 14:33:02 PDT)
Jean-Patrick Francoia
- Re: [AMBER] Load "library" of custom residues (Sun Jun 21 2015 - 08:43:50 PDT)
- [AMBER] Load "library" of custom residues (Sun Jun 21 2015 - 04:57:55 PDT)
- Re: [AMBER] Connect atoms in a pdb created with nab (Thu Jun 18 2015 - 07:09:19 PDT)
- Re: [AMBER] Connect atoms in a pdb created with nab (Thu Jun 18 2015 - 06:59:15 PDT)
- [AMBER] Connect atoms in a pdb created with nab (Thu Jun 18 2015 - 01:31:52 PDT)
- Re: [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' (Mon Jun 15 2015 - 02:02:41 PDT)
- Re: [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' (Mon Jun 15 2015 - 01:45:23 PDT)
- [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' (Sun Jun 14 2015 - 10:44:43 PDT)
Jeffrey Teillet
- [AMBER] torsions in parm10.dat (Tue Jun 02 2015 - 01:28:58 PDT)
Jim Wu
- Re: [AMBER] Compile Failure (Tue Jun 30 2015 - 21:12:54 PDT)
- Re: [AMBER] Compile Failure (Tue Jun 30 2015 - 19:44:41 PDT)
- [AMBER] Compile Failure (Tue Jun 30 2015 - 15:06:36 PDT)
- [AMBER] Installation Question - Missing file? (Mon Jun 29 2015 - 15:36:19 PDT)
Jinfeng Huang
- Re: [AMBER] How can I do a thermodynamic integration using Simpson's rules ? (Tue Jun 02 2015 - 07:04:07 PDT)
- Re: [AMBER] How can I do a thermodynamic integration using Simpson's rules ? (Tue Jun 02 2015 - 06:03:27 PDT)
- [AMBER] How can I do a thermodynamic integration using Simpson's rules ? (Tue Jun 02 2015 - 02:20:25 PDT)
Jiri Sponer
- Re: [AMBER] some doubts about simulation analysis (Sat Jun 27 2015 - 01:28:59 PDT)
- Re: [AMBER] accuracy of FEW free energy calculation (Sun Jun 21 2015 - 02:16:12 PDT)
- Re: [AMBER] accuracy of FEW free energy calculation (Sat Jun 20 2015 - 10:38:09 PDT)
John Dood
- Re: [AMBER] Output format in sander (Tue Jun 30 2015 - 11:38:17 PDT)
- [AMBER] Output format in sander (Tue Jun 30 2015 - 10:03:01 PDT)
Jonathan Gough
- Re: [AMBER] Freezing atoms in space during a simulation (Wed Jun 17 2015 - 06:22:54 PDT)
- [AMBER] Freezing atoms in space during a simulation (Tue Jun 16 2015 - 11:06:30 PDT)
- Re: [AMBER] basic question - sanity check (Wed Jun 10 2015 - 12:04:21 PDT)
- [AMBER] basic question - sanity check (Wed Jun 10 2015 - 10:48:32 PDT)
Jose Manuel Gally
- [AMBER] circle of correlation - PCA - AMBERtools (Wed Jun 03 2015 - 07:33:36 PDT)
Joseph Baker
- Re: [AMBER] Few queries about membrane protein simulations (Sat Jun 13 2015 - 17:04:26 PDT)
- Re: [AMBER] Few queries about membrane protein simulations (Fri Jun 12 2015 - 21:07:48 PDT)
- Re: [AMBER] Few queries about membrane protein simulations (Fri Jun 12 2015 - 07:25:47 PDT)
Juan Eiros Zamora
- Re: [AMBER] [cpptraj] Changing frames in a trajectory file (Tue Jun 16 2015 - 12:44:19 PDT)
- [AMBER] [cpptraj] Changing frames in a trajectory file (Tue Jun 16 2015 - 12:19:08 PDT)
- Re: [AMBER] Centre of Mass or geometry issue (Tue Jun 09 2015 - 02:14:20 PDT)
- Re: [AMBER] Centre of Mass or geometry issue (Tue Jun 09 2015 - 01:57:33 PDT)
- Re: [AMBER] Centre of Mass or geometry issue (Tue Jun 09 2015 - 01:55:58 PDT)
Julio Dominguez
- Re: [AMBER] Bug or feature of tleap (Tue Jun 02 2015 - 13:48:13 PDT)
- [AMBER] Bug or feature of tleap (Mon Jun 01 2015 - 16:01:27 PDT)
Jérémie Knoops
- [AMBER] Leap : problem with copying and combining DNA items (Sun Jun 07 2015 - 23:58:18 PDT)
Karl Debiec
- [AMBER] Use of OPLS-AA/M force field in AMBER via CHAMBER (Mon Jun 22 2015 - 08:54:31 PDT)
- Re: [AMBER] Torsion restraints with pmemd.amoeba (Thu Jun 04 2015 - 08:41:41 PDT)
Karl Kirschner
- Re: [AMBER] Experimental values about some orgnaic solvent BOX (Mon Jun 29 2015 - 05:04:36 PDT)
Kenneth Huang
- Re: [AMBER] Required time for a typical MD run (Mon Jun 22 2015 - 14:23:01 PDT)
- Re: [AMBER] amber 15 compiled with multiple GPUs (Fri Jun 19 2015 - 07:55:34 PDT)
- [AMBER] Energy contribution of phosphorylated residues (Thu Jun 18 2015 - 14:28:40 PDT)
- Re: [AMBER] Energy contribution of phosphorylated residues (Thu Jun 18 2015 - 09:06:25 PDT)
- Re: [AMBER] Dimer Rotations (Fri Jun 12 2015 - 15:18:33 PDT)
- Re: [AMBER] Error while running leap for a protein containing Co2+ (Mon Jun 08 2015 - 07:21:23 PDT)
- Re: [AMBER] Regarding creating Mg2+ ions topology and parameter file (Mon Jun 08 2015 - 07:12:55 PDT)
- Re: [AMBER] how to convert pdb to rst file ? (Fri Jun 05 2015 - 08:49:47 PDT)
Kshatresh Dutta Dubey
- Re: [AMBER] Population analysis (Mon Jun 15 2015 - 08:33:46 PDT)
- Re: [AMBER] Population analysis (Mon Jun 15 2015 - 07:51:11 PDT)
- [AMBER] Population analysis (Mon Jun 15 2015 - 00:54:25 PDT)
Lachele Foley
- Re: [AMBER] unsaturated sugars (Wed Jun 24 2015 - 10:31:25 PDT)
- Re: [AMBER] Charges for H-atoms in GLYCAM? (Wed Jun 10 2015 - 11:37:04 PDT)
- Re: [AMBER] Charges for H-atoms in GLYCAM? (Wed Jun 10 2015 - 10:44:33 PDT)
- Re: [AMBER] Fwd: Question about building a branched levan oligosaccharide (Tue Jun 09 2015 - 15:35:11 PDT)
- Re: [AMBER] Fwd: Question about building a branched levan oligosaccharide (Mon Jun 08 2015 - 11:42:19 PDT)
Lara rajam
- [AMBER] error in parallel run (Tue Jun 30 2015 - 10:20:37 PDT)
- Re: [AMBER] unsaturated sugars (Fri Jun 26 2015 - 09:08:47 PDT)
- Re: [AMBER] hbond lifetime cpptraj (Wed Jun 24 2015 - 13:32:44 PDT)
- [AMBER] hbond lifetime cpptraj (Wed Jun 24 2015 - 11:48:08 PDT)
- [AMBER] unsaturated sugars (Wed Jun 24 2015 - 07:06:07 PDT)
- [AMBER] distance restrain (Thu Jun 11 2015 - 13:11:38 PDT)
Lin Song
- [AMBER] Cpptraj failure (Tue Jun 30 2015 - 19:47:37 PDT)
loic etheve
- [AMBER] Get energy information (Thu Jun 18 2015 - 00:28:09 PDT)
- [AMBER] Issue Lennard jones interaction (Sat Jun 13 2015 - 02:01:33 PDT)
Marc van der Kamp
- [AMBER] About OH conformation in protonated Asp/Glu (ASH/GLH) (Fri Jun 19 2015 - 04:29:02 PDT)
- Re: [AMBER] To Add or Not To Add - Salt Conc in Explicit Solvent (Thu Jun 18 2015 - 01:10:20 PDT)
- Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER (Thu Jun 04 2015 - 02:20:35 PDT)
- Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER (Wed Jun 03 2015 - 01:41:57 PDT)
Marcos Serrou do Amaral
- Re: [AMBER] Steered Molecular Dynamics (Wed Jun 10 2015 - 13:35:09 PDT)
Marion, Antoine
- Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized (Wed Jun 17 2015 - 13:03:52 PDT)
- Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized (Wed Jun 17 2015 - 09:37:41 PDT)
- [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized (Wed Jun 17 2015 - 06:37:47 PDT)
Mary Varughese
- [AMBER] some doubts about simulation analysis (Sat Jun 27 2015 - 00:53:28 PDT)
Maryam Hamzehee
- [AMBER] binding energy for the frames (Wed Jun 17 2015 - 04:14:53 PDT)
- Re: [AMBER] problem with extraction of potential energy for the ligand (Thu Jun 11 2015 - 04:46:39 PDT)
- Re: [AMBER] problem with extraction of potential energy for the ligand (Wed Jun 10 2015 - 12:03:44 PDT)
- [AMBER] problem with extraction of potential energy for the ligand (Wed Jun 10 2015 - 10:45:29 PDT)
- [AMBER] problem with extraction of potential energy for the ligand (Wed Jun 10 2015 - 02:50:14 PDT)
- [AMBER] problem with extraction of potential energy for the ligand (Sun Jun 07 2015 - 10:14:26 PDT)
Michael Shokhen
- [AMBER] How to avoid protein drift? (Sun Jun 07 2015 - 05:08:36 PDT)
- [AMBER] During MD simulation protein drifts out of periodic cell (Sun Jun 07 2015 - 03:35:23 PDT)
- Re: [AMBER] Error unknown flag: –O (Sat Jun 06 2015 - 02:40:55 PDT)
- [AMBER] Error unknown flag: –O (Sat Jun 06 2015 - 01:24:19 PDT)
- [AMBER] How to generate Phi_Psi by cpptraj ? (Mon Jun 01 2015 - 12:27:19 PDT)
Miroslav Krepl
- Re: [AMBER] NMR restraints with pmemd.cuda problem (Wed Jun 17 2015 - 11:50:13 PDT)
- [AMBER] NMR restraints with pmemd.cuda problem (Tue Jun 16 2015 - 14:25:41 PDT)
MOHD HOMAIDUR RAHMAN
- [AMBER] Post processing of trajectory with sander (Tue Jun 30 2015 - 05:59:02 PDT)
- Re: [AMBER] Error during action on loaded multiple trajectory in cpptraj 15 (Mon Jun 29 2015 - 23:19:56 PDT)
- Re: [AMBER] Error during action on loaded multiple trajectory in cpptraj 15 (Mon Jun 29 2015 - 13:46:49 PDT)
- [AMBER] Regarding calculation of viscosity of system (Fri Jun 26 2015 - 05:09:56 PDT)
- Re: [AMBER] Error during action on loaded multiple trajectory in cpptraj 15 (Wed Jun 24 2015 - 14:09:01 PDT)
- [AMBER] Error during action on loaded multiple trajectory in cpptraj 15 (Wed Jun 24 2015 - 05:52:14 PDT)
- [AMBER] Regarding hydrogen bond time correlation function in cpptraj (Sat Jun 20 2015 - 03:27:34 PDT)
- Re: [AMBER] Pairwise Interaction Energy between two urea pairs (Fri Jun 12 2015 - 05:15:32 PDT)
- [AMBER] Pairwise Interaction Energy between two urea pairs (Thu Jun 11 2015 - 23:45:51 PDT)
- Re: [AMBER] Converting Gromacs topology files to Amber format (Sat Jun 06 2015 - 10:48:38 PDT)
Morteza Chehel Amirani
- [AMBER] Required time for a typical MD run (Mon Jun 22 2015 - 14:10:39 PDT)
- [AMBER] Spreading water molecules over the simulation time (Wed Jun 17 2015 - 12:40:34 PDT)
- [AMBER] A problem in using tLeap (Mon Jun 15 2015 - 11:12:50 PDT)
Mrinda Jones
- Re: [AMBER] Antechamber on regular nucleotides (Thu Jun 11 2015 - 22:58:14 PDT)
- [AMBER] Antechamber on regular nucleotides (Thu Jun 11 2015 - 05:58:14 PDT)
- Re: [AMBER] Density for a protein ligand complex run (Fri Jun 05 2015 - 11:12:40 PDT)
- Re: [AMBER] Density for a protein ligand complex run (Tue Jun 02 2015 - 23:26:00 PDT)
- [AMBER] Density for a protein ligand complex run (Tue Jun 02 2015 - 05:16:03 PDT)
muhammad tahir ayub
- [AMBER] savepdb command not working in xleap (Wed Jun 17 2015 - 08:20:02 PDT)
- [AMBER] Regarding the protonation states of Histidine (Wed Jun 10 2015 - 23:50:10 PDT)
Muthukumaran R
- Re: [AMBER] MMGBSA on Protein-DNA/RNA complex (Wed Jun 24 2015 - 09:58:45 PDT)
- Re: [AMBER] MMGBSA on Protein-DNA/RNA complex (Wed Jun 24 2015 - 01:02:59 PDT)
- Re: [AMBER] MMGBSA on Protein-DNA/RNA complex (Tue Jun 23 2015 - 09:04:31 PDT)
- [AMBER] MMGBSA on Protein-DNA/RNA complex (Tue Jun 23 2015 - 03:32:15 PDT)
nam kim
- Re: [AMBER] cuda7 not supported? (Mon Jun 29 2015 - 14:45:47 PDT)
- Re: [AMBER] amber 15 compiled with multiple GPUs (Thu Jun 25 2015 - 14:17:27 PDT)
- Re: [AMBER] amber 15 compiled with multiple GPUs (Fri Jun 19 2015 - 08:47:12 PDT)
- Re: [AMBER] amber 15 compiled with multiple GPUs (Fri Jun 19 2015 - 07:47:04 PDT)
- [AMBER] amber 15 compiled with multiple GPUs (Thu Jun 18 2015 - 22:43:01 PDT)
Neelanjana Sengupta
- [AMBER] RESP: charges on equivalent atoms (Tue Jun 30 2015 - 01:55:20 PDT)
- [AMBER] resp: errors in reading the electrostatic potential (Sun Jun 21 2015 - 05:29:47 PDT)
- [AMBER] resp: errors in reading the electrostatic potential (Sun Jun 21 2015 - 02:51:03 PDT)
- Re: [AMBER] RESP charge derivation (Fri Jun 19 2015 - 14:17:43 PDT)
- [AMBER] RESP charge derivation (Fri Jun 19 2015 - 10:56:08 PDT)
Neha Gandhi
- [AMBER] aMD and scaled MD simulation-NVT production runs (Sun Jun 21 2015 - 23:24:25 PDT)
newamber list
- Re: [AMBER] relaxation in t/xleap (Mon Jun 29 2015 - 03:46:04 PDT)
- Re: [AMBER] help in radial command (Fri Jun 26 2015 - 04:01:49 PDT)
- Re: [AMBER] relaxation in t/xleap (Thu Jun 25 2015 - 03:35:08 PDT)
- [AMBER] relaxation in t/xleap (Wed Jun 24 2015 - 15:33:51 PDT)
Nhai
- Re: [AMBER] amber 15 compiled with multiple GPUs (Fri Jun 19 2015 - 00:10:10 PDT)
- Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized (Wed Jun 17 2015 - 07:04:50 PDT)
Ning Xiang
- [AMBER] Lipid 14 force field (Fri Jun 26 2015 - 07:16:24 PDT)
Norbert GARNIER
- Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex (Mon Jun 29 2015 - 04:31:33 PDT)
- Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex (Wed Jun 24 2015 - 08:32:44 PDT)
- Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex (Tue Jun 23 2015 - 08:00:47 PDT)
- [AMBER] MMPBSA on DNA-Protein-Ligand complex (Tue Jun 23 2015 - 05:26:07 PDT)
Parker de Waal
- [AMBER] PCA Calculations (Mon Jun 29 2015 - 19:43:43 PDT)
- [AMBER] Quantifying Membrane Contact or insertion (Mon Jun 29 2015 - 11:39:35 PDT)
- Re: [AMBER] Energy contribution of phosphorylated residues (Thu Jun 18 2015 - 13:50:54 PDT)
- [AMBER] Energy contribution of phosphorylated residues (Thu Jun 18 2015 - 06:57:14 PDT)
- Re: [AMBER] Population analysis (Mon Jun 15 2015 - 06:39:44 PDT)
- [AMBER] Alternative Membrane System Tutorial (Sat Jun 13 2015 - 18:08:29 PDT)
- [AMBER] HMR (Tue Jun 09 2015 - 11:09:43 PDT)
Patrick McGrath
- Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? (Thu Jun 04 2015 - 05:35:51 PDT)
Pengfei Li
- Re: [AMBER] Arsenic force field parametrization (Fri Jun 26 2015 - 12:36:18 PDT)
- Re: [AMBER] Bug or feature of tleap (Tue Jun 02 2015 - 19:19:31 PDT)
- Re: [AMBER] Arsenic force field parametrization (Mon Jun 01 2015 - 15:56:59 PDT)
Peter Winn
- [AMBER] GPU machines in the UK. (Tue Jun 02 2015 - 06:49:33 PDT)
Pierre Bertin
- Re: [AMBER] ERROR while running XLEAP (Fri Jun 19 2015 - 07:49:47 PDT)
- [AMBER] ERROR while running XLEAP (Thu Jun 18 2015 - 11:13:29 PDT)
Rahul Ramesh
- [AMBER] Explicit Solvent Constant pH MD (Tue Jun 30 2015 - 13:53:13 PDT)
Ramin Ekhteiari
- Re: [AMBER] standard and non-standard residues (Sun Jun 21 2015 - 01:37:55 PDT)
- [AMBER] standard and non-standard residues (Sat Jun 20 2015 - 08:09:43 PDT)
- [AMBER] Entropy (Sun May 31 2015 - 23:25:36 PDT)
Ray Luo, Ph.D.
- Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex (Wed Jun 24 2015 - 10:06:34 PDT)
- Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex (Tue Jun 23 2015 - 10:35:57 PDT)
Robert Molt
- Re: [AMBER] accuracy of FEW free energy calculation (Sun Jun 21 2015 - 09:43:10 PDT)
Robin Jain
- [AMBER] help in radial command (Thu Jun 25 2015 - 22:20:22 PDT)
- [AMBER] Problem in Radial command (Wed Jun 24 2015 - 22:43:01 PDT)
- [AMBER] help in radial command (Wed Jun 17 2015 - 01:32:19 PDT)
ROOPALI VERMA
- [AMBER] Regarding creating Mg2+ ions topology and parameter file (Mon Jun 08 2015 - 03:31:53 PDT)
- Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER (Thu Jun 04 2015 - 02:04:24 PDT)
- Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER (Wed Jun 03 2015 - 21:58:18 PDT)
- Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER (Wed Jun 03 2015 - 21:51:08 PDT)
- [AMBER] ERROR WHILE RUNNING ANTECHAMBER (Wed Jun 03 2015 - 01:08:00 PDT)
Ross Walker
- Re: [AMBER] Amber14 compatibilty with GTX-760 GPU card (Fri Jun 26 2015 - 21:01:50 PDT)
- Re: [AMBER] accuracy of FEW free energy calculation (Sat Jun 20 2015 - 15:54:36 PDT)
- Re: [AMBER] accuracy of FEW free energy calculation (Fri Jun 19 2015 - 14:31:32 PDT)
- Re: [AMBER] amber 15 compiled with multiple GPUs (Fri Jun 19 2015 - 09:06:55 PDT)
- Re: [AMBER] NMR restraints with pmemd.cuda problem (Wed Jun 17 2015 - 08:00:52 PDT)
- Re: [AMBER] Few queries about membrane protein simulations (Sat Jun 13 2015 - 10:48:05 PDT)
- Re: [AMBER] Few queries about membrane protein simulations (Fri Jun 12 2015 - 19:46:50 PDT)
- [AMBER] Announcement: AMBER Workshop - London, Mon July 6th to Fri July 10th 2015 - Registration deadline June 15th (this coming Monday!) (Wed Jun 10 2015 - 09:23:17 PDT)
- Re: [AMBER] HMR (Tue Jun 09 2015 - 11:34:47 PDT)
- Re: [AMBER] Few queries about membrane protein simulations (Mon Jun 08 2015 - 09:17:38 PDT)
- Re: [AMBER] pmemd.cuda.MPI vs openmpi (Wed Jun 03 2015 - 13:42:43 PDT)
- Re: [AMBER] pmemd.cuda.MPI vs openmpi (Wed Jun 03 2015 - 12:29:00 PDT)
- Re: [AMBER] pmemd.cuda.MPI vs openmpi (Wed Jun 03 2015 - 11:31:48 PDT)
- Re: [AMBER] GPU machines in the UK. (Tue Jun 02 2015 - 08:53:15 PDT)
Sarah Witzke
- Re: [AMBER] Converting Gromacs topology files to Amber format (Mon Jun 15 2015 - 06:46:59 PDT)
Sheehan, Alice
- Re: [AMBER] Parmed.py_ImportError: No module named ParmedTools.logos (Thu Jun 11 2015 - 02:45:29 PDT)
- [AMBER] Parmed.py_ImportError: No module named ParmedTools.logos (Wed Jun 10 2015 - 08:54:20 PDT)
Soong Jiaxin
- Re: [AMBER] problem in .pdb after md simulation (Tue Jun 16 2015 - 00:52:22 PDT)
- Re: [AMBER] problem in .pdb after md simulation (Mon Jun 15 2015 - 23:55:01 PDT)
- Re: [AMBER] Problem with stripped combined mdcrd files (Fri Jun 12 2015 - 00:20:09 PDT)
- Re: [AMBER] Problem with stripped combined mdcrd files (Thu Jun 11 2015 - 21:04:57 PDT)
- Re: [AMBER] Problem with stripped combined mdcrd files (Thu Jun 11 2015 - 20:40:25 PDT)
- Re: [AMBER] Problem with stripped combined mdcrd files (Thu Jun 11 2015 - 20:29:50 PDT)
- [AMBER] Problem with stripped combined mdcrd files (Thu Jun 11 2015 - 19:48:06 PDT)
Soumendranath Bhakat
- Re: [AMBER] problem in .pdb after md simulation (Tue Jun 16 2015 - 00:54:25 PDT)
- Re: [AMBER] Regarding the protonation states of Histidine (Thu Jun 11 2015 - 01:13:13 PDT)
- Re: [AMBER] Centre of Mass or geometry issue (Tue Jun 09 2015 - 02:02:49 PDT)
- [AMBER] Centre of Mass or geometry issue (Tue Jun 09 2015 - 01:33:49 PDT)
- Re: [AMBER] Regarding dihedral scanning (Mon Jun 08 2015 - 02:48:09 PDT)
- Re: [AMBER] Regarding dihedral scanning (Fri Jun 05 2015 - 02:45:12 PDT)
- Re: [AMBER] Regarding dihedral scanning (Thu Jun 04 2015 - 08:49:40 PDT)
- [AMBER] Regarding dihedral scanning (Thu Jun 04 2015 - 01:36:21 PDT)
- Re: [AMBER] How to generate Phi_Psi by cpptraj ? (Mon Jun 01 2015 - 13:41:11 PDT)
srilaxmi reddy
- Re: [AMBER] How to Simulate Monoclinic crystal packing arrangement. (Mon Jun 01 2015 - 05:17:32 PDT)
- [AMBER] How to Simulate Monoclinic crystal packing arrangement. (Mon Jun 01 2015 - 02:55:20 PDT)
Suchetana Gupta
- [AMBER] Error while running leap for a protein containing Co2+ (Mon Jun 08 2015 - 05:05:38 PDT)
Suman Chakrabarty
- Re: [AMBER] RESP charge derivation (Sun Jun 21 2015 - 06:25:37 PDT)
Surasak Chunsrivirot
- Re: [AMBER] Fwd: Question about building a branched levan oligosaccharide (Tue Jun 09 2015 - 19:47:41 PDT)
- Re: [AMBER] Fwd: Question about building a branched levan oligosaccharide (Tue Jun 09 2015 - 04:05:08 PDT)
- [AMBER] Fwd: Question about building a branched levan oligosaccharide (Mon Jun 08 2015 - 07:26:17 PDT)
Sushi Shilpa
- Re: [AMBER] Arsenic force field parametrization (Tue Jun 02 2015 - 23:17:32 PDT)
Travis Hughes
- Re: [AMBER] tcorr and order parameters (Tue Jun 16 2015 - 12:49:48 PDT)
- [AMBER] tcorr and order parameters (Mon Jun 15 2015 - 16:08:30 PDT)
Victor Ma
- Re: [AMBER] pmemd.cuda.MPI vs openmpi (Wed Jun 03 2015 - 13:29:13 PDT)
- Re: [AMBER] pmemd.cuda.MPI vs openmpi (Wed Jun 03 2015 - 11:58:01 PDT)
- [AMBER] pmemd.cuda.MPI vs openmpi (Wed Jun 03 2015 - 10:54:44 PDT)
Vishal Nemaysh
- Re: [AMBER] problem in .pdb after md simulation (Tue Jun 16 2015 - 00:34:54 PDT)
- Re: [AMBER] problem in .pdb after md simulation (Tue Jun 16 2015 - 00:34:28 PDT)
- [AMBER] problem in .pdb after md simulation (Mon Jun 15 2015 - 23:52:58 PDT)
- Re: [AMBER] Converting Gromacs topology files to Amber format (Mon Jun 08 2015 - 22:30:42 PDT)
- Re: [AMBER] Converting Gromacs topology files to Amber format (Sun Jun 07 2015 - 02:12:49 PDT)
Vlad Cojocaru
- Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex (Mon Jun 29 2015 - 04:39:35 PDT)
- Re: [AMBER] MMGBSA on Protein-DNA/RNA complex (Wed Jun 24 2015 - 06:47:39 PDT)
- Re: [AMBER] MMGBSA on Protein-DNA/RNA complex (Wed Jun 24 2015 - 06:21:40 PDT)
- Re: [AMBER] MMGBSA on Protein-DNA/RNA complex (Tue Jun 23 2015 - 09:16:12 PDT)
- Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex (Tue Jun 23 2015 - 05:53:10 PDT)
- Re: [AMBER] MMGBSA on Protein-DNA/RNA complex (Tue Jun 23 2015 - 04:32:42 PDT)
- Re: [AMBER] Ligand entry and exit path (Mon Jun 22 2015 - 08:55:34 PDT)
- Re: [AMBER] aMD and scaled MD simulation-NVT production runs (Mon Jun 22 2015 - 00:43:57 PDT)
- [AMBER] write PCA mode trajectory with cpptraj (Fri Jun 05 2015 - 01:18:35 PDT)
- Re: [AMBER] Entropy (Mon Jun 01 2015 - 00:07:11 PDT)
wangmt
- [AMBER] Experimental values about some orgnaic solvent BOX (Sun Jun 28 2015 - 23:43:41 PDT)
windy
- [AMBER] how to export pdb in 'cluster' with 'autoimage' (Mon Jun 22 2015 - 02:11:32 PDT)
- Re: [AMBER] Spreading water molecules over the simulation time (Wed Jun 17 2015 - 18:30:28 PDT)
wliu
- [AMBER] Normal mode calculation was failed with MMPBSA.py (Mon Jun 29 2015 - 19:30:00 PDT)
Wu, Xiongwu (NIH/NHLBI) [E]
- Re: [AMBER] folding RNA using SGLD (Tue Jun 30 2015 - 07:44:37 PDT)
- Re: [AMBER] force-momentum based SGLD algorithm (Thu Jun 04 2015 - 08:14:51 PDT)
Yin, Guowei
- [AMBER] combine multiple trajectory (Wed Jun 17 2015 - 13:33:18 PDT)
Yin, Xing
- Re: [AMBER] Recover the water model and periodic box from built parm files (Tue Jun 23 2015 - 07:04:17 PDT)
- [AMBER] Recover the water model and periodic box from built parm files (Mon Jun 22 2015 - 07:01:10 PDT)
- Re: [AMBER] Recover .lib from .prmtop and .inpcrd (Thu Jun 18 2015 - 14:15:29 PDT)
- [AMBER] Recover .lib from .prmtop and .inpcrd (Thu Jun 18 2015 - 08:35:14 PDT)
Yip Yew Mun
- [AMBER] RESP Charge Fit - Intramolecular Hydrogen Bond (Tue Jun 30 2015 - 07:48:36 PDT)
- [AMBER] To Add or Not To Add - Salt Conc in Explicit Solvent (Thu Jun 18 2015 - 00:32:41 PDT)
Yogeeshwar Ajjugal
- [AMBER] Running amber forcefield in NAMD (Mon Jun 29 2015 - 05:02:32 PDT)
zahra khatti
- [AMBER] lifetime (Sun Jun 28 2015 - 15:06:50 PDT)
- [AMBER] lifetime (Sun Jun 28 2015 - 14:53:54 PDT)
- [AMBER] lifetime analysis (Sun Jun 28 2015 - 14:34:26 PDT)
- [AMBER] lifetime analysis (Sun Jun 28 2015 - 14:22:52 PDT)
- [AMBER] lifetime analysis (Sat Jun 27 2015 - 15:12:00 PDT)
- [AMBER] hbond (Wed Jun 24 2015 - 14:37:12 PDT)
zayan alhalabi
- [AMBER] problem (Sat Jun 20 2015 - 06:25:59 PDT)
- Re: [AMBER] problem (Wed Jun 17 2015 - 07:47:30 PDT)
- [AMBER] problem (Wed Jun 17 2015 - 06:52:01 PDT)
- [AMBER] Error: unspecified launch failure launching kernel kNLSkinTest (Wed Jun 17 2015 - 06:18:26 PDT)
Zhichao Lou
- Re: [AMBER] The respective references suggested by the developers of Amber and HADDOCK (Tue Jun 16 2015 - 20:38:19 PDT)
- [AMBER] The respective references suggested by the developers of Amber and HADDOCK (Tue Jun 16 2015 - 20:01:30 PDT)
Ziba Bahadori
- [AMBER] simulation phosphorylated complex of protein (Tue Jun 30 2015 - 07:24:36 PDT)
Åke Sandgren
- [AMBER] svdcmp in sander/ncsu-rmsd.F90 (AmberTools15) is sensitive to higher optimizations, suggest using lapack routine instead (Mon Jun 29 2015 - 23:41:35 PDT)

Amber Archive Jun 2015 by author