Amber Archive Jun 2016: by author

163邮箱
- [AMBER] Bad atom type: FE when calculating free energy using mmpbsa (Tue Jun 21 2016 - 01:08:34 PDT)
- [AMBER] [Amber] Build parameters on HEME-Fe-HIS system (Sun Jun 05 2016 - 08:28:22 PDT)
- [AMBER] Some problems about Heme (Sat Jun 04 2016 - 06:29:09 PDT)
- [AMBER] Some problems about heme (Fri Jun 03 2016 - 02:25:01 PDT)
Abdul-Rashid Iii Sampaco
- Re: [AMBER] Errors in my installation (Tue Jun 14 2016 - 20:52:26 PDT)
- Re: [AMBER] Errors in my installation (Tue Jun 14 2016 - 20:50:06 PDT)
- Re: [AMBER] Errors in my installation (Tue Jun 14 2016 - 20:21:57 PDT)
- Re: [AMBER] Errors in my installation (Tue Jun 14 2016 - 19:54:35 PDT)
- Re: [AMBER] Errors in my installation (Tue Jun 14 2016 - 19:06:50 PDT)
- [AMBER] Errors in my installation (Tue Jun 14 2016 - 01:22:56 PDT)
Adrian Roitberg
- Re: [AMBER] How to compare protein dynamics in free and bound-ligands states with cpptraj (Fri Jun 24 2016 - 11:42:54 PDT)
- Re: [AMBER] measures of data reliability in Steered MD (Thu Jun 23 2016 - 07:27:51 PDT)
- Re: [AMBER] QMMM-MD (Thu Jun 16 2016 - 06:05:48 PDT)
- Re: [AMBER] Dismal QM/MM Efficiency (Wed Jun 08 2016 - 12:14:04 PDT)
- Re: [AMBER] QMS-QMMM (Wed Jun 01 2016 - 06:30:37 PDT)
Airy Sanjeev
- [AMBER] umbrella sampling long axex problem (Mon Jun 13 2016 - 08:50:11 PDT)
- [AMBER] umbrella sampling with two degrees of freedom (Mon Jun 13 2016 - 05:06:29 PDT)
- [AMBER] Umbrella Sampling (Wed Jun 08 2016 - 09:15:58 PDT)
- [AMBER] Umbrella sampling with two degrees of freedom (Tue Jun 07 2016 - 21:16:50 PDT)
Aishani Prem
- [AMBER] Saving the coordinates during a simulation (Mon Jun 20 2016 - 11:31:12 PDT)
- Re: [AMBER] RMSD for the backbone atoms of residues (Thu Jun 09 2016 - 12:40:50 PDT)
- Re: [AMBER] RMSD for the backbone atoms of residues (Thu Jun 09 2016 - 12:31:46 PDT)
- [AMBER] RMSD for the backbone atoms of residues (Thu Jun 09 2016 - 12:14:32 PDT)
Albert
- Re: [AMBER] can we sample ligand conformation in Amber (Mon Jun 27 2016 - 01:13:57 PDT)
- Re: [AMBER] can we sample ligand conformation in Amber (Sun Jun 26 2016 - 11:45:41 PDT)
- [AMBER] can we sample ligand conformation in Amber (Sun Jun 26 2016 - 11:31:43 PDT)
Alessandro Contini
- Re: [AMBER] Stripping waters from trajectory on a distance-based criteria (Wed Jun 22 2016 - 03:27:07 PDT)
- [AMBER] Stripping waters from trajectory on a distance-based criteria (Tue Jun 21 2016 - 02:27:25 PDT)
Allen Zou
- [AMBER] Free energy decomposition of QM/MM-GBSA (Sat Jun 11 2016 - 07:48:37 PDT)
amir sadeghi
- [AMBER] RESP charges (Wed Jun 22 2016 - 11:53:14 PDT)
Angelina Malagodi
- Re: [AMBER] Radial Distribution Function (Mon Jun 13 2016 - 11:43:56 PDT)
- Re: [AMBER] Radial Distribution Function (Mon Jun 13 2016 - 11:32:38 PDT)
- Re: [AMBER] Radial Distribution Function (Mon Jun 13 2016 - 10:50:39 PDT)
- [AMBER] Radial Distribution Function (Mon Jun 13 2016 - 10:38:24 PDT)
- Re: [AMBER] Amber Cpptraj troubleshoot (Wed Jun 01 2016 - 16:37:08 PDT)
- Re: [AMBER] Amber Cpptraj troubleshoot (Wed Jun 01 2016 - 16:34:52 PDT)
- [AMBER] Amber Cpptraj troubleshoot (Wed Jun 01 2016 - 15:55:50 PDT)
ankita mehta
- Re: [AMBER] RMSD PLot (Wed Jun 29 2016 - 21:27:52 PDT)
- [AMBER] RMSD PLot (Wed Jun 29 2016 - 02:22:14 PDT)
Anton Perera
- [AMBER] AMBER support for gtx1080 (Tue Jun 21 2016 - 21:56:06 PDT)
anu chandra
- [AMBER] Using Gromcas trajectories with CPPTRAJ (Wed Jun 29 2016 - 02:57:01 PDT)
arthivenkat2.gmail.com
- [AMBER] Protein - ligand tutorials - reg (Sun Jun 05 2016 - 11:13:59 PDT)
Asmita Gupta
- [AMBER] measures of data reliability in Steered MD (Thu Jun 23 2016 - 07:25:30 PDT)
Atila Petrosian
- [AMBER] charge of aminoacids in an special pH (Tue Jun 28 2016 - 00:18:01 PDT)
- [AMBER] Which of charge methods in antechamber are appropriate? (Wed Jun 15 2016 - 11:10:54 PDT)
ATUL KUMAR
- Re: [AMBER] Problem in Calculating Rotational diffusion (Sun Jun 12 2016 - 22:44:47 PDT)
- [AMBER] Problem in Calculating Rotational diffusion (Sun Jun 12 2016 - 06:22:52 PDT)
Batuhan Kav
- Re: [AMBER] Lipidorder/No output (Wed Jun 15 2016 - 06:42:40 PDT)
- Re: [AMBER] Lipidorder/No output (Wed Jun 15 2016 - 05:23:28 PDT)
- Re: [AMBER] Lipidorder/No output (Wed Jun 15 2016 - 03:24:49 PDT)
- [AMBER] Lipidorder/No output (Wed Jun 15 2016 - 02:56:31 PDT)
Beavil, Andrew
- [AMBER] Amber16 + GTX1080 - working well (Thu Jun 23 2016 - 13:49:26 PDT)
bharat gupta
- Re: [AMBER] Slow performance of Amber12 on cluster (Wed Jun 29 2016 - 01:56:28 PDT)
- Re: [AMBER] QM/MM simulation (Wed Jun 29 2016 - 01:44:46 PDT)
- Re: [AMBER] QM/MM - SCF converge error (Tue Jun 28 2016 - 02:12:06 PDT)
- Re: [AMBER] SHAKE Error (Mon Jun 27 2016 - 17:41:38 PDT)
- Re: [AMBER] AMBER Digest, Vol 1618, Issue 1 (Mon Jun 27 2016 - 06:06:42 PDT)
- Re: [AMBER] AMBER Digest, Vol 1618, Issue 1 (Sun Jun 26 2016 - 18:06:36 PDT)
- Re: [AMBER] AMBER Digest, Vol 1616, Issue 1 (Sun Jun 26 2016 - 08:09:49 PDT)
- Re: [AMBER] SHAKE Error (Fri Jun 24 2016 - 03:42:55 PDT)
Bill Ross
- Re: [AMBER] solvent equilibration (Sat Jun 25 2016 - 06:08:52 PDT)
- Re: [AMBER] Replacing water with a H2O2 and restart the simulation (Thu Jun 02 2016 - 15:02:45 PDT)
- Re: [AMBER] Unreadable rst7 (Thu Jun 02 2016 - 03:50:00 PDT)
- Re: [AMBER] Unreadable rst7 (Thu Jun 02 2016 - 03:20:16 PDT)
- Re: [AMBER] Unreadable rst7 (Thu Jun 02 2016 - 02:17:22 PDT)
Bisignano, Paola
- Re: [AMBER] cutoff and switching (Wed Jun 29 2016 - 18:00:40 PDT)
- Re: [AMBER] cutoff and switching (Wed Jun 29 2016 - 17:59:56 PDT)
- [AMBER] cutoff and switching (Wed Jun 29 2016 - 17:24:15 PDT)
Bruno Falcone
- [AMBER] bad atom type decomp (Thu Jun 30 2016 - 11:33:39 PDT)
Budhathoki, Dipesh
- Re: [AMBER] proper box size to calculate binding enthalpy of host-guest (Mon Jun 06 2016 - 20:32:01 PDT)
- Re: [AMBER] proper box size to calculate binding enthalpy of host-guest (Mon Jun 06 2016 - 18:36:40 PDT)
- Re: [AMBER] proper box size to calculate binding enthalpy of host-guest (Mon Jun 06 2016 - 11:06:55 PDT)
- [AMBER] proper box size to calculate binding enthalpy of host-guest in explicit solvent (Sun Jun 05 2016 - 14:16:12 PDT)
- [AMBER] proper box size to calculate binding enthalpy of host-guest in explicit solvent (Fri Jun 03 2016 - 10:27:42 PDT)
Carlos Simmerling
- Re: [AMBER] Progress with testing GB-neck2 MD with nucleic acids (Thu Jun 30 2016 - 17:27:17 PDT)
- Re: [AMBER] GB-neck2 MD with nucleic acids (Thu Jun 30 2016 - 12:02:46 PDT)
- Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids (Wed Jun 29 2016 - 08:29:58 PDT)
- Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids (Wed Jun 29 2016 - 07:33:21 PDT)
- Re: [AMBER] can we sample ligand conformation in Amber (Sun Jun 26 2016 - 11:45:09 PDT)
- Re: [AMBER] Query regarding dihedral angles (Wed Jun 22 2016 - 03:19:38 PDT)
- Re: [AMBER] Imaging problem? (Fri Jun 17 2016 - 04:08:21 PDT)
- Re: [AMBER] FF14SB implementation (Tue Jun 14 2016 - 06:46:40 PDT)
- Re: [AMBER] FF14SB implementation (Tue Jun 14 2016 - 06:17:33 PDT)
- Re: [AMBER] Umbrella Sampling (Wed Jun 08 2016 - 09:43:51 PDT)
- Re: [AMBER] Umbrella sampling with two degrees of freedom (Wed Jun 08 2016 - 04:27:04 PDT)
Charles Lin
- Re: [AMBER] AMBER support for gtx1080 (Wed Jun 22 2016 - 02:17:40 PDT)
- Re: [AMBER] test 4096wat (Sun Jun 05 2016 - 22:20:22 PDT)
- Re: [AMBER] test 4096wat (Sun Jun 05 2016 - 22:19:00 PDT)
chemjxn
- [AMBER] problem:hydrogen bonding analysis contain water molecular (Mon Jun 27 2016 - 21:35:00 PDT)
- [AMBER] HYDROGEN BONDING ANALYSIS (Fri Jun 24 2016 - 04:35:19 PDT)
- [AMBER] mmgbsa calculation (Wed Jun 01 2016 - 17:25:53 PDT)
Chloe Renard
- Re: [AMBER] Une demande d'aide avec GAFF ( 2 ) (Mon Jun 20 2016 - 08:45:22 PDT)
- [AMBER] Une demande d'aide avec GAFF ( 2 ) (Fri Jun 17 2016 - 01:36:44 PDT)
Christina Bergonzo
- Re: [AMBER] TIP3PFBOX: water model (Wed Jun 29 2016 - 07:21:51 PDT)
colvin
- Re: [AMBER] Imaging problem? (Fri Jun 17 2016 - 00:06:52 PDT)
- Re: [AMBER] Imaging problem? (Fri Jun 17 2016 - 00:02:04 PDT)
- [AMBER] Imaging problem? (Wed Jun 15 2016 - 21:11:39 PDT)
Conor Parks
- Re: [AMBER] radial distribution function tails for liquids using GAFF (Sat Jun 11 2016 - 11:41:49 PDT)
- [AMBER] radial distribution function tails for liquids using GAFF (Fri Jun 10 2016 - 18:51:35 PDT)
Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Saving the coordinates during a simulation (Mon Jun 20 2016 - 11:39:41 PDT)
Damiano Spadoni
- Re: [AMBER] setMolecules failed (Tue Jun 07 2016 - 05:00:48 PDT)
- [AMBER] setMolecules failed (Mon Jun 06 2016 - 13:01:52 PDT)
Daniel Roe
- Re: [AMBER] Using Gromcas trajectories with CPPTRAJ (Wed Jun 29 2016 - 07:12:15 PDT)
- Re: [AMBER] problem:hydrogen bonding analysis contain water molecular (Tue Jun 28 2016 - 05:32:52 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Sat Jun 25 2016 - 05:42:57 PDT)
- Re: [AMBER] Issue with with the nocenter in tLeap (Fri Jun 24 2016 - 10:33:47 PDT)
- Re: [AMBER] cpptraj analysis of water in cavity (Fri Jun 24 2016 - 10:31:49 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Thu Jun 23 2016 - 10:30:27 PDT)
- Re: [AMBER] Issue with with the nocenter in tLeap (Thu Jun 23 2016 - 08:09:28 PDT)
- Re: [AMBER] MMPBSA.PY Error :LengthError: length mismatch in energy vectors (Thu Jun 23 2016 - 07:18:46 PDT)
- Re: [AMBER] Running pmemd.MPI across the nodes (Thu Jun 23 2016 - 07:17:42 PDT)
- Re: [AMBER] MMPBSA.py nmode output problem (Thu Jun 23 2016 - 07:17:09 PDT)
- Re: [AMBER] convergence criteria in enhanced md techniques (Wed Jun 22 2016 - 06:07:42 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Wed Jun 22 2016 - 04:50:50 PDT)
- Re: [AMBER] Problem with PCA projection (cont) (Tue Jun 21 2016 - 10:50:49 PDT)
- Re: [AMBER] Problem with PCA projection (Tue Jun 21 2016 - 10:01:06 PDT)
- Re: [AMBER] Principle component analysis: percentage contribution of eigenvectors (Tue Jun 21 2016 - 07:21:51 PDT)
- Re: [AMBER] Stripping waters from trajectory on a distance-based criteria (Tue Jun 21 2016 - 07:16:45 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Mon Jun 20 2016 - 11:45:06 PDT)
- Re: [AMBER] Saving the coordinates during a simulation (Mon Jun 20 2016 - 11:34:03 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Sat Jun 18 2016 - 07:17:09 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Fri Jun 17 2016 - 12:44:43 PDT)
- Re: [AMBER] extremely slow cluster analysis with cpptraj (Thu Jun 16 2016 - 07:39:56 PDT)
- Re: [AMBER] amber16 pmemd cuda rst file (Wed Jun 15 2016 - 08:32:16 PDT)
- Re: [AMBER] Lipidorder/No output (Wed Jun 15 2016 - 07:09:29 PDT)
- Re: [AMBER] amber16 pmemd cuda rst file (Tue Jun 14 2016 - 14:59:10 PDT)
- Re: [AMBER] amber16 pmemd cuda rst file (Tue Jun 14 2016 - 14:34:56 PDT)
- Re: [AMBER] Difference between radius of gyration and max radius of gyration (Tue Jun 14 2016 - 07:45:13 PDT)
- Re: [AMBER] Radial Distribution Function (Mon Jun 13 2016 - 11:46:23 PDT)
- Re: [AMBER] Radial Distribution Function (Mon Jun 13 2016 - 11:02:18 PDT)
- Re: [AMBER] Radial Distribution Function (Mon Jun 13 2016 - 10:44:37 PDT)
- Re: [AMBER] Problem in Calculating Rotational diffusion (Mon Jun 13 2016 - 07:39:18 PDT)
- Re: [AMBER] Error in tleap for the atom type of OCT1 and OCT2 of glutamic acid at C-terminal (Mon Jun 13 2016 - 07:36:14 PDT)
- Re: [AMBER] Choose reference frame for rmsd (Mon Jun 13 2016 - 07:18:46 PDT)
- Re: [AMBER] Problem in Calculating Rotational diffusion (Sun Jun 12 2016 - 08:44:10 PDT)
- Re: [AMBER] RMSD for the backbone atoms of residues (Fri Jun 10 2016 - 07:41:25 PDT)
- Re: [AMBER] RMSD for the backbone atoms of residues (Thu Jun 09 2016 - 12:33:14 PDT)
- Re: [AMBER] RMSD for the backbone atoms of residues (Thu Jun 09 2016 - 12:17:43 PDT)
- Re: [AMBER] PCA error not (Thu Jun 09 2016 - 11:41:27 PDT)
- Re: [AMBER] cpptraj reading a reference coordinate for analyses (Tue Jun 07 2016 - 07:56:29 PDT)
- Re: [AMBER] setMolecules failed (Mon Jun 06 2016 - 13:04:27 PDT)
- Re: [AMBER] Clustering of MD trajectories: ptraj, cpptraj (Mon Jun 06 2016 - 12:57:41 PDT)
- Re: [AMBER] Principle Component Analysis (PCA) in cpptraj (Sun Jun 05 2016 - 12:42:14 PDT)
- Re: [AMBER] Principle Component Analysis (PCA) in cpptraj (Sun Jun 05 2016 - 10:58:08 PDT)
- Re: [AMBER] radial (rdf) computation time (Thu Jun 02 2016 - 08:50:27 PDT)
- Re: [AMBER] Amber Cpptraj troubleshoot (Wed Jun 01 2016 - 16:25:37 PDT)
- Re: [AMBER] rdf or watershell (Wed Jun 01 2016 - 07:47:45 PDT)
- Re: [AMBER] cpptraj clustering based on ligand cavity (Wed Jun 01 2016 - 07:45:51 PDT)
- Re: [AMBER] radial (rdf) computation time (Wed Jun 01 2016 - 07:42:49 PDT)
David A Case
- [AMBER] one more point about gcc6 (Thu Jun 30 2016 - 06:06:24 PDT)
- [AMBER] compiling reduce with gcc6 (Thu Jun 30 2016 - 05:45:07 PDT)
- Re: [AMBER] 9. Hidden parameters for tleap (Thu Jun 30 2016 - 05:29:52 PDT)
- Re: [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt (Thu Jun 30 2016 - 05:25:49 PDT)
- Re: [AMBER] Structural refinement of the protein complexed with metalo-ions (Thu Jun 30 2016 - 05:13:03 PDT)
- Re: [AMBER] Library errors while using NAB on Amber16 (Wed Jun 29 2016 - 18:53:19 PDT)
- Re: [AMBER] prepin to mol2 (Tue Jun 28 2016 - 10:18:31 PDT)
- Re: [AMBER] Hidden parameters for tleap (Tue Jun 28 2016 - 07:10:19 PDT)
- Re: [AMBER] QM/MM - SCF converge error (Tue Jun 28 2016 - 04:35:52 PDT)
- Re: [AMBER] SHAKE Error (Mon Jun 27 2016 - 19:15:30 PDT)
- Re: [AMBER] Distorted and clumped structures after cpptraj average structure calculation (Mon Jun 27 2016 - 05:10:49 PDT)
- Re: [AMBER] Thermodynamic Integration with QM/MM Hamiltonian (Mon Jun 27 2016 - 05:07:18 PDT)
- [AMBER] Problem with SHAKE in water molecule (Sun Jun 26 2016 - 10:53:58 PDT)
- Re: [AMBER] Regarding run.rst file generation (Sun Jun 26 2016 - 10:42:50 PDT)
- Re: [AMBER] solvent equilibration (Sun Jun 26 2016 - 10:38:00 PDT)
- Re: [AMBER] SHAKE Error (Fri Jun 24 2016 - 06:38:46 PDT)
- Re: [AMBER] Issue with with the nocenter in tLeap (Wed Jun 22 2016 - 20:22:04 PDT)
- Re: [AMBER] Problem analysing output with process_mdout.perl script (Tue Jun 21 2016 - 10:25:30 PDT)
- Re: [AMBER] GAFF2 setup (Tue Jun 21 2016 - 05:49:11 PDT)
- Re: [AMBER] NMR restraints on GPU (asterisks in output) (Tue Jun 21 2016 - 05:34:25 PDT)
- Re: [AMBER] Bad atom type: FE when calculating free energy using mmpbsa (Tue Jun 21 2016 - 05:29:02 PDT)
- Re: [AMBER] amber16 pmemd cuda rst file (Mon Jun 20 2016 - 11:41:10 PDT)
- Re: [AMBER] amber16 pmemd cuda rst file (Sat Jun 18 2016 - 05:33:16 PDT)
- Re: [AMBER] amber16 pmemd cuda rst file (Fri Jun 17 2016 - 05:01:04 PDT)
- Re: [AMBER] Une demande d'aide avec GAFF ( 2 ) (Fri Jun 17 2016 - 04:50:50 PDT)
- Re: [AMBER] script for calculation of dihedral angle frequency (Fri Jun 17 2016 - 04:47:52 PDT)
- Re: [AMBER] QMMM-MD (Thu Jun 16 2016 - 06:01:41 PDT)
- Re: [AMBER] Density File (Wed Jun 15 2016 - 04:49:45 PDT)
- Re: [AMBER] antechamber error message (Tue Jun 14 2016 - 09:27:29 PDT)
- Re: [AMBER] FF14SB implementation (Tue Jun 14 2016 - 05:04:30 PDT)
- Re: [AMBER] Errors in my installation (Tue Jun 14 2016 - 05:00:47 PDT)
- Re: [AMBER] antechamber error message (Tue Jun 14 2016 - 04:55:24 PDT)
- Re: [AMBER] Can I turn off group coordinate averaging? (Mon Jun 13 2016 - 10:54:50 PDT)
- Re: [AMBER] Help me with double ambiguous noe.map files!!! PLEASE (Sun Jun 12 2016 - 06:09:52 PDT)
- Re: [AMBER] addition of hydrogen to unionised the -COO group (Sat Jun 11 2016 - 18:18:45 PDT)
- Re: [AMBER] radial distribution function tails for liquids using GAFF (Sat Jun 11 2016 - 10:26:24 PDT)
- Re: [AMBER] addition of hydrogen to unionised the -COO group (Sat Jun 11 2016 - 09:53:04 PDT)
- Re: [AMBER] Error in tleap for the atom type of OCT1 and OCT2 of glutamic acid at C-terminal (Sat Jun 11 2016 - 09:50:01 PDT)
- Re: [AMBER] energy decomposition (Thu Jun 09 2016 - 08:13:13 PDT)
- Re: [AMBER] setMolecules failed (Tue Jun 07 2016 - 10:04:46 PDT)
- Re: [AMBER] setMolecules failed (Tue Jun 07 2016 - 01:14:34 PDT)
- Re: [AMBER] restarting a run (Tue Jun 07 2016 - 01:04:10 PDT)
- Re: [AMBER] restarting a run (Mon Jun 06 2016 - 10:06:33 PDT)
- Re: [AMBER] Issue of AMBER 2016 with CUDA (Mon Jun 06 2016 - 08:05:49 PDT)
- Re: [AMBER] Protein - ligand tutorials - reg (Sun Jun 05 2016 - 13:04:07 PDT)
- Re: [AMBER] Ambertools16 test failed for leap (Sat Jun 04 2016 - 21:46:51 PDT)
- Re: [AMBER] Some problems about Heme (Sat Jun 04 2016 - 21:26:51 PDT)
- Re: [AMBER] Some problems about heme (Fri Jun 03 2016 - 13:33:57 PDT)
- Re: [AMBER] Unreadable rst7 (Thu Jun 02 2016 - 06:16:34 PDT)
- Re: [AMBER] parmchk and parmchk2 segmentation fault (Wed Jun 01 2016 - 20:50:48 PDT)
- Re: [AMBER] Amber Cpptraj troubleshoot (Wed Jun 01 2016 - 17:04:42 PDT)
David Cerutti
- Re: [AMBER] the meaning of NONBON in frcmod (Wed Jun 29 2016 - 02:11:53 PDT)
- Re: [AMBER] the meaning of NONBON in frcmod (Wed Jun 29 2016 - 02:11:06 PDT)
- Re: [AMBER] the meaning of NONBON in frcmod (Tue Jun 28 2016 - 21:44:15 PDT)
- Re: [AMBER] hanging test mdgx/1p7e for installation to 'long' path (Wed Jun 08 2016 - 14:53:29 PDT)
- Re: [AMBER] Umbrella Sampling (Wed Jun 08 2016 - 09:30:19 PDT)
- Re: [AMBER] Umbrella sampling with two degrees of freedom (Tue Jun 07 2016 - 21:41:11 PDT)
Debodyuti Dutta
- [AMBER] QM/MM MD problem (Thu Jun 09 2016 - 21:31:55 PDT)
Dr. Andreas W. Goetz
- Re: [AMBER] Thermodynamic Integration with QM/MM Hamiltonian (Mon Jun 27 2016 - 14:08:14 PDT)
- Re: [AMBER] Visualizing QM/MM Simulations (Tue Jun 14 2016 - 19:42:32 PDT)
- Re: [AMBER] Dismal QM/MM Efficiency (Wed Jun 08 2016 - 13:51:05 PDT)
- Re: [AMBER] Dismal QM/MM Efficiency (Wed Jun 08 2016 - 12:16:36 PDT)
Dr. Anselm Horn
- Re: [AMBER] Distorted and clumped structures after cpptraj average structure calculation (Mon Jun 27 2016 - 04:44:15 PDT)
- Re: [AMBER] Imaging problem? (Fri Jun 17 2016 - 03:48:31 PDT)
- Re: [AMBER] Imaging problem? (Thu Jun 16 2016 - 03:31:06 PDT)
- Re: [AMBER] RMSD for the backbone atoms of residues (Fri Jun 10 2016 - 01:21:01 PDT)
Duggan, Brendan
- Re: [AMBER] Help me with double ambiguous noe.map files!!! PLEASE (Mon Jun 13 2016 - 10:26:18 PDT)
Elisa Pieri
- Re: [AMBER] cpinutil.py problem (Mon Jun 06 2016 - 07:30:33 PDT)
- Re: [AMBER] cpinutil.py problem (Mon Jun 06 2016 - 07:21:43 PDT)
- [AMBER] cpinutil.py problem (Mon Jun 06 2016 - 06:46:53 PDT)
- Re: [AMBER] Unreadable rst7 (Thu Jun 02 2016 - 06:18:35 PDT)
- Re: [AMBER] Unreadable rst7 (Thu Jun 02 2016 - 04:02:46 PDT)
- Re: [AMBER] Unreadable rst7 (Thu Jun 02 2016 - 02:23:33 PDT)
- [AMBER] Unreadable rst7 (Thu Jun 02 2016 - 01:51:14 PDT)
Esteban Gabriel Vega Hissi
- [AMBER] Ambertools16 error compiling (Wed Jun 29 2016 - 10:43:36 PDT)
esther nehu
- Re: [AMBER] equilibration problem (Wed Jun 29 2016 - 09:43:48 PDT)
- Re: [AMBER] equilibration problem (Wed Jun 29 2016 - 09:24:05 PDT)
- Re: [AMBER] equilibration problem (Wed Jun 29 2016 - 08:39:35 PDT)
- Re: [AMBER] equilibration problem (Wed Jun 29 2016 - 08:07:01 PDT)
- [AMBER] Fwd: equilibration problem (Tue Jun 28 2016 - 22:41:51 PDT)
- [AMBER] equilibration problem (Tue Jun 28 2016 - 22:40:59 PDT)
Fabian gmail
- Re: [AMBER] pulling a zn ion with SMD (Tue Jun 07 2016 - 02:04:42 PDT)
- [AMBER] pulling a zn ion with SMD (Sun Jun 05 2016 - 04:29:05 PDT)
Fabrício Bracht
- Re: [AMBER] MCPB (Wed Jun 29 2016 - 12:00:55 PDT)
- Re: [AMBER] MCPB (Wed Jun 29 2016 - 09:50:15 PDT)
- Re: [AMBER] MCPB (Wed Jun 29 2016 - 09:32:57 PDT)
- [AMBER] MCPB (Mon Jun 27 2016 - 12:56:17 PDT)
- Re: [AMBER] Error in MCPB.py (Thu Jun 23 2016 - 10:38:27 PDT)
- [AMBER] Error in MCPB.py (Thu Jun 23 2016 - 09:19:31 PDT)
Feng Pan
- Re: [AMBER] MD simulations with jar=1 and more than one nmropt restraint (Wed Jun 08 2016 - 09:01:14 PDT)
- Re: [AMBER] Umbrella sampling with two degrees of freedom (Tue Jun 07 2016 - 21:34:58 PDT)
FyD
- Re: [AMBER] convert mol2 to pdb (Wed Jun 29 2016 - 23:27:26 PDT)
- Re: [AMBER] convert mol2 to pdb (Wed Jun 29 2016 - 23:22:27 PDT)
- Re: [AMBER] prepin to mol2 (Wed Jun 29 2016 - 07:38:01 PDT)
- Re: [AMBER] RESP charges (Wed Jun 22 2016 - 23:08:44 PDT)
galileo.galile22.yahoo.com
- [AMBER] INDIGO-DataCloud Newsletter, May 2016 (Thu Jun 09 2016 - 02:28:03 PDT)
George Tzotzos
- [AMBER] Entropy normal mode error (Thu Jun 16 2016 - 08:08:16 PDT)
Gerald Monard
- Re: [AMBER] convert mol2 to pdb (Wed Jun 29 2016 - 08:08:39 PDT)
Gulsevin,Alican
- Re: [AMBER] Amber16 won't install (Fri Jun 03 2016 - 10:58:43 PDT)
- Re: [AMBER] Amber16 won't install (Fri Jun 03 2016 - 10:22:41 PDT)
- [AMBER] Amber16 won't install (Fri Jun 03 2016 - 04:01:23 PDT)
Gustavo Seabra
- Re: [AMBER] Slow performance of Amber12 on cluster (Wed Jun 29 2016 - 06:57:01 PDT)
- Re: [AMBER] QM/MM simulation (Wed Jun 29 2016 - 06:54:42 PDT)
- Re: [AMBER] RMSD PLot (Wed Jun 29 2016 - 06:49:35 PDT)
- Re: [AMBER] QMMM-MD (Thu Jun 16 2016 - 08:08:28 PDT)
- Re: [AMBER] Which of charge methods in antechamber are appropriate? (Wed Jun 15 2016 - 11:32:55 PDT)
Hai Nguyen
- Re: [AMBER] how to calculate the correlation function for first water shell? (Thu Jun 30 2016 - 19:29:19 PDT)
- Re: [AMBER] bad atom type decomp (Thu Jun 30 2016 - 19:12:33 PDT)
- Re: [AMBER] Progress with testing GB-neck2 MD with nucleic acids (Thu Jun 30 2016 - 13:48:16 PDT)
- Re: [AMBER] GB-neck2 MD with nucleic acids (Thu Jun 30 2016 - 12:23:39 PDT)
- Re: [AMBER] GB-neck2 MD with nucleic acids (Thu Jun 30 2016 - 11:48:00 PDT)
- Re: [AMBER] convert mol2 to pdb (Wed Jun 29 2016 - 23:56:56 PDT)
- Re: [AMBER] RMSD PLot (Wed Jun 29 2016 - 22:55:36 PDT)
- Re: [AMBER] Ambertools16 error compiling (Wed Jun 29 2016 - 10:56:48 PDT)
- Re: [AMBER] convert mol2 to pdb (Wed Jun 29 2016 - 08:15:12 PDT)
- Re: [AMBER] convert mol2 to pdb (Wed Jun 29 2016 - 08:02:46 PDT)
- Re: [AMBER] Error: [cluster] Not all arguments handled: [ pdb ] (Tue Jun 28 2016 - 14:07:54 PDT)
- Re: [AMBER] HYDROGEN BONDING ANALYSIS (Fri Jun 24 2016 - 07:41:38 PDT)
- Re: [AMBER] Problem analysing output with process_mdout.perl script (Wed Jun 22 2016 - 10:25:05 PDT)
- Re: [AMBER] Query regarding dihedral angles (Tue Jun 21 2016 - 22:29:59 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Thu Jun 16 2016 - 10:41:48 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Thu Jun 16 2016 - 10:07:42 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Thu Jun 16 2016 - 07:54:55 PDT)
- Re: [AMBER] Errors in my installation (Tue Jun 14 2016 - 20:26:23 PDT)
- Re: [AMBER] Errors in my installation (Tue Jun 14 2016 - 19:59:33 PDT)
- Re: [AMBER] Errors in my installation (Tue Jun 14 2016 - 19:48:28 PDT)
- [AMBER] [ANN] Release of NGLView for interactive trajectory visualization in Jupyter notebooks. (Tue Jun 14 2016 - 11:05:11 PDT)
- Re: [AMBER] Errors in my installation (Tue Jun 14 2016 - 07:25:08 PDT)
- Re: [AMBER] Radial Distribution Function (Mon Jun 13 2016 - 11:37:12 PDT)
- Re: [AMBER] RMSD for the backbone atoms of residues (Thu Jun 09 2016 - 12:47:42 PDT)
- Re: [AMBER] Protein - ligand tutorials - reg (Sun Jun 05 2016 - 12:53:07 PDT)
- Re: [AMBER] Amber16 won't install (Fri Jun 03 2016 - 11:43:08 PDT)
- Re: [AMBER] Amber16 won't install (Fri Jun 03 2016 - 10:25:02 PDT)
- Re: [AMBER] Amber16 won't install (Fri Jun 03 2016 - 10:11:40 PDT)
- Re: [AMBER] Amber16 won't install (Fri Jun 03 2016 - 10:11:00 PDT)
- Re: [AMBER] re imaging doubt (Fri Jun 03 2016 - 07:36:13 PDT)
- Re: [AMBER] Amber Cpptraj troubleshoot (Wed Jun 01 2016 - 16:40:45 PDT)
- Re: [AMBER] Amber Cpptraj troubleshoot (Wed Jun 01 2016 - 16:38:15 PDT)
- Re: [AMBER] Amber Cpptraj troubleshoot (Wed Jun 01 2016 - 16:02:59 PDT)
- Re: [AMBER] FW: MMPBSA.py issue with complex prmtop file (Wed Jun 01 2016 - 11:43:37 PDT)
- Re: [AMBER] FW: MMPBSA.py issue with complex prmtop file (Wed Jun 01 2016 - 11:40:57 PDT)
Hannes Loeffler
- Re: [AMBER] amber16 pmemd cuda rst file (Mon Jun 20 2016 - 08:28:10 PDT)
- Re: [AMBER] amber16 pmemd cuda rst file (Fri Jun 17 2016 - 03:35:09 PDT)
- Re: [AMBER] Lipidorder/No output (Wed Jun 15 2016 - 07:04:35 PDT)
- Re: [AMBER] Lipidorder/No output (Wed Jun 15 2016 - 06:11:39 PDT)
- Re: [AMBER] Lipidorder/No output (Wed Jun 15 2016 - 04:13:14 PDT)
- Re: [AMBER] Lipidorder/No output (Wed Jun 15 2016 - 03:19:14 PDT)
- Re: [AMBER] TI calculation with ligand dimer (Sat Jun 04 2016 - 03:01:16 PDT)
Hector A. Baldoni
- Re: [AMBER] solvent equilibration (Sat Jun 25 2016 - 18:18:29 PDT)
Himanshu Joshi
- [AMBER] Running pmemd.MPI across the nodes (Thu Jun 23 2016 - 04:30:35 PDT)
- Re: [AMBER] Principle Component Analysis (PCA) in cpptraj (Sun Jun 05 2016 - 12:17:54 PDT)
- Re: [AMBER] Principle Component Analysis (PCA) in cpptraj (Sun Jun 05 2016 - 11:28:48 PDT)
- Re: [AMBER] pulling a zn ion with SMD (Sun Jun 05 2016 - 06:58:57 PDT)
- [AMBER] Principle Component Analysis (PCA) in cpptraj (Sat Jun 04 2016 - 06:14:43 PDT)
Hirdesh Kumar
- [AMBER] Principle component analysis: percentage contribution of eigenvectors (Tue Jun 21 2016 - 05:52:11 PDT)
Hu, Yuan
- Re: [AMBER] TI calculation with ligand dimer (Mon Jun 06 2016 - 07:33:59 PDT)
- [AMBER] TI calculation with ligand dimer (Fri Jun 03 2016 - 15:39:31 PDT)
Huian Li
- Re: [AMBER] Issue of AMBER 2016 with CUDA (Tue Jun 07 2016 - 08:23:05 PDT)
- [AMBER] Issue of AMBER 2016 with CUDA (Mon Jun 06 2016 - 06:24:07 PDT)
Igor Marques
- Re: [AMBER] GAFF2 setup (Fri Jun 03 2016 - 12:40:19 PDT)
Ilyas Yildirim
- Re: [AMBER] can we sample ligand conformation in Amber (Sun Jun 26 2016 - 11:39:33 PDT)
Irfan Alibay
- Re: [AMBER] Amber14 & Cuda 7.5 (Tue Jun 07 2016 - 07:16:08 PDT)
James Murdock
- [AMBER] MD simulations with jar=1 and more than one nmropt restraint (Wed Jun 08 2016 - 03:39:46 PDT)
James Starlight
- Re: [AMBER] Structural refinement of the protein complexed with metalo-ions (Thu Jun 30 2016 - 06:05:03 PDT)
- Re: [AMBER] Structural refinement of the protein complexed with metalo-ions (Thu Jun 30 2016 - 03:44:47 PDT)
- [AMBER] Structural refinement of the protein complexed with metalo-ions (Wed Jun 29 2016 - 07:39:21 PDT)
Jason Swails
- Re: [AMBER] Error in MMPBSA (Thu Jun 23 2016 - 10:00:39 PDT)
- Re: [AMBER] volmap: densities too low (Mon Jun 20 2016 - 08:48:25 PDT)
- Re: [AMBER] volmap: densities too low (Sat Jun 18 2016 - 04:33:04 PDT)
- Re: [AMBER] Free energy decomposition of QM/MM-GBSA (Tue Jun 14 2016 - 20:12:07 PDT)
- Re: [AMBER] Principal Component Analysis (Wed Jun 08 2016 - 19:36:05 PDT)
- Re: [AMBER] Dismal QM/MM Efficiency (Wed Jun 08 2016 - 13:14:11 PDT)
- Re: [AMBER] Error while trying to upgrade AmberTools 15 (Wed Jun 08 2016 - 03:31:16 PDT)
- Re: [AMBER] Issue of AMBER 2016 with CUDA (Tue Jun 07 2016 - 20:51:14 PDT)
- Re: [AMBER] setMolecules failed (Tue Jun 07 2016 - 11:26:36 PDT)
- Re: [AMBER] setMolecules failed (Tue Jun 07 2016 - 07:31:02 PDT)
- Re: [AMBER] cpinutil.py problem (Mon Jun 06 2016 - 07:16:07 PDT)
- Re: [AMBER] iwrap and mmpbsa (Fri Jun 03 2016 - 12:04:41 PDT)
- Re: [AMBER] mmpbsa analys (Thu Jun 02 2016 - 10:44:20 PDT)
- Re: [AMBER] Unreadable rst7 (Thu Jun 02 2016 - 06:33:46 PDT)
- Re: [AMBER] Unreadable rst7 (Thu Jun 02 2016 - 06:13:48 PDT)
- Re: [AMBER] mmgbsa calculation (Thu Jun 02 2016 - 06:11:56 PDT)
Jean-Patrick Francoia
- Re: [AMBER] volmap: densities too low (Mon Jun 20 2016 - 05:18:17 PDT)
- [AMBER] volmap: densities too low (Sat Jun 18 2016 - 03:38:35 PDT)
- Re: [AMBER] Difference between radius of gyration and max radius of gyration (Tue Jun 14 2016 - 08:11:47 PDT)
- [AMBER] Difference between radius of gyration and max radius of gyration (Tue Jun 14 2016 - 04:42:12 PDT)
- Re: [AMBER] Choose reference frame for rmsd (Mon Jun 13 2016 - 12:43:42 PDT)
- [AMBER] Choose reference frame for rmsd (Mon Jun 13 2016 - 05:55:31 PDT)
Jingyi Yan
- Re: [AMBER] mdl file for 1d-rism (Thu Jun 02 2016 - 14:51:58 PDT)
Jose Manuel Gally
- [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt (Thu Jun 30 2016 - 00:48:14 PDT)
Kalenkiewicz, Andrew (NIH/NICHD) [F]
- [AMBER] FW: MMPBSA.py issue with complex prmtop file (Wed Jun 01 2016 - 11:34:44 PDT)
Karolina Markowska
- [AMBER] Does Amber14 work with CUDA higher than 6.5? (Wed Jun 29 2016 - 00:25:44 PDT)
Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] Progress with testing GB-neck2 MD with nucleic acids (Thu Jun 30 2016 - 13:16:19 PDT)
- Re: [AMBER] GB-neck2 MD with nucleic acids (Thu Jun 30 2016 - 12:09:59 PDT)
- [AMBER] GB-neck2 MD with nucleic acids (Thu Jun 30 2016 - 11:29:48 PDT)
- Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids (Wed Jun 29 2016 - 08:47:45 PDT)
- Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids (Wed Jun 29 2016 - 08:04:16 PDT)
- [AMBER] Advice for Implicit Solvent MD with Nucleic Acids (Wed Jun 29 2016 - 07:22:16 PDT)
Kat G
- [AMBER] How to compare protein dynamics in free and bound-ligands states with cpptraj (Fri Jun 24 2016 - 11:38:37 PDT)
- [AMBER] Problem with PCA projection (cont) (Tue Jun 21 2016 - 10:41:32 PDT)
- [AMBER] Problem with PCA projection (Tue Jun 21 2016 - 09:26:01 PDT)
- [AMBER] Principal Component Analysis (Wed Jun 08 2016 - 18:10:47 PDT)
Kenneth Hoste
- Re: [AMBER] hanging test mdgx/1p7e for installation to 'long' path (Fri Jun 10 2016 - 04:19:14 PDT)
- [AMBER] hanging test mdgx/1p7e for installation to 'long' path (Wed Jun 08 2016 - 13:28:23 PDT)
koushik kasavajhala
- Re: [AMBER] Errors in my installation (Tue Jun 14 2016 - 20:44:48 PDT)
Lachele Foley
- Re: [AMBER] neuraminic acid (Wed Jun 08 2016 - 00:52:47 PDT)
- Re: [AMBER] Some problems about Heme (Mon Jun 06 2016 - 06:52:11 PDT)
Lara rajam
- [AMBER] PCA error not (Thu Jun 09 2016 - 11:28:30 PDT)
Lea Natalia Toledo Carvajal
- [AMBER] addAtomType problem (Thu Jun 30 2016 - 08:58:49 PDT)
- Re: [AMBER] 9. Hidden parameters for tleap (Wed Jun 29 2016 - 03:09:26 PDT)
- [AMBER] Hidden parameters for tleap (Tue Jun 28 2016 - 04:22:01 PDT)
Marc van der Kamp
- Re: [AMBER] QM/MM simulation (Wed Jun 29 2016 - 02:09:09 PDT)
- Re: [AMBER] charge of aminoacids in an special pH (Tue Jun 28 2016 - 01:29:20 PDT)
- Re: [AMBER] amber16 pmemd cuda rst file (Fri Jun 17 2016 - 03:07:25 PDT)
Marcelo Andrade Chagas
- Re: [AMBER] MCPB (Wed Jun 29 2016 - 09:57:35 PDT)
- Re: [AMBER] Error in MCPB.py (Thu Jun 23 2016 - 10:27:58 PDT)
- Re: [AMBER] Errors in my installation (Tue Jun 14 2016 - 04:47:26 PDT)
Mark Abraham
- Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 (Sat Jun 04 2016 - 10:43:08 PDT)
- Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 (Sat Jun 04 2016 - 07:31:11 PDT)
Markowska
- Re: [AMBER] Does Amber14 work with CUDA higher than 6.5? (Wed Jun 29 2016 - 11:13:18 PDT)
Martina Devi
- Re: [AMBER] convert mol2 to pdb (Wed Jun 29 2016 - 08:24:40 PDT)
- Re: [AMBER] convert mol2 to pdb (Wed Jun 29 2016 - 08:04:56 PDT)
- [AMBER] convert mol2 to pdb (Wed Jun 29 2016 - 07:57:36 PDT)
- [AMBER] convert mol2 to prepin (Tue Jun 28 2016 - 09:40:39 PDT)
- [AMBER] prepin to mol2 (Tue Jun 28 2016 - 09:37:23 PDT)
- Re: [AMBER] antechamber error message (Tue Jun 14 2016 - 08:04:31 PDT)
- [AMBER] antechamber error message (Tue Jun 14 2016 - 00:02:07 PDT)
- Re: [AMBER] addition of hydrogen to unionised the -COO group (Mon Jun 13 2016 - 23:59:53 PDT)
- Re: [AMBER] addition of hydrogen to unionised the -COO group (Sat Jun 11 2016 - 11:00:32 PDT)
- [AMBER] addition of hydrogen to unionised the -COO group (Fri Jun 10 2016 - 08:00:42 PDT)
Mary Varughese
- [AMBER] mmpbsa doubt (Thu Jun 16 2016 - 00:42:36 PDT)
- [AMBER] re imaging doubt (Fri Jun 03 2016 - 03:58:20 PDT)
- [AMBER] iwrap and mmpbsa (Fri Jun 03 2016 - 03:16:40 PDT)
Michael Shokhen
- [AMBER] cpptraj analysis of water in cavity (Fri Jun 24 2016 - 00:58:04 PDT)
- [AMBER] extremely slow cluster analysis with cpptraj (Thu Jun 16 2016 - 01:17:18 PDT)
Miroslav Krepl
- [AMBER] NMR restraints on GPU (asterisks in output) (Fri Jun 17 2016 - 02:21:15 PDT)
- Re: [AMBER] FF14SB implementation (Tue Jun 14 2016 - 06:14:23 PDT)
- [AMBER] FF14SB implementation (Fri Jun 10 2016 - 06:37:38 PDT)
mish
- [AMBER] buffer OR buffer_xyz_list in setBox command (Wed Jun 08 2016 - 18:35:35 PDT)
- [AMBER] Energy decomposition in MM/GBSA (Tue Jun 07 2016 - 22:35:21 PDT)
mmaestre
- [AMBER] problems with building sulfo sialil-lacnac (Mon Jun 13 2016 - 01:00:37 PDT)
- Re: [AMBER] neuraminic acid (Wed Jun 08 2016 - 01:01:41 PDT)
- [AMBER] neuraminic acid (Wed Jun 08 2016 - 00:44:00 PDT)
- [AMBER] test 4096wat (Sun Jun 05 2016 - 22:16:35 PDT)
- Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 (Sat Jun 04 2016 - 21:08:43 PDT)
- [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 (Fri Jun 03 2016 - 22:41:40 PDT)
MOHD HOMAIDUR RAHMAN
- [AMBER] Regarding ho parameter in gaff (Thu Jun 30 2016 - 11:01:35 PDT)
- [AMBER] Regarding error in MMPBSA (Fri Jun 10 2016 - 14:35:26 PDT)
Morteza Chehel Amirani
- Re: [AMBER] Replacing water with a H2O2 and restart the simulation (Thu Jun 02 2016 - 13:37:09 PDT)
Neha Gandhi
- [AMBER] convergence criteria in enhanced md techniques (Wed Jun 22 2016 - 05:43:18 PDT)
- Re: [AMBER] ABOUT the GaMD patch for Amber14 (Wed Jun 15 2016 - 09:36:05 PDT)
- Re: [AMBER] amber16 pmemd cuda rst file (Tue Jun 14 2016 - 14:49:15 PDT)
- [AMBER] amber16 pmemd cuda rst file (Tue Jun 14 2016 - 14:29:43 PDT)
- [AMBER] cpptraj reading a reference coordinate for analyses (Tue Jun 07 2016 - 01:43:18 PDT)
- Re: [AMBER] radial (rdf) computation time (Wed Jun 01 2016 - 20:58:19 PDT)
- [AMBER] parmchk and parmchk2 segmentation fault (Wed Jun 01 2016 - 18:41:51 PDT)
- [AMBER] radial (rdf) computation time (Wed Jun 01 2016 - 00:28:03 PDT)
- [AMBER] rdf or watershell (Tue May 31 2016 - 18:31:54 PDT)
- Re: [AMBER] cpptraj clustering based on ligand cavity (Tue May 31 2016 - 18:28:22 PDT)
Nhai
- Re: [AMBER] Using Gromcas trajectories with CPPTRAJ (Wed Jun 29 2016 - 09:58:56 PDT)
- Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids (Wed Jun 29 2016 - 09:07:07 PDT)
- Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids (Wed Jun 29 2016 - 08:37:18 PDT)
Niel Henriksen
- Re: [AMBER] proper box size to calculate binding enthalpy of host-guest (Mon Jun 06 2016 - 18:56:07 PDT)
- Re: [AMBER] proper box size to calculate binding enthalpy of host-guest (Mon Jun 06 2016 - 12:58:04 PDT)
Nikolay N. Kuzmich
- [AMBER] Error while trying to upgrade AmberTools 15 (Wed Jun 08 2016 - 02:48:28 PDT)
- [AMBER] Amber14 & Cuda 7.5 (Tue Jun 07 2016 - 05:03:52 PDT)
Nisler, Collin R.
- [AMBER] Visualizing QM/MM Simulations (Tue Jun 14 2016 - 19:26:07 PDT)
- Re: [AMBER] Dismal QM/MM Efficiency (Wed Jun 08 2016 - 12:31:30 PDT)
- Re: [AMBER] Dismal QM/MM Efficiency (Wed Jun 08 2016 - 12:29:29 PDT)
- [AMBER] Dismal QM/MM Efficiency (Wed Jun 08 2016 - 11:52:45 PDT)
Norbert GARNIER
- [AMBER] THF parametrization (Thu Jun 09 2016 - 05:39:54 PDT)
Odin Zeus
- [AMBER] QMMM-MD (Wed Jun 15 2016 - 22:36:37 PDT)
- [AMBER] QMS-QMMM (Tue May 31 2016 - 20:51:50 PDT)
Parviz Seifpanahi Shabane
- [AMBER] how to calculate the correlation function for first water shell? (Thu Jun 30 2016 - 09:20:10 PDT)
Pengfei Li
- Re: [AMBER] MCPB (Thu Jun 30 2016 - 09:51:41 PDT)
- Re: [AMBER] MCPB (Thu Jun 30 2016 - 09:42:27 PDT)
- Re: [AMBER] Structural refinement of the protein complexed with metalo-ions (Thu Jun 30 2016 - 09:20:42 PDT)
- Re: [AMBER] MCPB (Tue Jun 28 2016 - 07:33:03 PDT)
- Re: [AMBER] Error in MCPB.py (Thu Jun 23 2016 - 14:51:35 PDT)
- Re: [AMBER] Some problems about Heme (Tue Jun 07 2016 - 19:54:02 PDT)
Prayagraj Fandilolu
- [AMBER] Distorted and clumped structures after cpptraj average structure calculation (Mon Jun 27 2016 - 03:52:57 PDT)
Ross Walker
- Re: [AMBER] cutoff and switching (Wed Jun 29 2016 - 17:48:20 PDT)
- Re: [AMBER] Does Amber14 work with CUDA higher than 6.5? (Wed Jun 29 2016 - 09:25:33 PDT)
- Re: [AMBER] Amber16 + GTX1080 - working well (Fri Jun 24 2016 - 06:11:50 PDT)
- Re: [AMBER] ABOUT the GaMD patch for Amber14 (Wed Jun 15 2016 - 09:05:52 PDT)
- Re: [AMBER] Problem: Do not receive mails from Amber list but Amber digest (Tue Jun 14 2016 - 10:44:04 PDT)
- Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 (Sat Jun 04 2016 - 12:18:52 PDT)
- Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 (Sat Jun 04 2016 - 09:36:52 PDT)
Ruth Helena Tichauer
- Re: [AMBER] Problem analysing output with process_mdout.perl script (Thu Jun 23 2016 - 08:10:22 PDT)
- Re: [AMBER] Problem analysing output with process_mdout.perl script (Wed Jun 22 2016 - 06:22:44 PDT)
- [AMBER] Problem analysing output with process_mdout.perl script (Tue Jun 21 2016 - 08:46:40 PDT)
Sanjib Paul
- [AMBER] GIST calculation (Sat Jun 18 2016 - 04:46:05 PDT)
- Re: [AMBER] energy decomposition (Fri Jun 17 2016 - 03:22:46 PDT)
- [AMBER] energy decomposition (Wed Jun 08 2016 - 23:55:35 PDT)
Sehrish Naz Aijaz
- [AMBER] Query regarding dihedral angles (Tue Jun 21 2016 - 22:17:51 PDT)
- [AMBER] script for calculation of dihedral angle frequency (Fri Jun 17 2016 - 00:36:14 PDT)
SHAILESH KUMAR
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Sat Jun 25 2016 - 09:02:27 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Sat Jun 25 2016 - 02:36:40 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Wed Jun 22 2016 - 01:00:06 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Sat Jun 18 2016 - 02:44:15 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Thu Jun 16 2016 - 11:56:34 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Thu Jun 16 2016 - 10:52:50 PDT)
- Re: [AMBER] Entropy normal mode error (Thu Jun 16 2016 - 10:10:23 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd (Thu Jun 16 2016 - 09:53:28 PDT)
- [AMBER] Reading and Writing mdfrc files generated by pmemd (Thu Jun 16 2016 - 06:33:21 PDT)
- Re: [AMBER] Problem: Do not receive mails from Amber list but Amber digest (Tue Jun 14 2016 - 11:12:05 PDT)
- [AMBER] Problem: Do not receive mails from Amber list but Amber digest (Tue Jun 14 2016 - 02:10:42 PDT)
Shilpa Gupta
- [AMBER] TIP3PFBOX: water model (Wed Jun 29 2016 - 05:32:49 PDT)
- [AMBER] solvent equilibration (Sat Jun 25 2016 - 06:03:57 PDT)
Shreeramesh
- [AMBER] Error in MMPBSA (Thu Jun 23 2016 - 07:50:16 PDT)
- Re: [AMBER] Error in tleap for the atom type of OCT1 and OCT2 of glutamic acid at C-terminal (Mon Jun 13 2016 - 03:11:57 PDT)
- [AMBER] Error in tleap for the atom type of OCT1 and OCT2 of glutamic acid at C-terminal (Fri Jun 10 2016 - 07:16:49 PDT)
Shuntaro Chiba
- [AMBER] How to define COM group of atoms greater than 1024 atoms when nmropt=1 and pmemd.cuda.MPI (Wed Jun 08 2016 - 08:07:55 PDT)
Slava Chushak
- [AMBER] Library errors while using NAB on Amber16 (Wed Jun 29 2016 - 12:01:04 PDT)
Sushil Mishra
- Re: [AMBER] Issue with with the nocenter in tLeap (Thu Jun 23 2016 - 16:49:36 PDT)
- Re: [AMBER] Issue with with the nocenter in tLeap (Wed Jun 22 2016 - 21:58:23 PDT)
- [AMBER] Issue with with the nocenter in tLeap (Thu Jun 09 2016 - 23:39:02 PDT)
tanfei777.sina.cn
- [AMBER] 回复：Re: Help me with double ambiguous noe.map files!!! PLEASE (Mon Jun 13 2016 - 20:06:30 PDT)
- [AMBER] Can I turn off group coordinate averaging? (Sun Jun 12 2016 - 21:59:17 PDT)
- [AMBER] 回复：Re: Help me with double ambiguous noe.map files!!! PLEASE (Sun Jun 12 2016 - 21:15:45 PDT)
- [AMBER] Help me with double ambiguous noe.map files!!! PLEASE (Sun Jun 12 2016 - 00:28:05 PDT)
Thakur, Abhishek
- Re: [AMBER] equilibration problem (Wed Jun 29 2016 - 09:34:19 PDT)
- Re: [AMBER] equilibration problem (Wed Jun 29 2016 - 09:00:09 PDT)
- Re: [AMBER] equilibration problem (Wed Jun 29 2016 - 08:17:54 PDT)
- Re: [AMBER] equilibration problem (Wed Jun 29 2016 - 07:27:51 PDT)
- Re: [AMBER] Does Amber14 work with CUDA higher than 6.5? (Wed Jun 29 2016 - 07:16:25 PDT)
- Re: [AMBER] TIP3PFBOX: water model (Wed Jun 29 2016 - 07:12:23 PDT)
- Re: [AMBER] Error: [cluster] Not all arguments handled: [ pdb ] (Tue Jun 28 2016 - 14:36:32 PDT)
- [AMBER] Error: [cluster] Not all arguments handled: [ pdb ] (Tue Jun 28 2016 - 13:59:18 PDT)
- [AMBER] difference in ptraj for ambertools-12 and 15 (Tue Jun 28 2016 - 13:54:54 PDT)
Thiago Lipinski Paes
- Re: [AMBER] RMSD PLot (Wed Jun 29 2016 - 07:05:42 PDT)
Thomas Exner
- [AMBER] Reminder: Training and Innovation Course in Drug Design (Tue Jun 14 2016 - 23:59:22 PDT)
- [AMBER] Fwd: eChemInfo Workshop on Rational Drug Design in Milano (Mon Jun 13 2016 - 23:01:44 PDT)
Thomas Pochapsky
- Re: [AMBER] restarting a run (Tue Jun 07 2016 - 05:50:35 PDT)
- Re: [AMBER] restarting a run (Mon Jun 06 2016 - 10:26:35 PDT)
- [AMBER] restarting a run (Mon Jun 06 2016 - 06:27:54 PDT)
Tyler Luchko (Lists)
- Re: [AMBER] mdl file for 1d-rism (Tue Jun 21 2016 - 10:37:31 PDT)
Vaibhav Dixit
- Re: [AMBER] Some problems about Heme (Sat Jun 04 2016 - 06:55:12 PDT)
- Re: [AMBER] Some problems about heme (Fri Jun 03 2016 - 04:23:30 PDT)
Vishal Nemaysh
- [AMBER] Regarding run.rst file generation (Sun Jun 26 2016 - 07:10:59 PDT)
Vlad Cojocaru
- Re: [AMBER] FF14SB implementation (Tue Jun 14 2016 - 06:41:42 PDT)
- Re: [AMBER] FF14SB implementation (Tue Jun 14 2016 - 05:53:25 PDT)
Wong Li Zhe
- [AMBER] Density File (Tue Jun 14 2016 - 19:27:36 PDT)
Xiangyu Jia
- Re: [AMBER] Thermodynamic Integration with QM/MM Hamiltonian (Mon Jun 27 2016 - 07:07:00 PDT)
- [AMBER] Thermodynamic Integration with QM/MM Hamiltonian (Mon Jun 27 2016 - 00:07:30 PDT)
Xiao-Lei Wang
- Re: [AMBER] MMPBSA.py nmode output problem (Thu Jun 23 2016 - 07:56:34 PDT)
- [AMBER] MMPBSA.py nmode output problem (Thu Jun 23 2016 - 05:38:00 PDT)
Yeng-Tseng Wang
- Re: [AMBER] ABOUT the GaMD patch for Amber14 (Wed Jun 15 2016 - 09:14:05 PDT)
- [AMBER] ABOUT the GaMD patch for Amber14 (Wed Jun 15 2016 - 08:50:45 PDT)
Zack Scholl
- Re: [AMBER] Amber16 + GTX1080 - working well (Wed Jun 29 2016 - 12:02:25 PDT)
- Re: [AMBER] AMBER support for gtx1080 (Thu Jun 23 2016 - 07:35:33 PDT)
- [AMBER] Amber16 and CUDA8.0 pmemd.cuda worked, and then stopped working, saying "cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" (Tue Jun 21 2016 - 09:44:14 PDT)
- [AMBER] Amber16+CUDA8.0 pmemd.cuda worked, and then stopped working, saying "cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" (Tue Jun 21 2016 - 08:03:19 PDT)
Zhenyu Meng
- Re: [AMBER] the meaning of NONBON in frcmod (Thu Jun 30 2016 - 05:07:26 PDT)
- Re: [AMBER] the meaning of NONBON in frcmod (Wed Jun 29 2016 - 02:30:55 PDT)
- Re: [AMBER] the meaning of NONBON in frcmod (Wed Jun 29 2016 - 01:34:36 PDT)
- [AMBER] the meaning of NONBON in frcmod (Tue Jun 28 2016 - 21:26:18 PDT)
Ziba Bahadori
- [AMBER] Mmpbsa problem (Sat Jun 25 2016 - 23:08:40 PDT)
- [AMBER] Fw: (Sat Jun 25 2016 - 23:00:04 PDT)
- [AMBER] mmpbsa problem (Sat Jun 04 2016 - 07:05:50 PDT)
- [AMBER] mmpbsa analys (Thu Jun 02 2016 - 10:05:21 PDT)
zmatovic.kg.ac.rs
- Re: [AMBER] Ambertools16 test failed for leap (Sat Jun 04 2016 - 23:50:31 PDT)
zoran matovic
- Re: [AMBER] addAtomType problem (Thu Jun 30 2016 - 10:00:32 PDT)
- Re: [AMBER] Structural refinement of the protein complexed withmetalo-ions (Thu Jun 30 2016 - 05:08:33 PDT)
- Re: [AMBER] the meaning of NONBON in frcmod (Wed Jun 29 2016 - 04:12:08 PDT)
- [AMBER] Ambertools16 test failed for leap (Sat Jun 04 2016 - 14:18:22 PDT)
徐明远
- [AMBER] MMPBSA.PY Error :LengthError: length mismatch in energy vectors (Thu Jun 23 2016 - 04:07:06 PDT)

Amber Archive Jun 2016 by author