Amber Archive Aug 2014: by author

Alan
- [AMBER] updates about ACPYPE (Sat Aug 30 2014 - 03:41:24 PDT)
Alessandro Contini
- Re: [AMBER] mmpbsa on charged sytem (Tue Aug 05 2014 - 09:04:49 PDT)
Amit Harode
- Re: [AMBER] Performance of RuBisCo (74, 916) atoms on NVIDIA Tesla K40 GPU (Tue Aug 12 2014 - 00:03:04 PDT)
- [AMBER] Performance of RuBisCo (74, 916) atoms on NVIDIA Tesla K40 GPU (Mon Aug 11 2014 - 05:34:30 PDT)
ammarah.ghaffar.comsats.edu.pk
- [AMBER] Error in making and running xleap (Thu Aug 28 2014 - 02:52:23 PDT)
- Re: [AMBER] Error in making and running xleap (Tue Aug 26 2014 - 01:16:09 PDT)
- [AMBER] Error in making and running xleap (Mon Aug 25 2014 - 02:25:46 PDT)
Andy Tsai
- [AMBER] Antechamber Error: Cannot open file CORR_NAME_TYPE.DAT, exit (Mon Aug 11 2014 - 16:41:42 PDT)
Annika Wittenbecher
- [AMBER] unfolding molecule after heating (Thu Aug 07 2014 - 22:16:03 PDT)
- [AMBER] unfolding molecule after heating (Thu Aug 07 2014 - 21:14:51 PDT)
Asaminew Haile
- Re: [AMBER] Script error in Umbrella tutorial (Sun Aug 03 2014 - 12:35:45 PDT)
Asmita Gupta
- Re: [AMBER] principal axes calculation in ptraj (Wed Aug 20 2014 - 00:45:37 PDT)
- [AMBER] principal axes calculation in ptraj (Tue Aug 19 2014 - 02:12:48 PDT)
- [AMBER] significance of attaching a dummy atom in smd (Thu Aug 07 2014 - 10:32:12 PDT)
Bajarang Kumbhar
- Re: [AMBER] AMBER Digest, Vol 956, Issue 1 (Sun Aug 24 2014 - 23:32:02 PDT)
- [AMBER] Implicit solvent simulation study (Sat Aug 23 2014 - 22:42:54 PDT)
BATUHAN KAV
- [AMBER] antechamber parametrization of desoxycorticosterone (Thu Aug 21 2014 - 06:14:41 PDT)
- [AMBER] antechamber parametrization of desoxycorticosterone (Thu Aug 21 2014 - 05:59:39 PDT)
- [AMBER] Parametrization of glycerol and desoxycorticosterone (Wed Aug 20 2014 - 10:59:16 PDT)
- [AMBER] Parametrization of glycerol and desoxycorticosterone (Wed Aug 20 2014 - 10:54:56 PDT)
bharat lakhani
- [AMBER] MM-PBSA ALA scanning module (Fri Aug 01 2014 - 14:17:36 PDT)
Bill Ross
- Re: [AMBER] Converting (rst) file to PDB using ambpdb (Tue Aug 05 2014 - 15:18:52 PDT)
Brian Radak
- Re: [AMBER] Mg 12-6-4 potential using parmed (Fri Aug 29 2014 - 06:39:19 PDT)
- Re: [AMBER] Mg 12-6-4 potential using parmed (Thu Aug 28 2014 - 16:47:35 PDT)
- [AMBER] Mg 12-6-4 potential using parmed (Thu Aug 28 2014 - 12:45:19 PDT)
- Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling (Tue Aug 26 2014 - 11:41:26 PDT)
- Re: [AMBER] QM/MM in Amber (Mon Aug 18 2014 - 11:13:21 PDT)
- Re: [AMBER] Questions for pH-REMD by Jason Swails (Wed Aug 06 2014 - 11:40:17 PDT)
- Re: [AMBER] Cluster results (Wed Aug 06 2014 - 06:37:44 PDT)
- Re: [AMBER] SCF convergence failed during QMMM (Wed Aug 06 2014 - 06:32:58 PDT)
- Re: [AMBER] SCF convergence failed during QMMM (Tue Aug 05 2014 - 11:12:00 PDT)
- Re: [AMBER] mmpbsa on charged sytem (Tue Aug 05 2014 - 07:42:00 PDT)
- Re: [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error) (Mon Aug 04 2014 - 11:27:30 PDT)
- Re: [AMBER] what's the difference between imin=1 and imin=5 when performing minimizations on structures from MD trajectory (Fri Aug 01 2014 - 06:16:41 PDT)
Caitlin Scott
- [AMBER] Using iwrap with a dimer (Thu Aug 21 2014 - 06:45:28 PDT)
Carlos Simmerling
- Re: [AMBER] Implicit solvent simulation study (Sun Aug 24 2014 - 08:06:47 PDT)
- Re: [AMBER] Potential Energy is positve for a normal ligand (Mon Aug 04 2014 - 07:53:34 PDT)
Chinh Su Tran To
- [AMBER] error: "STOP PMEMD terminated abnormally" (Wed Aug 13 2014 - 00:06:48 PDT)
Chris Gao
- Re: [AMBER] Prediction of the protonation state for the ensemble of pdb structures (Wed Aug 27 2014 - 05:00:57 PDT)
- Re: [AMBER] Prediction of the protonation state for the ensemble of pdb structures (Wed Aug 27 2014 - 02:33:54 PDT)
- Re: [AMBER] MCPB and sidechain.bcl problem (Mon Aug 25 2014 - 20:32:23 PDT)
- Re: [AMBER] MCPB and sidechain.bcl problem (Sun Aug 24 2014 - 04:21:10 PDT)
Covington, Cody Lance
- Re: [AMBER] Calculating electrostatic potential in cpptraj (Sat Aug 16 2014 - 13:20:42 PDT)
- Re: [AMBER] Calculating electrostatic potential in cpptraj (Sat Aug 16 2014 - 13:11:24 PDT)
- [AMBER] Calculating electrostatic potential in cpptraj (Fri Aug 15 2014 - 13:21:41 PDT)
Daniel Roe
- Re: [AMBER] Obtaining representative structures from clustering (Fri Aug 29 2014 - 09:21:33 PDT)
- Re: [AMBER] Obtaining representative structures from clustering (Fri Aug 29 2014 - 08:22:51 PDT)
- Re: [AMBER] antechamber error message (Wed Aug 27 2014 - 22:16:25 PDT)
- Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling (Tue Aug 26 2014 - 11:35:28 PDT)
- Re: [AMBER] Undocumented DSSP commands and torsional analysis (Tue Aug 26 2014 - 10:33:01 PDT)
- Re: [AMBER] Using iwrap with a dimer (Thu Aug 21 2014 - 06:52:02 PDT)
- Re: [AMBER] Contacts (Wed Aug 20 2014 - 08:23:06 PDT)
- Re: [AMBER] Calculating lipid diffusion (Wed Aug 20 2014 - 07:57:14 PDT)
- Re: [AMBER] principal axes calculation in ptraj (Wed Aug 20 2014 - 07:11:37 PDT)
- Re: [AMBER] principal axes calculation in ptraj (Tue Aug 19 2014 - 07:50:28 PDT)
- Re: [AMBER] PCA projection (Tue Aug 19 2014 - 07:32:32 PDT)
- Re: [AMBER] How to visualize PCA (Mon Aug 18 2014 - 20:11:24 PDT)
- Re: [AMBER] errors for surf command in cpptraj (Fri Aug 15 2014 - 13:15:32 PDT)
- Re: [AMBER] Cluster results (Fri Aug 15 2014 - 13:06:39 PDT)
- Re: [AMBER] Dynamic selection of donor and acceptor mask for hbond analysis (Fri Aug 15 2014 - 12:52:50 PDT)
- Re: [AMBER] errors for surf command in cpptraj (Fri Aug 15 2014 - 10:47:39 PDT)
- Re: [AMBER] Very high values of Diffusion coefficient of water (Fri Aug 15 2014 - 08:07:05 PDT)
- Re: [AMBER] Principal Component/Kullback-Leibler Analysis (Tue Aug 12 2014 - 12:33:12 PDT)
- Re: [AMBER] Principal Component/Kullback-Leibler Analysis (Tue Aug 12 2014 - 12:06:30 PDT)
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer (Tue Aug 12 2014 - 10:34:34 PDT)
- Re: [AMBER] Cluster results (Mon Aug 11 2014 - 09:02:22 PDT)
- Re: [AMBER] cpptraj.MPI running in 'ensemble' mode. (Sat Aug 09 2014 - 15:54:26 PDT)
- [AMBER] New CPPTRAJ Tutorials (Fri Aug 08 2014 - 12:49:19 PDT)
- Re: [AMBER] Principal Component/Kullback-Leibler Analysis (Fri Aug 08 2014 - 09:41:55 PDT)
- Re: [AMBER] Cluster results (Fri Aug 08 2014 - 08:00:52 PDT)
- Re: [AMBER] Cluster results (Fri Aug 08 2014 - 07:35:53 PDT)
- Re: [AMBER] Cluster results (Fri Aug 08 2014 - 07:25:36 PDT)
- Re: [AMBER] Cluster results (Fri Aug 08 2014 - 06:56:34 PDT)
- Re: [AMBER] Cluster results (Thu Aug 07 2014 - 07:18:09 PDT)
- Re: [AMBER] Cluster results (Wed Aug 06 2014 - 08:09:23 PDT)
- Re: [AMBER] help in analysis (Wed Aug 06 2014 - 07:55:05 PDT)
- Re: [AMBER] Visualyze avg structure in VMD (Tue Aug 05 2014 - 05:33:58 PDT)
- Re: [AMBER] AMBER14 Tutorial: Lipid14 Edition (Sat Aug 02 2014 - 09:46:22 PDT)
David A Case
- Re: [AMBER] Do the Charmm FF parameters apply to Amber? (Sun Aug 31 2014 - 10:56:24 PDT)
- Re: [AMBER] nab (Sat Aug 30 2014 - 05:28:58 PDT)
- Re: [AMBER] harmonic restraint (Wed Aug 27 2014 - 19:10:19 PDT)
- Re: [AMBER] Triply bonded oxygen (Wed Aug 27 2014 - 05:02:51 PDT)
- Re: [AMBER] pmemdTI test failure (Mon Aug 25 2014 - 18:00:01 PDT)
- Re: [AMBER] Error in making and running xleap (Mon Aug 25 2014 - 05:01:04 PDT)
- Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling (Fri Aug 22 2014 - 10:54:32 PDT)
- Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling (Thu Aug 21 2014 - 13:08:57 PDT)
- Re: [AMBER] clustering (Thu Aug 21 2014 - 11:14:47 PDT)
- Re: [AMBER] antechamber (Thu Aug 21 2014 - 07:42:54 PDT)
- Re: [AMBER] antechamber parametrization of desoxycorticosterone (Thu Aug 21 2014 - 06:30:08 PDT)
- Re: [AMBER] positive free energy (Wed Aug 20 2014 - 11:48:37 PDT)
- Re: [AMBER] Parametrization of glycerol and desoxycorticosterone (Wed Aug 20 2014 - 11:32:57 PDT)
- Re: [AMBER] ambpdb error (Tue Aug 19 2014 - 05:01:16 PDT)
- Re: [AMBER] 10 Error on OPEN: ANTECHAMBER.ESP (Tue Aug 19 2014 - 04:55:08 PDT)
- Re: [AMBER] nmode for chamber prmtop (Mon Aug 18 2014 - 07:26:57 PDT)
- Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization (Fri Aug 15 2014 - 07:17:16 PDT)
- Re: [AMBER] Antechamber error (Thu Aug 14 2014 - 08:47:09 PDT)
- Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization (Thu Aug 14 2014 - 08:44:38 PDT)
- Re: [AMBER] error: "STOP PMEMD terminated abnormally" (Wed Aug 13 2014 - 07:51:32 PDT)
- Re: [AMBER] Performance of RuBisCo (74, 916) atoms on NVIDIA Tesla K40 GPU (Tue Aug 12 2014 - 07:37:30 PDT)
- Re: [AMBER] Antechamber Error: Cannot open file CORR_NAME_TYPE.DAT, exit (Mon Aug 11 2014 - 17:43:19 PDT)
- Re: [AMBER] Question concerning a torsion parameter (Wed Aug 06 2014 - 20:55:52 PDT)
- Re: [AMBER] SQM error while preparing ATP with antechamber (Wed Aug 06 2014 - 09:04:30 PDT)
- Re: [AMBER] Hydrogen bond analysis (Tue Aug 05 2014 - 08:50:30 PDT)
- Re: [AMBER] this a very green neophyte's question. (Sat Aug 02 2014 - 05:27:46 PDT)
- Re: [AMBER] MMPBSA prmtop problem (Sat Aug 02 2014 - 05:27:38 PDT)
- Re: [AMBER] this a very green neophyte's question. (Fri Aug 01 2014 - 06:40:31 PDT)
de Manzanos Guinot, Angela
- [AMBER] PCA projection (Tue Aug 19 2014 - 02:52:42 PDT)
DEBOSTUTI GHOSHDASTIDAR
- Re: [AMBER] perl script to convert GIST output to .dx file (Mon Aug 18 2014 - 21:45:29 PDT)
- [AMBER] perl script to convert GIST output to .dx file (Mon Aug 18 2014 - 11:11:13 PDT)
- Re: [AMBER] Very high values of Diffusion coefficient of water (Sat Aug 16 2014 - 02:52:13 PDT)
- Re: [AMBER] Very high values of Diffusion coefficient of water (Fri Aug 15 2014 - 09:46:13 PDT)
- [AMBER] Dynamic selection of donor and acceptor mask for hbond analysis (Fri Aug 15 2014 - 03:11:22 PDT)
- [AMBER] Very high values of Diffusion coefficient of water (Wed Aug 13 2014 - 22:09:52 PDT)
Dhananjay
- [AMBER] MMPBSA.py -nan values. (Mon Aug 25 2014 - 09:36:58 PDT)
Dickson, Callum J
- Re: [AMBER] question about lipid tutorial (Fri Aug 01 2014 - 04:49:09 PDT)
Dr. Vitaly Chaban
- Re: [AMBER] QM/MM in Amber (Mon Aug 18 2014 - 12:47:46 PDT)
Eugene Yedvabny
- [AMBER] Undocumented DSSP commands and torsional analysis (Tue Aug 26 2014 - 00:48:53 PDT)
FyD
- Re: [AMBER] On combining different force-fields and charge-derivation methods (Sat Aug 30 2014 - 04:08:48 PDT)
- Re: [AMBER] [Private q4md] R.E.D. Server: Private assistance (Fri Aug 22 2014 - 12:27:23 PDT)
- Re: [AMBER] 10 Error on OPEN: ANTECHAMBER.ESP (Tue Aug 19 2014 - 04:43:04 PDT)
George Green
- Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling (Wed Aug 27 2014 - 13:16:18 PDT)
- Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling (Tue Aug 26 2014 - 10:58:46 PDT)
- Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling (Fri Aug 22 2014 - 10:25:21 PDT)
- [AMBER] Using setbox command to prepare files for Umbrella Sampling (Thu Aug 21 2014 - 12:28:45 PDT)
George Patargias
- [AMBER] Problem with Firefly optimisation in R.E.D server (Wed Aug 20 2014 - 02:06:44 PDT)
Gerald Monard
- Re: [AMBER] Performance of RuBisCo (74, 916) atoms on NVIDIA Tesla K40 GPU (Wed Aug 13 2014 - 12:36:08 PDT)
Gulsevin,Alican
- [AMBER] Triply bonded oxygen (Tue Aug 26 2014 - 15:21:05 PDT)
- Re: [AMBER] Question on Updating AMBER (Tue Aug 19 2014 - 08:42:34 PDT)
- [AMBER] Question on Updating AMBER (Tue Aug 19 2014 - 05:18:58 PDT)
Hallel Freedman
- Re: [AMBER] bad atom type o (Wed Aug 20 2014 - 14:36:51 PDT)
- Re: [AMBER] bad atom type o (Wed Aug 20 2014 - 14:11:11 PDT)
- Re: [AMBER] bad atom type o (Wed Aug 20 2014 - 12:17:40 PDT)
- Re: [AMBER] bad atom type o (Wed Aug 20 2014 - 10:56:47 PDT)
- Re: [AMBER] bad atom type o (Wed Aug 20 2014 - 10:37:57 PDT)
- Re: [AMBER] bad atom type o (Wed Aug 20 2014 - 10:24:05 PDT)
- Re: [AMBER] bad atom type o (Wed Aug 20 2014 - 09:44:45 PDT)
- Re: [AMBER] bad atom type o (Mon Aug 18 2014 - 09:58:58 PDT)
- [AMBER] bad atom type o (Sun Aug 17 2014 - 15:42:38 PDT)
Hirdesh Kumar
- Re: [AMBER] error: "STOP PMEMD terminated abnormally" (Wed Aug 13 2014 - 13:18:26 PDT)
- Re: [AMBER] error: "STOP PMEMD terminated abnormally" (Wed Aug 13 2014 - 13:15:40 PDT)
- Re: [AMBER] error: "STOP PMEMD terminated abnormally" (Wed Aug 13 2014 - 08:57:00 PDT)
- Re: [AMBER] Minimization and equilibration with SANDER.MPI and production with PMEMD.cuda ?? (Tue Aug 12 2014 - 07:45:57 PDT)
- Re: [AMBER] Minimization and equilibration with SANDER.MPI and production with PMEMD.cuda ?? (Tue Aug 12 2014 - 07:30:30 PDT)
- [AMBER] Minimization and equilibration with SANDER.MPI and production with PMEMD.cuda ?? (Tue Aug 12 2014 - 07:09:58 PDT)
- [AMBER] SQM error while preparing ATP with antechamber (Wed Aug 06 2014 - 07:47:54 PDT)
Hiromasa WATANABE
- Re: [AMBER] MMPBSA.py -make-mdins does not work with nmode (Tue Aug 05 2014 - 17:13:48 PDT)
- Re: [AMBER] MMPBSA.py -make-mdins does not work with nmode (Mon Aug 04 2014 - 18:55:23 PDT)
- [AMBER] MMPBSA.py -make-mdins does not work with nmode (Mon Aug 04 2014 - 03:57:36 PDT)
Hoshin Kim
- Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files (Mon Aug 11 2014 - 09:52:46 PDT)
- Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files (Fri Aug 08 2014 - 10:54:30 PDT)
- Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files (Tue Aug 05 2014 - 11:08:27 PDT)
- Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files (Tue Aug 05 2014 - 10:49:39 PDT)
- [AMBER] NaN and asterisks error in md.out, and mdinfo files (Mon Aug 04 2014 - 12:04:34 PDT)
Huang
- Re: [AMBER] pmemdTI test failure (Mon Aug 25 2014 - 02:37:24 PDT)
- Re: [AMBER] pmemdTI test failure (Tue Aug 19 2014 - 05:15:46 PDT)
Hugo Azurmendi
- Re: [AMBER] restraints with natural language (Fri Aug 15 2014 - 13:06:53 PDT)
- [AMBER] restraints with natural language (Fri Aug 15 2014 - 12:11:21 PDT)
Indrajit Deb
- Re: [AMBER] problem in understanding the K+ parameter (Tue Aug 26 2014 - 06:28:04 PDT)
- [AMBER] problem in understanding the K+ parameter (Tue Aug 26 2014 - 05:34:54 PDT)
J.W. Halley
- Re: [AMBER] this a very green neophyte's question. (Fri Aug 01 2014 - 18:02:27 PDT)
James Starlight
- Re: [AMBER] Prediction of the protonation state for the ensemble of pdb structures (Wed Aug 27 2014 - 03:27:47 PDT)
- Re: [AMBER] Prediction of the protonation state for the ensemble of pdb structures (Wed Aug 27 2014 - 02:39:39 PDT)
- [AMBER] Prediction of the protonation state for the ensemble of pdb structures (Wed Aug 27 2014 - 00:40:51 PDT)
- [AMBER] Testing of the convergence by means of PCA (Fri Aug 22 2014 - 10:00:13 PDT)
Jason Swails
- Re: [AMBER] On combining different force-fields and charge-derivation methods (Thu Aug 28 2014 - 18:03:47 PDT)
- Re: [AMBER] system size more than 1000 residues (Thu Aug 28 2014 - 13:53:14 PDT)
- Re: [AMBER] amber 14 tests errors (Thu Aug 28 2014 - 12:15:47 PDT)
- Re: [AMBER] Error in making and running xleap (Thu Aug 28 2014 - 04:34:59 PDT)
- Re: [AMBER] Question for residues.py to parameterize a nonstandard residue for constant pH MD (Wed Aug 27 2014 - 14:26:55 PDT)
- Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling (Tue Aug 26 2014 - 12:09:24 PDT)
- Re: [AMBER] problem in understanding the K+ parameter (Tue Aug 26 2014 - 06:25:33 PDT)
- Re: [AMBER] Error in making and running xleap (Tue Aug 26 2014 - 04:30:45 PDT)
- Re: [AMBER] MMPBSA.py -nan values. (Mon Aug 25 2014 - 10:27:02 PDT)
- Re: [AMBER] Implicit solvation method: problem with the rst file (Mon Aug 25 2014 - 05:10:17 PDT)
- Re: [AMBER] Implicit solvation method: problem with the rst file (Mon Aug 25 2014 - 04:33:41 PDT)
- Re: [AMBER] Implicit solvent simulation study (Sun Aug 24 2014 - 07:12:27 PDT)
- Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization (Fri Aug 22 2014 - 09:10:56 PDT)
- Re: [AMBER] antechamber parametrization of desoxycorticosterone (Fri Aug 22 2014 - 04:20:00 PDT)
- Re: [AMBER] antechamber (Thu Aug 21 2014 - 07:18:02 PDT)
- Re: [AMBER] antechamber parametrization of desoxycorticosterone (Thu Aug 21 2014 - 06:26:58 PDT)
- Re: [AMBER] antechamber parametrization of desoxycorticosterone (Thu Aug 21 2014 - 06:26:13 PDT)
- Re: [AMBER] bad atom type o (Wed Aug 20 2014 - 15:34:43 PDT)
- Re: [AMBER] positive free energy (Wed Aug 20 2014 - 15:29:46 PDT)
- Re: [AMBER] positive free energy (Wed Aug 20 2014 - 14:36:44 PDT)
- Re: [AMBER] bad atom type o (Wed Aug 20 2014 - 14:26:42 PDT)
- Re: [AMBER] bad atom type o (Wed Aug 20 2014 - 14:08:56 PDT)
- Re: [AMBER] positive free energy (Wed Aug 20 2014 - 11:34:17 PDT)
- Re: [AMBER] Parametrization of glycerol and desoxycorticosterone (Wed Aug 20 2014 - 11:21:51 PDT)
- Re: [AMBER] ATTN NEED REVISION error - reg (Wed Aug 20 2014 - 11:07:35 PDT)
- Re: [AMBER] bad atom type o (Wed Aug 20 2014 - 10:41:31 PDT)
- Re: [AMBER] bad atom type o (Wed Aug 20 2014 - 10:31:53 PDT)
- Re: [AMBER] bad atom type o (Wed Aug 20 2014 - 09:56:15 PDT)
- Re: [AMBER] error ambpdb - Old style inpcrd file read (Wed Aug 20 2014 - 07:48:21 PDT)
- Re: [AMBER] Contacts (Wed Aug 20 2014 - 06:58:32 PDT)
- Re: [AMBER] Contacts (Wed Aug 20 2014 - 05:34:54 PDT)
- Re: [AMBER] error ambpdb - Old style inpcrd file read (Wed Aug 20 2014 - 05:33:22 PDT)
- Re: [AMBER] error ambpdb - Old style inpcrd file read (Wed Aug 20 2014 - 05:09:52 PDT)
- Re: [AMBER] antechamber (Wed Aug 20 2014 - 04:41:36 PDT)
- Re: [AMBER] error ambpdb - Old style inpcrd file read (Wed Aug 20 2014 - 04:34:24 PDT)
- Re: [AMBER] error ambpdb - Old style inpcrd file read (Wed Aug 20 2014 - 04:30:55 PDT)
- Re: [AMBER] Question on Updating AMBER (Tue Aug 19 2014 - 09:16:24 PDT)
- Re: [AMBER] puckering of 6 member ring (Tue Aug 19 2014 - 07:11:17 PDT)
- Re: [AMBER] Question on Updating AMBER (Tue Aug 19 2014 - 05:51:45 PDT)
- Re: [AMBER] pmemdTI test failure (Tue Aug 19 2014 - 05:41:30 PDT)
- Re: [AMBER] ambpdb error (Tue Aug 19 2014 - 05:04:03 PDT)
- Re: [AMBER] 10 Error on OPEN: ANTECHAMBER.ESP (Tue Aug 19 2014 - 04:56:51 PDT)
- Re: [AMBER] ambpdb error (Tue Aug 19 2014 - 04:13:56 PDT)
- Re: [AMBER] bad atom type o (Mon Aug 18 2014 - 04:14:45 PDT)
- Re: [AMBER] Calculating electrostatic potential in cpptraj (Sat Aug 16 2014 - 18:05:24 PDT)
- Re: [AMBER] Calculating electrostatic potential in cpptraj (Fri Aug 15 2014 - 17:00:46 PDT)
- Re: [AMBER] restraints with natural language (Fri Aug 15 2014 - 15:49:46 PDT)
- Re: [AMBER] restraints with natural language (Fri Aug 15 2014 - 12:33:22 PDT)
- Re: [AMBER] Very high values of Diffusion coefficient of water (Fri Aug 15 2014 - 12:27:41 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Thu Aug 14 2014 - 10:37:46 PDT)
- Re: [AMBER] Fwd: problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Thu Aug 14 2014 - 09:48:09 PDT)
- Re: [AMBER] Kinase and ATP MD simulation (Thu Aug 14 2014 - 09:18:49 PDT)
- Re: [AMBER] Help on Normal Mode Analysis (Thu Aug 14 2014 - 08:19:10 PDT)
- Re: [AMBER] ATP and MG2+prep and frcmod files (Thu Aug 14 2014 - 05:15:31 PDT)
- Re: [AMBER] Parameters for ATP and MG2+ (Wed Aug 13 2014 - 09:24:23 PDT)
- Re: [AMBER] ATP and MG2+prep and frcmod files (Wed Aug 13 2014 - 09:21:34 PDT)
- Re: [AMBER] error: "STOP PMEMD terminated abnormally" (Wed Aug 13 2014 - 09:15:50 PDT)
- Re: [AMBER] amber/gaussian find the transition state (Wed Aug 13 2014 - 05:07:08 PDT)
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer (Wed Aug 13 2014 - 04:56:51 PDT)
- Re: [AMBER] build branched polymer in leap? (Tue Aug 12 2014 - 19:51:35 PDT)
- [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Tue Aug 12 2014 - 13:36:59 PDT)
- Re: [AMBER] Minimization and equilibration with SANDER.MPI and production with PMEMD.cuda ?? (Tue Aug 12 2014 - 09:15:24 PDT)
- Re: [AMBER] Minimization and equilibration with SANDER.MPI and production with PMEMD.cuda ?? (Tue Aug 12 2014 - 07:17:48 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Tue Aug 12 2014 - 07:16:06 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Tue Aug 12 2014 - 04:52:09 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Mon Aug 11 2014 - 19:37:48 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Mon Aug 11 2014 - 10:37:48 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Sun Aug 10 2014 - 14:44:19 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Sat Aug 09 2014 - 14:16:29 PDT)
- Re: [AMBER] cpptraj.MPI running in 'ensemble' mode. (Sat Aug 09 2014 - 11:55:14 PDT)
- Re: [AMBER] Cluster results (Fri Aug 08 2014 - 07:40:15 PDT)
- Re: [AMBER] chamber prmtop with changed LJ parameters not accepted by pmemd.cuda? (Fri Aug 08 2014 - 06:25:48 PDT)
- Re: [AMBER] significance of attaching a dummy atom in smd (Thu Aug 07 2014 - 10:52:20 PDT)
- Re: [AMBER] Percent occupancy of a hydrogen bond (Thu Aug 07 2014 - 08:32:05 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Thu Aug 07 2014 - 08:27:07 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Wed Aug 06 2014 - 11:54:34 PDT)
- Re: [AMBER] Adding new Bondi radii for mmpbsa (Wed Aug 06 2014 - 09:35:12 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Wed Aug 06 2014 - 09:18:46 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Wed Aug 06 2014 - 09:17:47 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Wed Aug 06 2014 - 08:44:59 PDT)
- Re: [AMBER] Converting (rst) file to PDB using ambpdb (Tue Aug 05 2014 - 14:57:48 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Tue Aug 05 2014 - 12:30:45 PDT)
- Re: [AMBER] MMPBSA.py -make-mdins does not work with nmode (Tue Aug 05 2014 - 07:10:37 PDT)
- Re: [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error) (Tue Aug 05 2014 - 07:03:25 PDT)
- Re: [AMBER] MMPBSA.py -make-mdins does not work with nmode (Mon Aug 04 2014 - 04:32:09 PDT)
- Re: [AMBER] Script error in Umbrella tutorial (Sun Aug 03 2014 - 13:03:34 PDT)
- Re: [AMBER] MMPBSA prmtop problem (Sat Aug 02 2014 - 15:16:00 PDT)
- Re: [AMBER] MMPBSA prmtop problem (Sat Aug 02 2014 - 05:00:51 PDT)
- Re: [AMBER] Zinc parameterization (Fri Aug 01 2014 - 15:15:03 PDT)
- Re: [AMBER] MM-PBSA ALA scanning module (Fri Aug 01 2014 - 14:41:53 PDT)
- Re: [AMBER] Metal parametrization problem!! (Fri Aug 01 2014 - 12:27:07 PDT)
- Re: [AMBER] Metal parametrization problem!! (Fri Aug 01 2014 - 11:29:48 PDT)
Jonathan Gough
- Re: [AMBER] Obtaining representative structures from clustering (Fri Aug 29 2014 - 09:22:39 PDT)
- Re: [AMBER] Obtaining representative structures from clustering (Fri Aug 29 2014 - 09:01:04 PDT)
- Re: [AMBER] Obtaining representative structures from clustering (Fri Aug 29 2014 - 08:40:10 PDT)
- [AMBER] Obtaining representative structures from clustering (Fri Aug 29 2014 - 07:56:06 PDT)
- Re: [AMBER] Principal Component/Kullback-Leibler Analysis (Tue Aug 12 2014 - 12:47:50 PDT)
- Re: [AMBER] Principal Component/Kullback-Leibler Analysis (Tue Aug 12 2014 - 12:17:11 PDT)
- Re: [AMBER] Principal Component/Kullback-Leibler Analysis (Tue Aug 12 2014 - 10:47:19 PDT)
- Re: [AMBER] cpptraj.MPI running in 'ensemble' mode. (Sat Aug 09 2014 - 12:53:24 PDT)
- Re: [AMBER] cpptraj.MPI running in 'ensemble' mode. (Sat Aug 09 2014 - 11:31:47 PDT)
- [AMBER] cpptraj.MPI running in 'ensemble' mode. (Sat Aug 09 2014 - 11:28:41 PDT)
- [AMBER] Principal Component/Kullback-Leibler Analysis (Fri Aug 08 2014 - 09:17:26 PDT)
- Re: [AMBER] question about lipid tutorial (Fri Aug 01 2014 - 07:24:15 PDT)
Jordi Bujons
- [AMBER] amber 14 tests errors (Thu Aug 28 2014 - 11:23:27 PDT)
Kshatresh Dutta Dubey
- [AMBER] Memory keyword for QM/MM using ORCA (Wed Aug 06 2014 - 00:43:53 PDT)
- Re: [AMBER] Script error in Umbrella tutorial (Sun Aug 03 2014 - 13:10:15 PDT)
- Re: [AMBER] Script error in Umbrella tutorial (Sun Aug 03 2014 - 12:42:58 PDT)
- [AMBER] Script error in Umbrella tutorial (Sun Aug 03 2014 - 11:56:46 PDT)
Lara rajam
- [AMBER] clustering (Thu Aug 21 2014 - 10:27:07 PDT)
- [AMBER] puckering of 6 member ring (Tue Aug 19 2014 - 06:06:31 PDT)
M Olivia Kim
- [AMBER] Question for residues.py to parameterize a nonstandard residue for constant pH MD (Wed Aug 27 2014 - 12:30:20 PDT)
- [AMBER] Questions for pH-REMD by Jason Swails (Wed Aug 06 2014 - 10:43:35 PDT)
M.Venkata Satish Kumar
- Re: [AMBER] Implicit solvation method: problem with the rst file (Mon Aug 25 2014 - 04:54:52 PDT)
- [AMBER] Implicit solvation method: problem with the rst file (Mon Aug 25 2014 - 04:08:51 PDT)
Manikanthan Bhavaraju
- [AMBER] Fwd: Unable to generate RESP charges for a charged ligand (Wed Aug 06 2014 - 07:36:44 PDT)
Marc van der Kamp
- Re: [AMBER] Cluster results (Wed Aug 13 2014 - 06:22:03 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Tue Aug 12 2014 - 09:20:13 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Tue Aug 12 2014 - 05:43:11 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Mon Aug 11 2014 - 22:50:03 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Mon Aug 11 2014 - 13:14:04 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Mon Aug 11 2014 - 06:40:53 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Sun Aug 10 2014 - 14:05:36 PDT)
- [AMBER] chamber prmtop with changed LJ parameters not accepted by pmemd.cuda? (Fri Aug 08 2014 - 04:12:44 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Thu Aug 07 2014 - 08:58:12 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Thu Aug 07 2014 - 04:53:23 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Wed Aug 06 2014 - 09:06:34 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Wed Aug 06 2014 - 05:01:25 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Wed Aug 06 2014 - 00:55:07 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Wed Aug 06 2014 - 00:39:39 PDT)
- [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Tue Aug 05 2014 - 09:27:19 PDT)
- Re: [AMBER] Visualyze avg structure in VMD (Tue Aug 05 2014 - 03:39:44 PDT)
Mark Williamson
- Re: [AMBER] antechamber (Wed Aug 20 2014 - 05:04:48 PDT)
Mary Varughese
- Re: [AMBER] nab (Sun Aug 31 2014 - 00:26:21 PDT)
- Re: [AMBER] nab (Fri Aug 29 2014 - 22:16:26 PDT)
- [AMBER] nab (Fri Aug 29 2014 - 01:56:39 PDT)
- [AMBER] mmpbsa on charged sytem (Tue Aug 05 2014 - 00:19:26 PDT)
menwer momo
- Re: [AMBER] Percent occupancy of a hydrogen bond (Thu Aug 07 2014 - 08:40:44 PDT)
- [AMBER] Percent occupancy of a hydrogen bond (Thu Aug 07 2014 - 05:00:46 PDT)
- Re: [AMBER] Converting (rst) file to PDB using ambpdb (Tue Aug 05 2014 - 15:24:44 PDT)
- Re: [AMBER] Converting (rst) file to PDB using ambpdb (Tue Aug 05 2014 - 15:23:33 PDT)
- [AMBER] Converting (rst) file to PDB using ambpdb (Tue Aug 05 2014 - 13:40:11 PDT)
- [AMBER] Hydrogen bond analysis (Tue Aug 05 2014 - 04:45:35 PDT)
mmaestre.gate.sinica.edu.tw
- Re: [AMBER] glycated residue parameter (Mon Aug 04 2014 - 02:45:56 PDT)
- Re: [AMBER] glycated residue parameter (Mon Aug 04 2014 - 00:35:39 PDT)
- Re: [AMBER] glycated residue parameter (Sun Aug 03 2014 - 23:45:49 PDT)
Mohammad Salem
- Re: [AMBER] On combining different force-fields and charge-derivation methods (Thu Aug 28 2014 - 21:13:35 PDT)
- [AMBER] On combining different force-fields and charge-derivation methods (Thu Aug 28 2014 - 16:27:29 PDT)
- Re: [AMBER] Question concerning a torsion parameter (Thu Aug 07 2014 - 12:14:58 PDT)
- Re: [AMBER] Question concerning a torsion parameter (Wed Aug 06 2014 - 21:47:53 PDT)
- Re: [AMBER] Question concerning a torsion parameter (Wed Aug 06 2014 - 17:35:47 PDT)
- [AMBER] Question concerning a torsion parameter (Wed Aug 06 2014 - 17:26:29 PDT)
Muthukumaran R
- [AMBER] QM/MM in Amber (Mon Aug 18 2014 - 10:12:00 PDT)
- Re: [AMBER] SCF convergence failed during QMMM (Tue Aug 05 2014 - 21:55:39 PDT)
- [AMBER] SCF convergence failed during QMMM (Tue Aug 05 2014 - 09:23:55 PDT)
Nadia Li
- Re: [AMBER] harmonic restraint (Wed Aug 27 2014 - 21:09:15 PDT)
- [AMBER] harmonic restraint (Wed Aug 27 2014 - 17:00:42 PDT)
- Re: [AMBER] MMPBSA prmtop problem (Sat Aug 02 2014 - 08:47:06 PDT)
- [AMBER] MMPBSA prmtop problem (Fri Aug 01 2014 - 23:40:59 PDT)
- Re: [AMBER] Zinc parameterization (Fri Aug 01 2014 - 15:20:44 PDT)
- Re: [AMBER] Zinc parameterization (Fri Aug 01 2014 - 15:11:18 PDT)
- Re: [AMBER] Zinc parameterization (Fri Aug 01 2014 - 10:34:41 PDT)
Nguyen, Crystal
- Re: [AMBER] perl script to convert GIST output to .dx file (Mon Aug 18 2014 - 11:23:04 PDT)
Niels Geudens
- Re: [AMBER] ScaledMD for proline dipeptide (Mon Aug 04 2014 - 05:20:59 PDT)
Pablo Ródenas
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer (Wed Aug 13 2014 - 06:31:58 PDT)
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer (Wed Aug 13 2014 - 04:11:39 PDT)
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer (Tue Aug 12 2014 - 23:59:17 PDT)
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer (Mon Aug 11 2014 - 23:00:26 PDT)
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer (Thu Aug 07 2014 - 07:54:05 PDT)
Parker de Waal
- Re: [AMBER] this a very green neophyte's question. (Thu Jul 31 2014 - 20:13:57 PDT)
Pedro A. Baldera Aguayo
- Re: [AMBER] Metal parametrization problem!! (Tue Aug 05 2014 - 14:01:25 PDT)
- Re: [AMBER] Metal parametrization problem!! (Tue Aug 05 2014 - 10:56:10 PDT)
- Re: [AMBER] Metal parametrization problem!! (Mon Aug 04 2014 - 19:46:58 PDT)
- Re: [AMBER] Metal parametrization problem!! (Mon Aug 04 2014 - 18:39:06 PDT)
- Re: [AMBER] Metal parametrization problem!! (Fri Aug 01 2014 - 13:13:27 PDT)
- Re: [AMBER] Metal parametrization problem!! (Fri Aug 01 2014 - 11:38:29 PDT)
- [AMBER] Metal parametrization problem!! (Fri Aug 01 2014 - 11:17:24 PDT)
Pengfei Li
- Re: [AMBER] Mg 12-6-4 potential using parmed (Fri Aug 29 2014 - 07:51:35 PDT)
- Re: [AMBER] Mg 12-6-4 potential using parmed (Thu Aug 28 2014 - 15:23:17 PDT)
- Re: [AMBER] MCPB and sidechain.bcl problem (Wed Aug 27 2014 - 07:47:14 PDT)
- Re: [AMBER] MCPB and sidechain.bcl problem (Tue Aug 26 2014 - 12:05:58 PDT)
- Re: [AMBER] MCPB and sidechain.bcl problem (Mon Aug 25 2014 - 06:26:37 PDT)
- Re: [AMBER] MCPB and sidechain.bcl problem (Sat Aug 23 2014 - 05:34:24 PDT)
- Re: [AMBER] Metal parametrization problem!! (Tue Aug 05 2014 - 13:33:05 PDT)
- Re: [AMBER] Metal parametrization problem!! (Mon Aug 04 2014 - 18:58:40 PDT)
- Re: [AMBER] Metal parametrization problem!! (Mon Aug 04 2014 - 18:51:30 PDT)
- Re: [AMBER] Zinc parameterization (Fri Aug 01 2014 - 14:54:40 PDT)
- Re: [AMBER] Metal parametrization problem!! (Fri Aug 01 2014 - 14:42:57 PDT)
Pengzhi Zhang
- [AMBER] system size more than 1000 residues (Thu Aug 28 2014 - 12:36:12 PDT)
Radhika Swathi
- [AMBER] ATTN NEED REVISION error - reg (Wed Aug 20 2014 - 10:49:45 PDT)
Rajeswari A.
- Re: [AMBER] Problem with atommap in cpptraj (Fri Aug 01 2014 - 22:03:23 PDT)
Ray Luo, Ph.D.
- Re: [AMBER] positive free energy (Wed Aug 20 2014 - 17:03:02 PDT)
- Re: [AMBER] positive free energy (Wed Aug 20 2014 - 12:21:13 PDT)
- Re: [AMBER] positive free energy (Wed Aug 20 2014 - 11:59:23 PDT)
Robin Betz
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Wed Aug 06 2014 - 08:50:34 PDT)
Robin Jain
- [AMBER] help in analysis (Wed Aug 06 2014 - 02:44:16 PDT)
- [AMBER] help in analysis (Wed Aug 06 2014 - 02:44:16 PDT)
Ross Walker
- Re: [AMBER] Performance of RuBisCo (74, 916) atoms on NVIDIA Tesla K40 GPU (Mon Aug 11 2014 - 10:08:16 PDT)
- Re: [AMBER] chamber prmtop with changed LJ parameters not accepted by pmemd.cuda? (Fri Aug 08 2014 - 08:49:31 PDT)
- Re: [AMBER] unfolding molecule after heating (Thu Aug 07 2014 - 22:35:15 PDT)
- Re: [AMBER] unfolding molecule after heating (Thu Aug 07 2014 - 22:33:47 PDT)
- Re: [AMBER] Question concerning a torsion parameter (Thu Aug 07 2014 - 10:23:09 PDT)
- Re: [AMBER] Question concerning a torsion parameter (Wed Aug 06 2014 - 18:42:58 PDT)
- Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files (Wed Aug 06 2014 - 11:38:15 PDT)
- Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files (Tue Aug 05 2014 - 10:55:44 PDT)
- Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files (Mon Aug 04 2014 - 12:14:14 PDT)
- Re: [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error) (Mon Aug 04 2014 - 09:23:06 PDT)
Saikat Dutta chowdhury
- Re: [AMBER] HELP Needed: AMBER12 cuda compilation ERROR (Thu Jul 31 2014 - 23:03:38 PDT)
Sally Pias
- [AMBER] build branched polymer in leap? (Tue Aug 12 2014 - 16:32:59 PDT)
Sangita Kachhap
- Re: [AMBER] glycated residue parameter (Mon Aug 04 2014 - 02:49:16 PDT)
- Re: [AMBER] glycated residue parameter (Mon Aug 04 2014 - 02:24:51 PDT)
- Re: [AMBER] glycated residue parameter (Sun Aug 03 2014 - 23:57:47 PDT)
- [AMBER] glycated residue parameter (Sun Aug 03 2014 - 22:10:39 PDT)
Sarah Witzke
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Thu Aug 14 2014 - 10:09:14 PDT)
- [AMBER] Fwd: problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Thu Aug 14 2014 - 09:31:16 PDT)
- [AMBER] Fwd: problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Thu Aug 07 2014 - 09:11:48 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Wed Aug 06 2014 - 13:56:24 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Wed Aug 06 2014 - 11:30:09 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Wed Aug 06 2014 - 08:27:08 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) (Wed Aug 06 2014 - 04:50:14 PDT)
Scott Le Grand
- Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files (Sat Aug 09 2014 - 08:23:49 PDT)
- Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files (Wed Aug 06 2014 - 12:24:15 PDT)
Sergey Samsonov
- Re: [AMBER] Adding new Bondi radii for mmpbsa (Wed Aug 06 2014 - 23:46:43 PDT)
- [AMBER] Adding new Bondi radii for mmpbsa (Wed Aug 06 2014 - 07:18:39 PDT)
Shekter, Lee R
- [AMBER] AMBER14 Tutorial: Lipid14 Edition (Fri Aug 01 2014 - 11:03:58 PDT)
Soumendranath Bhakat
- Re: [AMBER] Converting (rst) file to PDB using ambpdb (Wed Aug 06 2014 - 01:48:25 PDT)
Sourav Purohit
- Re: [AMBER] Contacts (Wed Aug 20 2014 - 09:56:12 PDT)
- Re: [AMBER] Contacts (Wed Aug 20 2014 - 07:26:04 PDT)
- Re: [AMBER] Contacts (Wed Aug 20 2014 - 06:14:30 PDT)
- [AMBER] Contacts (Wed Aug 20 2014 - 05:22:07 PDT)
Subrata Paul
- [AMBER] parameters for Mutant HP35 NelNel (PDB code 2F4K) (Fri Aug 01 2014 - 05:42:08 PDT)
Sun
- [AMBER] the force constant in umberlla simpling (Sun Aug 31 2014 - 01:35:42 PDT)
- Re: [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error) (Mon Aug 04 2014 - 10:06:14 PDT)
- [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error) (Mon Aug 04 2014 - 08:39:02 PDT)
- [AMBER] Potential Energy is positve for a normal ligand (Mon Aug 04 2014 - 07:49:06 PDT)
svrci
- Re: [AMBER] nab (Fri Aug 29 2014 - 03:37:36 PDT)
Tamara Meirelles
- [AMBER] How to visualize PCA (Mon Aug 18 2014 - 18:08:39 PDT)
Thomas Cheatham
- Re: [AMBER] Cluster results (Wed Aug 06 2014 - 11:28:34 PDT)
- Re: [AMBER] mmpbsa on charged sytem (Tue Aug 05 2014 - 08:24:41 PDT)
- Re: [AMBER] Ptraj cluster error (Mon Aug 04 2014 - 08:21:28 PDT)
Urszula Uciechowska
- Re: [AMBER] error ambpdb - Old style inpcrd file read (Wed Aug 20 2014 - 07:20:42 PDT)
- Re: [AMBER] error ambpdb - Old style inpcrd file read (Wed Aug 20 2014 - 05:15:08 PDT)
- Re: [AMBER] error ambpdb - Old style inpcrd file read (Wed Aug 20 2014 - 04:38:46 PDT)
- Re: [AMBER] error ambpdb - Old style inpcrd file read (Wed Aug 20 2014 - 04:22:51 PDT)
- Re: [AMBER] error ambpdb - Old style inpcrd file read (Wed Aug 20 2014 - 03:55:11 PDT)
- [AMBER] error ambpdb - Old style inpcrd file read (Wed Aug 20 2014 - 01:20:23 PDT)
- Re: [AMBER] ambpdb error (Tue Aug 19 2014 - 04:12:58 PDT)
- [AMBER] ambpdb error (Tue Aug 19 2014 - 04:01:13 PDT)
Valentina Romano
- Re: [AMBER] error ambpdb - Old style inpcrd file read (Wed Aug 20 2014 - 04:09:25 PDT)
- [AMBER] Kinase and ATP MD simulation (Thu Aug 14 2014 - 08:49:45 PDT)
- [AMBER] Antechamber error (Thu Aug 14 2014 - 02:38:24 PDT)
- Re: [AMBER] ATP and MG2+prep and frcmod files (Thu Aug 14 2014 - 00:59:39 PDT)
- [AMBER] ATP and MG2+prep and frcmod files (Wed Aug 13 2014 - 08:28:27 PDT)
- [AMBER] Parameters for ATP and MG2+ (Wed Aug 13 2014 - 07:56:32 PDT)
- Re: [AMBER] Cluster results (Wed Aug 13 2014 - 07:25:31 PDT)
- Re: [AMBER] Cluster results (Wed Aug 13 2014 - 05:59:34 PDT)
- Re: [AMBER] Cluster results (Mon Aug 11 2014 - 03:13:24 PDT)
- Re: [AMBER] Cluster results (Fri Aug 08 2014 - 07:30:39 PDT)
- Re: [AMBER] Cluster results (Fri Aug 08 2014 - 07:10:02 PDT)
- Re: [AMBER] Cluster results (Fri Aug 08 2014 - 04:42:49 PDT)
- Re: [AMBER] Cluster results (Thu Aug 07 2014 - 01:34:00 PDT)
- Re: [AMBER] Cluster results (Wed Aug 06 2014 - 07:27:40 PDT)
- [AMBER] Cluster results (Wed Aug 06 2014 - 05:22:41 PDT)
- [AMBER] Visualyze avg structure in VMD (Tue Aug 05 2014 - 03:23:16 PDT)
- [AMBER] Ptraj cluster error (Mon Aug 04 2014 - 07:58:42 PDT)
Vijay Manickam Achari
- [AMBER] Calculating lipid diffusion using mass weighted feature (Tue Aug 19 2014 - 00:02:09 PDT)
Vijyan Achari
- [AMBER] Calculating lipid diffusion (Tue Aug 19 2014 - 19:07:36 PDT)
Vlad Cojocaru
- Re: [AMBER] positive free energy (Wed Aug 20 2014 - 14:45:26 PDT)
- Re: [AMBER] positive free energy (Wed Aug 20 2014 - 13:32:03 PDT)
- Re: [AMBER] positive free energy (Wed Aug 20 2014 - 13:29:06 PDT)
Wei Chen
- [AMBER] nmode for chamber prmtop (Mon Aug 18 2014 - 07:01:01 PDT)
- Re: [AMBER] errors for surf command in cpptraj (Fri Aug 15 2014 - 12:58:49 PDT)
- [AMBER] errors for surf command in cpptraj (Fri Aug 15 2014 - 09:50:07 PDT)
xy21hb
- [AMBER] Help on Normal Mode Analysis (Thu Aug 14 2014 - 07:55:12 PDT)
ye renlo
- [AMBER] what's the difference between imin=1 and imin=5 when performing minimizations on structures from MD trajectory (Fri Aug 01 2014 - 01:18:56 PDT)
Ying-Chieh Sun
- Re: [AMBER] antechamber (Tue Aug 19 2014 - 21:06:29 PDT)
- Re: [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error) (Tue Aug 05 2014 - 22:28:03 PDT)
- Re: [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error) (Mon Aug 04 2014 - 19:45:27 PDT)
zahra khatti
- Re: [AMBER] Distance command (Tue Aug 26 2014 - 12:10:15 PDT)
- [AMBER] Distance command (Tue Aug 26 2014 - 05:30:38 PDT)
- [AMBER] positive free energy (Wed Aug 20 2014 - 11:11:29 PDT)
张冬冬
- [AMBER] Do the Charmm FF parameters apply to Amber? (Sun Aug 31 2014 - 08:09:42 PDT)
- Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization (Fri Aug 22 2014 - 07:56:01 PDT)
- Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization (Fri Aug 15 2014 - 02:26:33 PDT)
- [AMBER] Using polarized force field lead to large RMS in the second step of minimization (Thu Aug 14 2014 - 02:23:13 PDT)
王珍
- [AMBER] amber/gaussian find the transition state (Wed Aug 13 2014 - 02:03:19 PDT)
闫玉娜
- Re: [AMBER] antechamber (Thu Aug 21 2014 - 06:52:51 PDT)
- Re: [AMBER] antechamber (Wed Aug 20 2014 - 05:21:26 PDT)
- [AMBER] antechamber (Tue Aug 19 2014 - 19:31:10 PDT)
高彧辉
- Re: [AMBER] MCPB and sidechain.bcl problem (Tue Aug 26 2014 - 22:33:23 PDT)
- [AMBER] MCPB and sidechain.bcl problem (Fri Aug 22 2014 - 05:55:30 PDT)
전선희
- [AMBER] antechamber error message (Wed Aug 27 2014 - 20:02:13 PDT)
- [AMBER] 10 Error on OPEN: ANTECHAMBER.ESP (Mon Aug 18 2014 - 23:17:38 PDT)

Amber Archive Aug 2014 by author