Amber Archive Oct 2012: by author

Abderezak-EXT.Mekfouldji.sanofi.com
- [AMBER] compilation error on Amber 10 (Wed Oct 17 2012 - 03:41:44 PDT)
ABEL Stephane 175950
- [AMBER] RE : RE : Reference for the AMBER12SB force field (Thu Oct 11 2012 - 04:36:44 PDT)
- [AMBER] RE : Reference for the AMBER12SB force field (Mon Oct 08 2012 - 05:05:02 PDT)
- [AMBER] Reference for the AMBER12SB force field (Mon Oct 08 2012 - 04:13:57 PDT)
Abhishek Mukhopadhyay
- [AMBER] TI with shake (Wed Oct 03 2012 - 14:37:28 PDT)
Acoot Brett
- [AMBER] on salt bridge affinity by AMBER (Fri Oct 12 2012 - 20:28:31 PDT)
Adrian Roitberg
- Re: [AMBER] Estimating time in AMD (Mon Oct 08 2012 - 02:10:48 PDT)
- Re: [AMBER] Setting the random seed in Langevin dynamics (Wed Oct 03 2012 - 06:25:00 PDT)
Ake Sandgren
- Re: [AMBER] AmberTools12 unset variable in sqm/MNDOChargeSeparation.F90 (Mon Oct 22 2012 - 13:18:47 PDT)
- [AMBER] Amber12 uninitialized variable in sander/nmr.F90 (Fri Oct 19 2012 - 14:55:20 PDT)
- [AMBER] AmberTools12 unset variable in sqm/MNDOChargeSeparation.F90 (Fri Oct 19 2012 - 13:11:00 PDT)
Alan
- [AMBER] How dose ptraj calculate diffusion (Mon Oct 15 2012 - 04:56:51 PDT)
Albert
- Re: [AMBER] job failed for REMD in cluster (Mon Oct 15 2012 - 11:53:49 PDT)
- [AMBER] job failed for REMD in cluster (Mon Oct 15 2012 - 11:48:04 PDT)
- [AMBER] a question about replica exchange (Sun Oct 14 2012 - 23:19:36 PDT)
Aldo Segura
- Re: [AMBER] Vina Docking model is not accepted in Antechamber (Wed Oct 17 2012 - 07:36:11 PDT)
- Re: [AMBER] Vina Docking model is not accepted in Antechamber (Tue Oct 16 2012 - 15:52:02 PDT)
- Re: [AMBER] Vina Docking model is not accepted in Antechamber (Tue Oct 16 2012 - 13:35:43 PDT)
Amparo Garcia Lopez
- Re: [AMBER] RNA - build a mismatch and a loop with NAB (Wed Oct 24 2012 - 02:58:44 PDT)
- Re: [AMBER] RNA - build a mismatch and a loop with NAB (Tue Oct 23 2012 - 01:06:39 PDT)
- [AMBER] RNA - build a mismatch and a loop with NAB (Mon Oct 22 2012 - 07:11:13 PDT)
Amy Davenport
- Re: [AMBER] Calculation of single atom radius of gyration (Fri Oct 26 2012 - 14:04:04 PDT)
- [AMBER] Calculation of single atom radius of gyration (Thu Oct 25 2012 - 16:02:50 PDT)
- [AMBER] Calculation of single atom radius of gyration (Wed Oct 24 2012 - 14:50:20 PDT)
Andre Serobian
- Re: [AMBER] no prmtop created with closest (Wed Oct 10 2012 - 22:33:47 PDT)
- [AMBER] no prmtop created with closest (Wed Oct 10 2012 - 19:26:46 PDT)
Andreas Goetz
- Re: [AMBER] AmberTools12 unset variable in sqm/MNDOChargeSeparation.F90 (Mon Oct 22 2012 - 15:02:28 PDT)
- Re: [AMBER] AmberTools12 unset variable in sqm/MNDOChargeSeparation.F90 (Mon Oct 22 2012 - 13:11:24 PDT)
André C. Stiel
- Re: [AMBER] idecomp and so on.... (Tue Oct 09 2012 - 13:59:12 PDT)
- Re: [AMBER] idecomp and so on.... (Tue Oct 09 2012 - 09:35:56 PDT)
- [AMBER] idecomp and so on.... (Mon Oct 08 2012 - 09:52:36 PDT)
Anna Bauß
- Re: [AMBER] vlimit exceeded on step.. error (Thu Oct 11 2012 - 01:43:38 PDT)
Anogna
- [AMBER] Request for MMPBSA files. (Tue Oct 30 2012 - 04:50:45 PDT)
- Re: [AMBER] unable to find mopac charges (Wed Oct 10 2012 - 23:07:45 PDT)
- Re: [AMBER] unable to find mopac charges (Wed Oct 10 2012 - 03:39:36 PDT)
- Re: [AMBER] unable to find mopac charges (Thu Oct 04 2012 - 23:55:20 PDT)
- [AMBER] unable to find mopac charges (Wed Oct 03 2012 - 03:03:53 PDT)
- Re: [AMBER] Molecular Dynamic production (Mon Oct 01 2012 - 22:51:28 PDT)
Anselm Horn
- Re: [AMBER] Nonstandard residue: phosphotyrosine (Mon Oct 29 2012 - 07:24:02 PDT)
- Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling (Tue Oct 23 2012 - 00:50:07 PDT)
- Re: [AMBER] unable to find mopac charges (Mon Oct 15 2012 - 00:07:38 PDT)
Antonija Tomić
- [AMBER] deprotonated serine (Mon Oct 29 2012 - 07:27:06 PDT)
anyiphysics.gmail.com
- [AMBER] antechamber limitation on molecule size (Mon Oct 29 2012 - 12:37:25 PDT)
Aron Broom
- Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling (Fri Oct 19 2012 - 11:30:18 PDT)
- Re: [AMBER] NaN question (Fri Oct 19 2012 - 07:51:35 PDT)
- Re: [AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? (Fri Oct 19 2012 - 07:45:13 PDT)
- Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling (Thu Oct 18 2012 - 21:36:08 PDT)
- Re: [AMBER] Probelms encountered when creating non-standard residue (Thu Oct 18 2012 - 21:25:20 PDT)
- Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling (Thu Oct 18 2012 - 18:30:02 PDT)
- Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling (Thu Oct 18 2012 - 12:30:30 PDT)
- Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling (Thu Oct 18 2012 - 09:53:40 PDT)
- Re: [AMBER] Concerning nonbonded exclusions and MMPBSA (Thu Oct 18 2012 - 09:35:24 PDT)
- [AMBER] Concerning nonbonded exclusions and MMPBSA (Thu Oct 18 2012 - 08:45:25 PDT)
- Re: [AMBER] Leap ditribution (Wed Oct 17 2012 - 09:05:48 PDT)
- Re: [AMBER] Incorrect Bond Assignment in AMBERTools 12 LeAP (Tue Oct 16 2012 - 16:26:15 PDT)
- Re: [AMBER] Atom-type for aromatic carbon attached by amide nitrogen (Tue Oct 16 2012 - 15:21:45 PDT)
- Re: [AMBER] Incorrect Bond Assignment in AMBERTools 12 LeAP (Tue Oct 16 2012 - 11:40:04 PDT)
- [AMBER] Incorrect Bond Assignment in AMBERTools 12 LeAP (Tue Oct 16 2012 - 09:59:55 PDT)
Aronica, Pietro
- Re: [AMBER] Possible bug in LEaP with ff12SB (Thu Oct 25 2012 - 05:36:11 PDT)
- [AMBER] Possible bug in LEaP with ff12SB (Thu Oct 25 2012 - 04:23:32 PDT)
ashley chen
- Re: [AMBER] Antechamber Warning Atomtype (Tue Oct 23 2012 - 23:37:40 PDT)
BALA SUBRAMANI G L
- [AMBER] forefield for Pyridoxal 5-phosphate (Fri Oct 12 2012 - 07:39:35 PDT)
baogen duan
- [AMBER] "Bad value during floating point read" of processing dihedral using chamber (Fri Oct 19 2012 - 05:56:57 PDT)
- [AMBER] "istrng" option in MMPBSA calculation (Thu Oct 18 2012 - 03:57:29 PDT)
- [AMBER] error while using chamber (AmberTools1.5) to convert charmm psf and pdb to amber crd and top (Thu Oct 11 2012 - 19:16:03 PDT)
Bashford, Donald
- Re: [AMBER] Atom selection for restraints. .. . (Tue Oct 30 2012 - 14:07:50 PDT)
Ben Roberts
- Re: [AMBER] difference in amino94.xml (MCPB) and all_amino94.lib (leap) for CYM (Tue Oct 09 2012 - 13:14:52 PDT)
- Re: [AMBER] Errors in Amber12 installation (Mon Oct 08 2012 - 18:57:18 PDT)
- Re: [AMBER] Errors in Amber12 installation (Mon Oct 08 2012 - 16:46:09 PDT)
- Re: [AMBER] Problem related to the parallel installation og Amber11 (Sun Sep 30 2012 - 20:55:32 PDT)
- Re: [AMBER] Problem related to the parallel installation og Amber11 (Sun Sep 30 2012 - 14:15:10 PDT)
BERGY
- [AMBER] MMPBSA error (Mon Oct 01 2012 - 02:15:17 PDT)
Bill Miller III
- Re: [AMBER] problem with decompostion energy (Wed Oct 17 2012 - 08:36:05 PDT)
- Re: [AMBER] Pairwise decoposition (MMPBSA) (Wed Oct 17 2012 - 08:19:51 PDT)
- Re: [AMBER] bad atom type: cl error in MMPBSA decomp (Fri Oct 12 2012 - 05:12:05 PDT)
Bill Ross
- Re: [AMBER] Possible bug in LEaP with ff12SB (Thu Oct 25 2012 - 23:47:25 PDT)
- Re: [AMBER] Meaning of the term "pre-equilibrated" waters (Sun Oct 21 2012 - 17:31:24 PDT)
- Re: [AMBER] XLeap Install Issue (Fri Oct 12 2012 - 18:58:41 PDT)
- Re: [AMBER] Centering a multimeric protein with solvateOct (Sat Oct 06 2012 - 15:09:05 PDT)
Binwu Zhao
- [AMBER] radgyr of ptraj or cpptraj (Mon Oct 29 2012 - 09:57:45 PDT)
bio lab
- Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling (Fri Oct 19 2012 - 10:11:16 PDT)
- Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling (Thu Oct 18 2012 - 17:05:47 PDT)
- Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling (Thu Oct 18 2012 - 11:10:58 PDT)
- [AMBER] cis form: avoiding atom overlap in all-atom modeling (Thu Oct 18 2012 - 09:42:13 PDT)
Brian Radak
- Re: [AMBER] extract velocities (Mon Oct 22 2012 - 13:47:05 PDT)
- Re: [AMBER] Random Seed (Wed Oct 17 2012 - 10:39:14 PDT)
- Re: [AMBER] Temperature in TI run (Tue Oct 16 2012 - 12:07:39 PDT)
- Re: [AMBER] QM method (Tue Oct 09 2012 - 08:45:20 PDT)
- Re: [AMBER] effect neutralizing ions on value of "saltcon" in generalized Born model (Mon Oct 01 2012 - 13:58:22 PDT)
Brown, Kyle
- [AMBER] Maintaining Chain ID (Mon Oct 15 2012 - 10:26:52 PDT)
Cao Yang
- [AMBER] Asterisks in the restart file (Mon Oct 08 2012 - 05:08:41 PDT)
Carlos Romero
- Re: [AMBER] residue split (Thu Oct 18 2012 - 00:22:36 PDT)
- Re: [AMBER] residue split (Tue Oct 16 2012 - 22:11:04 PDT)
- Re: [AMBER] residue split (Tue Oct 16 2012 - 07:20:33 PDT)
- [AMBER] residue split (Mon Oct 15 2012 - 22:16:42 PDT)
- [AMBER] about results (Fri Oct 12 2012 - 18:28:18 PDT)
Carlos Simmerling
- Re: [AMBER] short bonds in average pdb (Thu Oct 18 2012 - 07:52:39 PDT)
- Re: [AMBER] short bonds in average pdb (Thu Oct 18 2012 - 07:24:47 PDT)
- [AMBER] ACS awards deadline Oct 23 (Tue Oct 16 2012 - 07:05:50 PDT)
- Re: [AMBER] residue split (Tue Oct 16 2012 - 03:13:57 PDT)
- Re: [AMBER] job failed for REMD in cluster (Mon Oct 15 2012 - 12:01:47 PDT)
- Re: [AMBER] a question about replica exchange (Mon Oct 15 2012 - 03:12:10 PDT)
- Re: [AMBER] on salt bridge affinity by AMBER (Sat Oct 13 2012 - 06:08:02 PDT)
- Re: [AMBER] Fwd: Notes and warnings in the generalized Born calculation (Fri Oct 12 2012 - 14:26:55 PDT)
- Re: [AMBER] RE : Reference for the AMBER12SB force field (Thu Oct 11 2012 - 04:28:58 PDT)
- Re: [AMBER] Reference for the AMBER12SB force field (Mon Oct 08 2012 - 04:57:33 PDT)
- Re: [AMBER] Meaning of setting gbsa=0 in generalized Born calculations (Fri Oct 05 2012 - 04:48:26 PDT)
- Re: [AMBER] phosphate moiety & igb model (Fri Oct 05 2012 - 04:43:50 PDT)
Catein Catherine
- [AMBER] Error Message in running MM/GBSA (Mon Oct 29 2012 - 22:51:59 PDT)
- [AMBER] How to read the PairwiseDistance file after clustering analysis? (Fri Oct 19 2012 - 10:54:28 PDT)
- [AMBER] How to convert ptraj cluster commands to cpptraj (Fri Oct 19 2012 - 10:49:28 PDT)
- [AMBER] Should we exclude "equilibri?um state" conformers? (Wed Oct 17 2012 - 19:48:54 PDT)
- [AMBER] clustering error message (Wed Oct 17 2012 - 10:29:13 PDT)
- [AMBER] Clustering VS constant rmsd (Wed Oct 17 2012 - 10:23:50 PDT)
Changqing Yan
- Re: [AMBER] How Can I modify a amino acid in Amber (Sun Oct 21 2012 - 19:22:19 PDT)
- [AMBER] Probelms encountered when creating non-standard residue (Thu Oct 18 2012 - 20:07:59 PDT)
- Re: [AMBER] How Can I modify a amino acid in Amber? (Sun Oct 14 2012 - 20:11:17 PDT)
- [AMBER] How Can I modify a amino acid in Amber? (Fri Oct 12 2012 - 19:17:02 PDT)
- [AMBER] How to express a right-handed amino acid in leap (Thu Oct 11 2012 - 05:36:49 PDT)
chenkai_szpku
- [AMBER] Amber12 Parrell Installation Error (Wed Oct 31 2012 - 04:52:01 PDT)
Chiara Pallara
- Re: [AMBER] Trajectory Clustering (Fri Oct 26 2012 - 09:04:24 PDT)
- [AMBER] Trajectory Clustering (Fri Oct 26 2012 - 05:08:38 PDT)
Chris Chris
- Re: [AMBER] Vina Docking model is not accepted in Antechamber (Tue Oct 16 2012 - 21:09:12 PDT)
- Re: [AMBER] Vina Docking model is not accepted in Antechamber (Tue Oct 16 2012 - 14:55:02 PDT)
- [AMBER] Vina Docking model is not accepted in Antechamber (Tue Oct 16 2012 - 11:47:09 PDT)
- [AMBER] RESTARTED DUE TO LINMIN FAILURE (Sun Oct 14 2012 - 21:55:55 PDT)
Dail Chapman
- Re: [AMBER] Umbrella Sampling with Z-axis as Reaction Coordinate (Sun Oct 14 2012 - 22:23:00 PDT)
- [AMBER] Umbrella Sampling with Z-axis as Reaction Coordinate (Sun Oct 07 2012 - 16:57:08 PDT)
Daniel Roe
- Re: [AMBER] antechamber limitation on molecule size (Wed Oct 31 2012 - 17:06:57 PDT)
- Re: [AMBER] questions about thermodynamic integration atom name and order (Wed Oct 31 2012 - 08:43:24 PDT)
- Re: [AMBER] Atom selection for restraints (Mon Oct 29 2012 - 16:10:52 PDT)
- Re: [AMBER] radgyr of ptraj or cpptraj (Mon Oct 29 2012 - 11:17:23 PDT)
- Re: [AMBER] If i strip water from the trajectory files, would it influence the analysis results? (Mon Oct 29 2012 - 07:28:25 PDT)
- Re: [AMBER] Calculation of single atom radius of gyration (Fri Oct 26 2012 - 14:34:40 PDT)
- Re: [AMBER] Trajectory Clustering (Fri Oct 26 2012 - 07:22:05 PDT)
- Re: [AMBER] Hydrogen bond time series in cpptraj (Thu Oct 25 2012 - 08:16:03 PDT)
- Re: [AMBER] Calculation of single atom radius of gyration (Wed Oct 24 2012 - 15:51:46 PDT)
- Re: [AMBER] intdiel / extdiel (Thu Oct 18 2012 - 16:48:10 PDT)
- Re: [AMBER] clustering the trajectories (Thu Oct 18 2012 - 08:57:52 PDT)
- Re: [AMBER] clustering the trajectories (Wed Oct 17 2012 - 13:09:42 PDT)
- Re: [AMBER] clustering error message (Wed Oct 17 2012 - 13:08:02 PDT)
- Re: [AMBER] Maintaining Chain ID (Wed Oct 17 2012 - 07:04:15 PDT)
- Re: [AMBER] calculating intramolecular hydrogen bonding (Wed Oct 17 2012 - 06:57:44 PDT)
- Re: [AMBER] How dose ptraj calculate diffusion (Mon Oct 15 2012 - 14:23:57 PDT)
- Re: [AMBER] clustering the trajectories (Thu Oct 11 2012 - 07:43:10 PDT)
- Re: [AMBER] Average structure of trajectories as pdb file? (Thu Oct 11 2012 - 07:40:37 PDT)
- Re: [AMBER] no prmtop created with closest (Wed Oct 10 2012 - 21:56:45 PDT)
- Re: [AMBER] Problem related to the radial distribution function (Wed Oct 10 2012 - 10:41:53 PDT)
- Re: [AMBER] vlimit exceeded on step.. error (Tue Oct 09 2012 - 09:05:55 PDT)
- Re: [AMBER] how to create crd file from my tra file? (Tue Oct 09 2012 - 09:00:02 PDT)
- Re: [AMBER] Distance calculations with ptraj (Mon Oct 08 2012 - 15:07:15 PDT)
- Re: [AMBER] diff. between avg/rep structures & connectivity problem in PDB files (Mon Oct 08 2012 - 07:39:42 PDT)
- Re: [AMBER] Distance calculations with ptraj (Mon Oct 08 2012 - 07:28:49 PDT)
- Re: [AMBER] PairwiseDistance file location (Fri Oct 05 2012 - 10:47:55 PDT)
- Re: [AMBER] calculating intramolecular hydrogen bonding (Fri Oct 05 2012 - 10:43:11 PDT)
- Re: [AMBER] Problem related to the analysis of mdcrd (Thu Oct 04 2012 - 07:39:29 PDT)
- Re: [AMBER] PairwiseDistance file location (Thu Oct 04 2012 - 07:35:35 PDT)
Daniel Sindhikara
- Re: [AMBER] Calculation of single atom radius of gyration (Thu Oct 25 2012 - 18:54:15 PDT)
Date, Mihir
- Re: [AMBER] Atom selection for restraints. . (Tue Oct 30 2012 - 07:18:22 PDT)
- [AMBER] Atom selection for restraints (Mon Oct 29 2012 - 15:41:10 PDT)
David A Case
- Re: [AMBER] Amber and P450 cytochromes (Wed Oct 31 2012 - 07:55:54 PDT)
- Re: [AMBER] Download problem of amber12 (Wed Oct 31 2012 - 07:49:31 PDT)
- Re: [AMBER] Problem in running parallel (Wed Oct 31 2012 - 07:46:17 PDT)
- Re: [AMBER] Antechamber preparartion (Mon Oct 29 2012 - 07:18:55 PDT)
- Re: [AMBER] Inquiry about how writing out pressure tensor (Mon Oct 29 2012 - 07:10:30 PDT)
- Re: [AMBER] Misleading leaprc with ff12 (Fri Oct 26 2012 - 04:49:47 PDT)
- Re: [AMBER] [PATCH 5/8] test/nab: Use paths to scripts (Thu Oct 25 2012 - 16:58:56 PDT)
- Re: [AMBER] Possible bug in LEaP with ff12SB (Thu Oct 25 2012 - 05:32:43 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Tue Oct 23 2012 - 06:29:28 PDT)
- Re: [AMBER] compilation aborted for ncsu-umbrella.F90 (code 1) (Tue Oct 23 2012 - 06:18:41 PDT)
- Re: [AMBER] [PATCH 0/8] AmberTools cleanups (Tue Oct 23 2012 - 05:43:36 PDT)
- Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling (Tue Oct 23 2012 - 05:26:28 PDT)
- Re: [AMBER] RNA - build a mismatch and a loop with NAB (Tue Oct 23 2012 - 05:20:17 PDT)
- Re: [AMBER] Clustering VS constant rmsd (Thu Oct 18 2012 - 04:39:06 PDT)
- Re: [AMBER] Clustering VS constant rmsd (Wed Oct 17 2012 - 18:09:53 PDT)
- Re: [AMBER] Leap ditribution (Wed Oct 17 2012 - 09:37:02 PDT)
- Re: [AMBER] Side chain correction for Asp (Wed Oct 17 2012 - 09:32:16 PDT)
- Re: [AMBER] distortion of the ligand during MD (Wed Oct 17 2012 - 06:44:06 PDT)
- Re: [AMBER] compilation error on Amber 10 (Wed Oct 17 2012 - 06:39:24 PDT)
- Re: [AMBER] clustering the trajectories (Wed Oct 17 2012 - 06:26:56 PDT)
- Re: [AMBER] residue split (Wed Oct 17 2012 - 06:19:14 PDT)
- Re: [AMBER] X11 problems on Mac OS X 10.8 (Tue Oct 16 2012 - 18:38:01 PDT)
- Re: [AMBER] genmetalFF.sh (Tue Oct 16 2012 - 18:33:18 PDT)
- Re: [AMBER] residue split (Tue Oct 16 2012 - 18:27:34 PDT)
- Re: [AMBER] job failed for REMD in cluster (Mon Oct 15 2012 - 12:53:18 PDT)
- Re: [AMBER] Maintaining Chain ID (Mon Oct 15 2012 - 12:45:36 PDT)
- Re: [AMBER] XLeap Install Issue (Sat Oct 13 2012 - 06:05:18 PDT)
- Re: [AMBER] Fwd: Notes and warnings in the generalized Born calculation (Fri Oct 12 2012 - 17:48:35 PDT)
- Re: [AMBER] TI problem (Fri Oct 12 2012 - 08:13:00 PDT)
- Re: [AMBER] completing C-term atoms after strip in ptraj (Fri Oct 12 2012 - 04:56:18 PDT)
- Re: [AMBER] TI problem (Thu Oct 11 2012 - 18:37:14 PDT)
- Re: [AMBER] the origin of ELEC DV/DL in the case of softcore TIcalculation of the solute with no charge by crgmask (Thu Oct 11 2012 - 07:45:40 PDT)
- Re: [AMBER] problem with antechamber and ESP (Thu Oct 11 2012 - 06:57:25 PDT)
- Re: [AMBER] unable to find mopac charges (Thu Oct 11 2012 - 05:00:01 PDT)
- Re: [AMBER] Basis of sander of Amber11 and Amber9 (Wed Oct 10 2012 - 05:49:05 PDT)
- Re: [AMBER] unable to find mopac charges (Wed Oct 10 2012 - 05:47:53 PDT)
- Re: [AMBER] vlimit exceeded on step.. error (Wed Oct 10 2012 - 04:16:51 PDT)
- Re: [AMBER] spce water (Wed Oct 10 2012 - 04:13:36 PDT)
- Re: [AMBER] Using NMR restraints for G-Quadruplex structure (Wed Oct 10 2012 - 04:11:37 PDT)
- Re: [AMBER] NVE ensemble for solvation (Wed Oct 10 2012 - 04:08:50 PDT)
- Re: [AMBER] Problems in Amber12 parallel installation (Tue Oct 09 2012 - 07:26:32 PDT)
- Re: [AMBER] Errors in Amber12 installation (Mon Oct 08 2012 - 13:33:19 PDT)
- Re: [AMBER] Reg: error in equilibration (Mon Oct 08 2012 - 05:47:49 PDT)
- Re: [AMBER] Asterisks in the restart file (Mon Oct 08 2012 - 05:43:29 PDT)
- Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" (Fri Oct 05 2012 - 05:13:04 PDT)
- Re: [AMBER] unable to find mopac charges (Fri Oct 05 2012 - 05:07:58 PDT)
- Re: [AMBER] vlimit exceeded on step.. error (Fri Oct 05 2012 - 04:58:43 PDT)
- Re: [AMBER] X11 problems on Mac OS X 10.8 (Thu Oct 04 2012 - 09:30:29 PDT)
- Re: [AMBER] the origin of ELEC DV/DL in the case of softcore TI calculation of the solute with no charge by crgmask (Thu Oct 04 2012 - 07:16:44 PDT)
- Re: [AMBER] Obtain trajectory in NAB (Thu Oct 04 2012 - 07:10:02 PDT)
- Re: [AMBER] vlimit exceeded on step.. error (Wed Oct 03 2012 - 06:53:42 PDT)
- Re: [AMBER] unable to find mopac charges (Wed Oct 03 2012 - 04:58:18 PDT)
- Re: [AMBER] To which ensemble does generalized Born trajectory fall? (Wed Oct 03 2012 - 04:56:17 PDT)
- Re: [AMBER] X11 problems on Mac OS X 10.8 (Wed Oct 03 2012 - 04:49:30 PDT)
- Re: [AMBER] X11 problems on Mac OS X 10.8 (Tue Oct 02 2012 - 18:01:37 PDT)
- Re: [AMBER] different between PBSA and MMPBSA ? (Tue Oct 02 2012 - 05:25:30 PDT)
- Re: [AMBER] Antechamber + SQM/DFTB (Mon Oct 01 2012 - 05:32:28 PDT)
- Re: [AMBER] TI Softcore potentials and SHAKE (Mon Oct 01 2012 - 05:25:21 PDT)
David Condon
- Re: [AMBER] Trajectory Clustering (Fri Oct 26 2012 - 05:43:40 PDT)
davide.savy.unina.it
- [AMBER] Leap ditribution (Wed Oct 17 2012 - 08:49:01 PDT)
- [AMBER] AMBER (Tue Oct 16 2012 - 06:28:27 PDT)
Deák Robert
- Re: [AMBER] Setting the random seed in Langevin dynamics (Wed Oct 03 2012 - 07:25:50 PDT)
- Re: [AMBER] Setting the random seed in Langevin dynamics (Wed Oct 03 2012 - 02:54:52 PDT)
Dickson, Callum
- [AMBER] Compiling amber parallel (Fri Oct 26 2012 - 08:11:18 PDT)
Diego Javier Alonso de Armiño
- [AMBER] Hydrogen bond time series in cpptraj (Thu Oct 25 2012 - 06:23:33 PDT)
duanbg
- [AMBER] error while using chamber (AmberTools1.5) to convert charmm psf and pdb to amber crd and top (Tue Oct 02 2012 - 20:05:09 PDT)
Edgar Mixcoha
- Re: [AMBER] Antechamber + SQM/DFTB (Mon Oct 01 2012 - 06:56:52 PDT)
- [AMBER] Antechamber + SQM/DFTB (Mon Oct 01 2012 - 03:12:14 PDT)
Elisa Frezza
- Re: [AMBER] umbrella sampling (Wed Oct 17 2012 - 07:13:55 PDT)
- Re: [AMBER] umbrella sampling (Wed Oct 17 2012 - 07:06:42 PDT)
- Re: [AMBER] umbrella sampling (Wed Oct 17 2012 - 06:16:56 PDT)
- [AMBER] problem umbrella sampling and gpus (Wed Oct 17 2012 - 06:08:38 PDT)
- [AMBER] umbrella sampling (Wed Oct 17 2012 - 02:32:01 PDT)
- Re: [AMBER] umbrella sampling (Mon Oct 15 2012 - 05:13:28 PDT)
- [AMBER] umbrella sampling (Mon Oct 15 2012 - 00:32:26 PDT)
- Re: [AMBER] problem restraint (Thu Oct 11 2012 - 08:12:04 PDT)
- Re: [AMBER] problem restraint (Thu Oct 11 2012 - 07:51:17 PDT)
- Re: [AMBER] problem restraint (Thu Oct 11 2012 - 07:45:43 PDT)
- [AMBER] problem restraint (Thu Oct 11 2012 - 06:53:45 PDT)
- [AMBER] restraint and NMR (Thu Oct 11 2012 - 04:38:59 PDT)
- Re: [AMBER] spce water (Wed Oct 10 2012 - 04:40:51 PDT)
- [AMBER] spce water (Wed Oct 10 2012 - 02:02:06 PDT)
Eng H Yap
- [AMBER] positional restraint to within stipulated distance (Mon Oct 29 2012 - 20:00:01 PDT)
Esam Tolba
- [AMBER] Computer specification for Amber 12 (Thu Oct 18 2012 - 02:03:32 PDT)
- Re: [AMBER] clustering the trajectories (Thu Oct 18 2012 - 00:38:24 PDT)
- Re: [AMBER] clustering the trajectories (Wed Oct 17 2012 - 12:49:09 PDT)
- [AMBER] Accessible surface area (Wed Oct 17 2012 - 01:47:10 PDT)
- Re: [AMBER] clustering the trajectories (Wed Oct 17 2012 - 01:44:51 PDT)
- [AMBER] clustering the trajectories (Thu Oct 11 2012 - 07:37:05 PDT)
- [AMBER] Average structure of trajectories as pdb file? (Thu Oct 11 2012 - 06:44:01 PDT)
- [AMBER] how to create crd file from my tra file? (Tue Oct 09 2012 - 02:07:26 PDT)
Fabrício Bracht
- [AMBER] Temperature in TI run (Tue Oct 16 2012 - 11:49:36 PDT)
- Re: [AMBER] TI problem (Fri Oct 12 2012 - 06:12:53 PDT)
- [AMBER] TI problem (Thu Oct 11 2012 - 11:15:04 PDT)
- [AMBER] Question regarding COM and atom pulling (Tue Oct 09 2012 - 10:11:25 PDT)
Federica Chiappori
- Re: [AMBER] MMPBSA.py (Wed Oct 17 2012 - 02:03:17 PDT)
- [AMBER] MMPBSA.py (Tue Oct 16 2012 - 08:58:16 PDT)
FyD
- Re: [AMBER] Fwd: Re: files for RED (Wed Oct 31 2012 - 03:57:55 PDT)
- Re: [AMBER] Fwd: Re: files for RED (Tue Oct 30 2012 - 03:54:57 PDT)
- Re: [AMBER] Antechamber preparartion (Tue Oct 30 2012 - 01:35:31 PDT)
- [AMBER] Fwd: Re: files for RED (Sun Oct 28 2012 - 09:58:34 PDT)
- Re: [AMBER] files for RED (Sun Oct 28 2012 - 09:53:44 PDT)
- Re: [AMBER] files for RED (Thu Oct 25 2012 - 05:34:49 PDT)
- Re: [AMBER] files for RED (Wed Oct 24 2012 - 05:13:03 PDT)
- Re: [AMBER] files for RED (Mon Oct 22 2012 - 08:44:09 PDT)
- Re: [AMBER] How Can I modify a amino acid in Amber (Sun Oct 21 2012 - 22:59:59 PDT)
- Re: [AMBER] about reproduction of HIS RESP charge (Thu Oct 18 2012 - 12:39:39 PDT)
- Re: [AMBER] RESP charge of the ligand (Tue Oct 16 2012 - 01:44:50 PDT)
- Re: [AMBER] NPA charge for the ligand (Mon Oct 15 2012 - 01:37:11 PDT)
- Re: [AMBER] How Can I modify a amino acid in Amber? (Sun Oct 14 2012 - 22:22:59 PDT)
- Re: [AMBER] How Can I modify a amino acid in Amber? (Sat Oct 13 2012 - 03:42:41 PDT)
- Re: [AMBER] forefield for Pyridoxal 5-phosphate (Fri Oct 12 2012 - 13:02:08 PDT)
- Re: [AMBER] QM method (Tue Oct 09 2012 - 09:03:48 PDT)
- [AMBER] Release of the R.E.D.-III.52 tools (Mon Oct 01 2012 - 02:32:02 PDT)
Gannett, Peter
- Re: [AMBER] Trajectory Clustering (Fri Oct 26 2012 - 05:47:03 PDT)
George Tzotzos
- Re: [AMBER] Trajectory Clustering (Fri Oct 26 2012 - 05:47:16 PDT)
- Re: [AMBER] Clustering VS constant rmsd (Thu Oct 18 2012 - 10:33:57 PDT)
- Re: [AMBER] Clustering VS constant rmsd (Wed Oct 17 2012 - 18:19:33 PDT)
Giulia
- [AMBER] extract velocities (Mon Oct 22 2012 - 09:11:48 PDT)
Guanglei Cui
- [AMBER] NMR restraints based on order parameters (Thu Oct 11 2012 - 07:42:45 PDT)
Gustavo Seabra
- Re: [AMBER] Trajectory Clustering (Fri Oct 26 2012 - 05:39:06 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Tue Oct 23 2012 - 12:51:43 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Tue Oct 23 2012 - 11:56:42 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Tue Oct 23 2012 - 08:50:57 PDT)
- Re: [AMBER] intdiel / extdiel (Thu Oct 18 2012 - 17:12:49 PDT)
- Re: [AMBER] intdiel / extdiel (Thu Oct 18 2012 - 15:35:40 PDT)
- [AMBER] intdiel / extdiel (Thu Oct 18 2012 - 11:01:02 PDT)
hari krishna
- [AMBER] Problem in running parallel (Tue Oct 30 2012 - 21:56:22 PDT)
- [AMBER] compilation aborted for ncsu-umbrella.F90 (code 1) (Tue Oct 23 2012 - 04:48:44 PDT)
hironori.kokubo.takeda.com
- [AMBER] different restraint_wt settings possble? (Thu Oct 18 2012 - 02:12:15 PDT)
- Re: [AMBER] the origin of ELEC DV/DL in the case of softcoreTIcalculation of the solute with no charge by crgmask (Sun Oct 14 2012 - 23:11:49 PDT)
- Re: [AMBER] the origin of ELEC DV/DL in the case of softcore TIcalculation of the solute with no charge by crgmask (Thu Oct 04 2012 - 20:27:07 PDT)
Ignacio J. General
- Re: [AMBER] umbrella sampling (Wed Oct 17 2012 - 07:22:31 PDT)
- Re: [AMBER] umbrella sampling (Wed Oct 17 2012 - 07:04:39 PDT)
- Re: [AMBER] umbrella sampling (Wed Oct 17 2012 - 05:13:19 PDT)
Ilyas Yildirim
- Re: [AMBER] Trajectory Clustering (Fri Oct 26 2012 - 05:47:15 PDT)
Ismail, Mohd F.
- Re: [AMBER] Cuda test hangs with Amber12 compiled with CUDA5 (Fri Oct 19 2012 - 11:12:59 PDT)
Jacopo Sgrignani
- Re: [AMBER] Joining two files (Mon Oct 29 2012 - 05:31:06 PDT)
Jason Swails
- Re: [AMBER] Request for MMPBSA files. (Tue Oct 30 2012 - 07:15:25 PDT)
- Re: [AMBER] Nonstandard residue: phosphotyrosine (Mon Oct 29 2012 - 08:05:43 PDT)
- Re: [AMBER] can i strip water energy from .out ? (Mon Oct 29 2012 - 06:12:03 PDT)
- Re: [AMBER] NetCDF and MTK++ configuration issues after applying bugfixes 15-27 (Fri Oct 26 2012 - 09:19:44 PDT)
- Re: [AMBER] can i strip water energy from .out ? (Fri Oct 26 2012 - 06:32:29 PDT)
- Re: [AMBER] Calculation of single atom radius of gyration (Wed Oct 24 2012 - 15:52:22 PDT)
- Re: [AMBER] Antechamber Warning Atomtype (Wed Oct 24 2012 - 12:55:43 PDT)
- Re: [AMBER] RNA - build a mismatch and a loop with NAB (Wed Oct 24 2012 - 04:30:27 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Tue Oct 23 2012 - 16:20:49 PDT)
- Re: [AMBER] compilation aborted for ncsu-umbrella.F90 (code 1) (Tue Oct 23 2012 - 06:19:01 PDT)
- Re: [AMBER] RNA - build a mismatch and a loop with NAB (Mon Oct 22 2012 - 11:40:34 PDT)
- [AMBER] MMPBSA.py error in AmberTools 12 fixed (Mon Oct 22 2012 - 08:57:10 PDT)
- Re: [AMBER] Bad atom type (Sat Oct 20 2012 - 19:42:49 PDT)
- Re: [AMBER] configure problem during installation (Sat Oct 20 2012 - 05:41:26 PDT)
- Re: [AMBER] Amber12 uninitialized variable in sander/nmr.F90 (Fri Oct 19 2012 - 15:21:51 PDT)
- Re: [AMBER] NaN question (Fri Oct 19 2012 - 10:07:32 PDT)
- Re: [AMBER] NaN question (Fri Oct 19 2012 - 07:49:50 PDT)
- Re: [AMBER] intdiel / extdiel (Thu Oct 18 2012 - 15:59:25 PDT)
- Re: [AMBER] intdiel / extdiel (Thu Oct 18 2012 - 12:26:22 PDT)
- Re: [AMBER] Concerning nonbonded exclusions and MMPBSA (Thu Oct 18 2012 - 08:57:58 PDT)
- Re: [AMBER] problem umbrella sampling and gpus (Thu Oct 18 2012 - 07:15:08 PDT)
- Re: [AMBER] short bonds in average pdb (Thu Oct 18 2012 - 06:44:31 PDT)
- Re: [AMBER] cuda pmemd failed (Thu Oct 18 2012 - 06:39:17 PDT)
- Re: [AMBER] "istrng" option in MMPBSA calculation (Thu Oct 18 2012 - 05:00:50 PDT)
- Re: [AMBER] distortion of the ligand during MD (Wed Oct 17 2012 - 08:35:52 PDT)
- Re: [AMBER] Accessible surface area (Wed Oct 17 2012 - 06:53:36 PDT)
- Re: [AMBER] ambpdb problems (Tue Oct 16 2012 - 10:17:24 PDT)
- Re: [AMBER] Incorrect Bond Assignment in AMBERTools 12 LeAP (Tue Oct 16 2012 - 10:15:35 PDT)
- Re: [AMBER] MMPBSA.py (Tue Oct 16 2012 - 10:01:29 PDT)
- Re: [AMBER] Input files for MMPBSA (Tue Oct 16 2012 - 04:25:43 PDT)
- Re: [AMBER] details of energy values for individual frames in MMPBSA.py calculations... (Mon Oct 15 2012 - 14:20:44 PDT)
- Re: [AMBER] job failed for REMD in cluster (Mon Oct 15 2012 - 13:09:01 PDT)
- Re: [AMBER] job failed for REMD in cluster (Mon Oct 15 2012 - 12:47:14 PDT)
- Re: [AMBER] details of energy values for individual frames in MMPBSA.py calculations... (Mon Oct 15 2012 - 12:42:00 PDT)
- Re: [AMBER] details of energy values for individual frames in MMPBSA.py calculations... (Mon Oct 15 2012 - 12:40:53 PDT)
- Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU (Mon Oct 15 2012 - 12:38:16 PDT)
- Re: [AMBER] umbrella sampling (Mon Oct 15 2012 - 05:07:24 PDT)
- Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE (Mon Oct 15 2012 - 05:05:55 PDT)
- Re: [AMBER] Input files for MMPBSA (Mon Oct 15 2012 - 04:52:56 PDT)
- Re: [AMBER] problem with calculating decomposition energy (Mon Oct 15 2012 - 04:50:34 PDT)
- Re: [AMBER] problems with the keyword "append" in trajout command... (Sat Oct 13 2012 - 11:39:43 PDT)
- Re: [AMBER] Notes and warnings in the generalized Born calculation (Fri Oct 12 2012 - 17:12:25 PDT)
- Re: [AMBER] XLeap Install Issue (Fri Oct 12 2012 - 16:47:40 PDT)
- Re: [AMBER] AmberTools 12 Build Issue (Fri Oct 12 2012 - 08:23:46 PDT)
- Re: [AMBER] completing C-term atoms after strip in ptraj (Thu Oct 11 2012 - 23:38:08 PDT)
- Re: [AMBER] problem restraint (Thu Oct 11 2012 - 08:10:06 PDT)
- Re: [AMBER] problem restraint (Thu Oct 11 2012 - 07:30:43 PDT)
- Re: [AMBER] How to express a right-handed amino acid in leap (Thu Oct 11 2012 - 07:03:04 PDT)
- Re: [AMBER] pmemd installation error (Thu Oct 11 2012 - 05:11:42 PDT)
- Re: [AMBER] unable to find mopac charges (Thu Oct 11 2012 - 01:22:20 PDT)
- Re: [AMBER] unable to find mopac charges (Wed Oct 10 2012 - 05:42:29 PDT)
- Re: [AMBER] idecomp and so on.... (Tue Oct 09 2012 - 14:11:49 PDT)
- Re: [AMBER] Question regarding COM and atom pulling (Tue Oct 09 2012 - 12:54:09 PDT)
- Re: [AMBER] idecomp and so on.... (Tue Oct 09 2012 - 12:26:07 PDT)
- Re: [AMBER] Problem related to the Amber11 installation in user account (Tue Oct 09 2012 - 05:15:53 PDT)
- Re: [AMBER] difference in amino94.xml (MCPB) and all_amino94.lib (leap) for CYM (Tue Oct 09 2012 - 04:47:48 PDT)
- Re: [AMBER] Problem related to the Amber11 installation in user account (Tue Oct 09 2012 - 02:03:25 PDT)
- Re: [AMBER] Problem related to the Amber11 installation in user account (Tue Oct 09 2012 - 01:06:30 PDT)
- Re: [AMBER] Problem related to the Amber11 installation in user account (Tue Oct 09 2012 - 00:22:37 PDT)
- Re: [AMBER] idecomp and so on.... (Mon Oct 08 2012 - 14:40:49 PDT)
- Re: [AMBER] Queastions Regarding Tutorial A11 NCSU Method (Mon Oct 08 2012 - 14:26:44 PDT)
- Re: [AMBER] Umbrella Sampling with Z-axis as Reaction Coordinate (Mon Oct 08 2012 - 03:38:44 PDT)
- Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" (Mon Oct 08 2012 - 03:37:18 PDT)
- Re: [AMBER] different between PBSA and MMPBSA ? (Mon Oct 08 2012 - 03:26:37 PDT)
- Re: [AMBER] Meaning of setting gbsa=0 in generalized Born calculations (Fri Oct 05 2012 - 07:27:42 PDT)
- Re: [AMBER] unable to find mopac charges (Fri Oct 05 2012 - 04:59:54 PDT)
- Re: [AMBER] Meaning of setting gbsa=0 in generalized Born calculations (Fri Oct 05 2012 - 04:45:19 PDT)
- Re: [AMBER] How do I generate prmtop files with bondi radii? (Thu Oct 04 2012 - 15:28:08 PDT)
- Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" (Thu Oct 04 2012 - 11:42:50 PDT)
- Re: [AMBER] X11 problems on Mac OS X 10.8 (Thu Oct 04 2012 - 09:02:56 PDT)
- Re: [AMBER] Problem in Installing Amber12/Tools in parallel (Thu Oct 04 2012 - 05:12:16 PDT)
- Re: [AMBER] simulation box shape changed (Thu Oct 04 2012 - 04:44:00 PDT)
- Re: [AMBER] Problem related to the trajectory analysis (Wed Oct 03 2012 - 18:38:23 PDT)
- Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" (Wed Oct 03 2012 - 18:33:04 PDT)
- Re: [AMBER] different between PBSA and MMPBSA ? (Tue Oct 02 2012 - 04:45:54 PDT)
- Re: [AMBER] Molecular Dynamic production (Tue Oct 02 2012 - 04:42:15 PDT)
- Re: [AMBER] Difference between ntx5 and ntx 7 (Tue Oct 02 2012 - 04:36:44 PDT)
- Re: [AMBER] different between PBSA and MMPBSA ? (Tue Oct 02 2012 - 04:31:00 PDT)
- Re: [AMBER] X11 problems on Mac OS X 10.8 (Mon Oct 01 2012 - 16:14:17 PDT)
- Re: [AMBER] Problem related to the parallel installation of Amber11 (Mon Oct 01 2012 - 13:10:09 PDT)
- Re: [AMBER] Problem related to the parallel installation of Amber11 (Mon Oct 01 2012 - 12:14:54 PDT)
- Re: [AMBER] Problem related to the parallel installation of Amber11 (Mon Oct 01 2012 - 11:04:19 PDT)
- Re: [AMBER] parallel MMPBSA: no of cores versus no of frames analyzed (Mon Oct 01 2012 - 10:18:21 PDT)
- Re: [AMBER] parallel MMPBSA: no of cores versus no of frames analyzed (Mon Oct 01 2012 - 09:32:04 PDT)
- Re: [AMBER] Problem related to the parallel installation of Amber11 (Mon Oct 01 2012 - 04:25:52 PDT)
- Re: [AMBER] MMPBSA error (Mon Oct 01 2012 - 04:23:46 PDT)
Jean-Christophe Ducom
- Re: [AMBER] Cuda test hangs with Amber12 compiled with CUDA5 (Fri Oct 19 2012 - 11:18:46 PDT)
- [AMBER] Cuda test hangs with Amber12 compiled with CUDA5 (Fri Oct 19 2012 - 10:40:27 PDT)
Jesper Sørensen
- [AMBER] Misleading leaprc with ff12 (Thu Oct 25 2012 - 10:00:24 PDT)
Jitesh Doshi
- Re: [AMBER] vlimit exceeded on step.. error (Thu Oct 18 2012 - 04:39:35 PDT)
- Re: [AMBER] vlimit exceeded on step.. error (Wed Oct 10 2012 - 05:24:00 PDT)
- Re: [AMBER] vlimit exceeded on step.. error (Wed Oct 10 2012 - 03:19:16 PDT)
- Re: [AMBER] vlimit exceeded on step.. error (Tue Oct 09 2012 - 04:18:50 PDT)
- Re: [AMBER] vlimit exceeded on step.. error (Fri Oct 05 2012 - 05:11:37 PDT)
- Re: [AMBER] vlimit exceeded on step.. error (Thu Oct 04 2012 - 23:44:22 PDT)
- [AMBER] vlimit exceeded on step.. error (Wed Oct 03 2012 - 06:19:52 PDT)
Joaquin Barroso Flores
- [AMBER] Error 'Created a new atom named:' (Thu Oct 25 2012 - 18:26:03 PDT)
Jocelyne Sogotongo
- [AMBER] about reproduction of HIS RESP charge (Wed Oct 17 2012 - 08:23:44 PDT)
Jodi Ann Hadden
- Re: [AMBER] questions about thermodynamic integration atom name and order (Tue Oct 30 2012 - 13:48:16 PDT)
Jonathan Gough
- Re: [AMBER] X11 problems on Mac OS X 10.8 (Thu Oct 04 2012 - 10:24:51 PDT)
- Re: [AMBER] X11 problems on Mac OS X 10.8 (Thu Oct 04 2012 - 08:08:32 PDT)
- Re: [AMBER] X11 problems on Mac OS X 10.8 (Tue Oct 02 2012 - 19:36:45 PDT)
Jonathan Sheehan
- Re: [AMBER] Centering a multimeric protein with solvateOct (Sat Oct 06 2012 - 18:07:47 PDT)
- Re: [AMBER] Centering a multimeric protein with solvateOct (Thu Oct 04 2012 - 12:24:29 PDT)
Jordan, Brad
- [AMBER] Random Seed (Wed Oct 17 2012 - 10:08:09 PDT)
Julio Dominguez
- Re: [AMBER] X11 problems on Mac OS X 10.8 (Wed Oct 03 2012 - 19:47:31 PDT)
- Re: [AMBER] AMBER Digest, Vol 292, Issue 2 (Tue Oct 02 2012 - 21:03:57 PDT)
- Re: [AMBER] X11 problems on Mac OS X 10.8 (Tue Oct 02 2012 - 15:09:29 PDT)
- [AMBER] X11 problems on Mac OS X 10.8 (Mon Oct 01 2012 - 13:59:59 PDT)
Kepa K. Burusco
- Re: [AMBER] TI Softcore potentials and SHAKE (Mon Oct 01 2012 - 09:02:03 PDT)
- Re: [AMBER] TI Softcore potentials and SHAKE (Mon Oct 01 2012 - 03:17:52 PDT)
- Re: [AMBER] TI Softcore potentials and SHAKE (Sun Sep 30 2012 - 16:12:10 PDT)
Kira Armacost
- Re: [AMBER] Distance calculations with ptraj (Mon Oct 08 2012 - 13:18:03 PDT)
- [AMBER] Distance calculations with ptraj (Sun Oct 07 2012 - 12:23:43 PDT)
Lachele Foley (Lists)
- [AMBER] Updated GLYCAM parameters (Mon Oct 29 2012 - 11:15:04 PDT)
- Re: [AMBER] glyco (Wed Oct 17 2012 - 18:27:22 PDT)
- Re: [AMBER] glyco (Mon Oct 15 2012 - 17:26:50 PDT)
- Re: [AMBER] glycoprotein (Sun Oct 14 2012 - 20:54:55 PDT)
- Re: [AMBER] glycoprotein (Sun Oct 14 2012 - 09:24:53 PDT)
Lorenzo Gontrani
- Re: [AMBER] Joining two files (Wed Oct 31 2012 - 05:45:13 PDT)
- Re: [AMBER] Joining two files (Mon Oct 29 2012 - 07:32:47 PDT)
M. L. Dodson
- Re: [AMBER] RNA - build a mismatch and a loop with NAB (Tue Oct 23 2012 - 05:31:59 PDT)
Mannan
- [AMBER] Hydrophobic cleft is solvent-exposed (Sun Oct 21 2012 - 19:06:17 PDT)
- [AMBER] QM method (Tue Oct 09 2012 - 06:24:04 PDT)
marawan hussain
- [AMBER] NVE ensemble for solvation (Tue Oct 09 2012 - 17:12:04 PDT)
Marc van der Kamp
- Re: [AMBER] Problem with CHAMBER (for RNA molecule) (Tue Oct 30 2012 - 05:09:20 PDT)
- [AMBER] Problem with CHAMBER (for RNA molecule) (Fri Oct 26 2012 - 01:59:17 PDT)
- [AMBER] aMD with implicit solvent? (Fri Oct 05 2012 - 08:30:52 PDT)
- [AMBER] phosphate moiety & igb model (Fri Oct 05 2012 - 03:10:21 PDT)
Marco Malvaldi
- Re: [AMBER] Joining two files (Wed Oct 31 2012 - 05:00:03 PDT)
- [AMBER] Joining two files (Mon Oct 29 2012 - 03:47:35 PDT)
Maria Ana Castro
- Re: [AMBER] X11 problems on Mac OS X 10.8 (Tue Oct 16 2012 - 08:11:51 PDT)
Mark Williamson
- Re: [AMBER] error when Chamber dealing with DNA, RNA and ATP (Tue Oct 30 2012 - 04:48:27 PDT)
- Re: [AMBER] Problem with CHAMBER (for RNA molecule) (Fri Oct 26 2012 - 08:28:04 PDT)
- Re: [AMBER] CHAMBER: error in finding bond type (Wed Oct 17 2012 - 05:29:17 PDT)
- Re: [AMBER] CHAMBER: error in finding bond type (Tue Oct 16 2012 - 05:24:38 PDT)
Mark Zottola
- Re: [AMBER] XLeap Install Issue (Fri Oct 12 2012 - 18:11:00 PDT)
- [AMBER] Part 2 of xleap (Fri Oct 12 2012 - 10:57:45 PDT)
- [AMBER] XLeap Install Issue (Fri Oct 12 2012 - 10:32:52 PDT)
- [AMBER] AmberTools 12 Build Issue (Fri Oct 12 2012 - 07:57:54 PDT)
Mary Varughese
- [AMBER] missing bonds and angles (Sun Oct 07 2012 - 22:36:17 PDT)
Maryam Hamzehee
- [AMBER] problem with decompostion energy (Wed Oct 17 2012 - 08:27:14 PDT)
- [AMBER] problem with calculating decomposition energy (Sun Oct 14 2012 - 23:23:27 PDT)
Maximilian Ebert
- Re: [AMBER] Amber and P450 cytochromes (Wed Oct 31 2012 - 08:53:56 PDT)
- [AMBER] Amber and P450 cytochromes (Wed Oct 31 2012 - 07:05:21 PDT)
mehdi bagherpoor
- [AMBER] pmemd installation error (Thu Oct 11 2012 - 04:10:30 PDT)
mhclewett.msn.com
- Re: [AMBER] NaN question (Sat Oct 20 2012 - 08:43:59 PDT)
- Re: [AMBER] NaN question (Fri Oct 19 2012 - 09:48:09 PDT)
- Re: [AMBER] NaN question (Fri Oct 19 2012 - 09:46:58 PDT)
- [AMBER] NaN question (Fri Oct 19 2012 - 07:36:49 PDT)
Miguel Ortiz Lombardia
- Re: [AMBER] NetCDF and MTK++ configuration issues after applying bugfixes 15-27 (Fri Oct 26 2012 - 14:39:17 PDT)
Miguel Ortiz Lombardía
- [AMBER] NetCDF and MTK++ configuration issues after applying bugfixes 15-27 (Fri Oct 26 2012 - 08:42:51 PDT)
Mike Limb
- [AMBER] CHAMBER: error in finding bond type (Tue Oct 16 2012 - 04:28:26 PDT)
Mo Chen
- Re: [AMBER] Inquiry about how writing out pressure tensor (Mon Oct 29 2012 - 12:29:50 PDT)
- Re: [AMBER] Inquiry about how writing out pressure tensor (Mon Oct 29 2012 - 00:13:12 PDT)
- Re: [AMBER] Inquiry about how writing out pressure tensor (Mon Oct 29 2012 - 00:04:03 PDT)
- Re: [AMBER] Inquiry about how writing out pressure tensor (Fri Oct 26 2012 - 18:57:51 PDT)
- [AMBER] Inquiry about how writing out pressure tensor (Fri Oct 26 2012 - 15:57:17 PDT)
Mu Xia
- [AMBER] Computational methods to explain the small regioselectivity (Wed Oct 24 2012 - 01:21:55 PDT)
- [AMBER] short bonds in average pdb (Thu Oct 18 2012 - 02:40:34 PDT)
- Re: [AMBER] distortion of the ligand during MD (Wed Oct 17 2012 - 07:02:42 PDT)
- [AMBER] distortion of the ligand during MD (Wed Oct 17 2012 - 04:12:45 PDT)
- [AMBER] RESP charge of the ligand (Mon Oct 15 2012 - 07:08:17 PDT)
- [AMBER] NPA charge for the ligand (Mon Oct 15 2012 - 00:58:30 PDT)
Nadine Homeyer
- Re: [AMBER] MMPBSA error (Mon Oct 01 2012 - 05:49:38 PDT)
Niel Henriksen
- Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU (Tue Oct 16 2012 - 10:06:17 PDT)
- Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU (Mon Oct 15 2012 - 12:58:48 PDT)
- Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU (Mon Oct 15 2012 - 12:07:39 PDT)
- Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU (Mon Oct 15 2012 - 09:39:12 PDT)
Nihal Korkmaz
- Re: [AMBER] completing C-term atoms after strip in ptraj (Fri Oct 12 2012 - 11:48:36 PDT)
- [AMBER] completing C-term atoms after strip in ptraj (Thu Oct 11 2012 - 16:53:56 PDT)
Olguin, Marco A
- Re: [AMBER] Error 'Created a new atom named:' (Thu Oct 25 2012 - 18:43:24 PDT)
Osman, Roman
- Re: [AMBER] Bad atom type (Sun Oct 21 2012 - 17:58:56 PDT)
- [AMBER] Bad atom type (Sat Oct 20 2012 - 17:12:46 PDT)
PAUL NEWMAN
- Re: [AMBER] Nonstandard residue: phosphotyrosine (Mon Oct 29 2012 - 07:46:41 PDT)
- [AMBER] Nonstandard residue: phosphotyrosine (Mon Oct 29 2012 - 07:03:47 PDT)
pavel.banas.upol.cz
- Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU (Tue Oct 16 2012 - 13:57:04 PDT)
- Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU (Mon Oct 15 2012 - 11:25:17 PDT)
- [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU (Mon Oct 15 2012 - 00:22:33 PDT)
peter.stauffert.boehringer-ingelheim.com
- Re: [AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? (Tue Oct 23 2012 - 05:42:10 PDT)
Pyle, Ronald
- [AMBER] ambpdb problems (Tue Oct 16 2012 - 07:59:00 PDT)
Rahul Banerjee
- [AMBER] Amber12 installation and testing (Tue Oct 30 2012 - 10:47:09 PDT)
Rajiv
- [AMBER] Using NMR restraints for G-Quadruplex structure (Tue Oct 09 2012 - 23:07:48 PDT)
Ray Luo, Ph.D.
- Re: [AMBER] Non-polar solvation free energy in AMBER11 MMPBSA.py (Fri Oct 12 2012 - 10:25:22 PDT)
- Re: [AMBER] Non-polar solvation free energy in AMBER11 MMPBSA.py (Thu Oct 11 2012 - 14:25:38 PDT)
Rebeca García Fandiño
- [AMBER] problem with antechamber and ESP (Thu Oct 11 2012 - 05:31:12 PDT)
Reinis
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Wed Oct 24 2012 - 15:55:05 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Wed Oct 24 2012 - 11:30:25 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Wed Oct 24 2012 - 01:09:25 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Tue Oct 23 2012 - 13:55:26 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Tue Oct 23 2012 - 12:41:11 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Tue Oct 23 2012 - 09:33:54 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Tue Oct 23 2012 - 09:21:05 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Tue Oct 23 2012 - 08:37:25 PDT)
- Re: [AMBER] [PATCH 0/8] AmberTools cleanups (Tue Oct 23 2012 - 08:08:25 PDT)
Reinis Danne
- [AMBER] [PATCH 8/8] amber_outputs.py: Format floats in csv output (Mon Oct 22 2012 - 15:15:01 PDT)
- [AMBER] [PATCH 7/8] AmberTools: Fix parallel tests (Mon Oct 22 2012 - 15:15:00 PDT)
- [AMBER] [PATCH 6/8] AmberTools: Tests should fail when they fail (Mon Oct 22 2012 - 15:14:59 PDT)
- [AMBER] [PATCH 5/8] test/nab: Use paths to scripts (Mon Oct 22 2012 - 15:14:58 PDT)
- [AMBER] [PATCH 2/8] dsarpack.f: Move into sff to allow build against arpack-ng (Mon Oct 22 2012 - 15:14:55 PDT)
- [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Mon Oct 22 2012 - 15:14:57 PDT)
- [AMBER] [PATCH 3/8] nab.c: Don't hardcode CPP path (Mon Oct 22 2012 - 15:14:56 PDT)
- [AMBER] [PATCH 1/8] AmberTools: Fix buffer overflows in mdgx, nab and ptraj (Mon Oct 22 2012 - 15:14:54 PDT)
- [AMBER] [PATCH 0/8] AmberTools cleanups (Mon Oct 22 2012 - 15:14:53 PDT)
Renuka Ganesan
- [AMBER] genmetalFF.sh (Tue Oct 16 2012 - 07:34:19 PDT)
Robert Crovella
- Re: [AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? (Fri Oct 19 2012 - 06:50:05 PDT)
Romelia Salomon
- Re: [AMBER] Estimating time in AMD (Mon Oct 08 2012 - 01:25:49 PDT)
Ross Walker
- Re: [AMBER] error when Chamber dealing with DNA, RNA and ATP (Tue Oct 30 2012 - 11:03:56 PDT)
- Re: [AMBER] Amber12 installation and testing (Tue Oct 30 2012 - 10:59:58 PDT)
- Re: [AMBER] Inquiry about how writing out pressure tensor (Fri Oct 26 2012 - 16:48:16 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Wed Oct 24 2012 - 12:52:03 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Wed Oct 24 2012 - 09:15:18 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Tue Oct 23 2012 - 10:00:36 PDT)
- Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build (Tue Oct 23 2012 - 09:26:34 PDT)
- Re: [AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? (Tue Oct 23 2012 - 09:21:14 PDT)
- Re: [AMBER] cuda pmemd failed (Fri Oct 19 2012 - 11:31:05 PDT)
- Re: [AMBER] Cuda test hangs with Amber12 compiled with CUDA5 (Fri Oct 19 2012 - 11:19:59 PDT)
- Re: [AMBER] NaN question (Fri Oct 19 2012 - 11:19:04 PDT)
- Re: [AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? (Fri Oct 19 2012 - 11:09:32 PDT)
- [AMBER] Request: Tell us your CUDA story (Tue Oct 16 2012 - 10:19:30 PDT)
- Re: [AMBER] GPU accelerated - accelerated MD (Was: Count number of frames in any trajectory file) (Mon Oct 15 2012 - 13:44:07 PDT)
- Re: [AMBER] job failed for REMD in cluster (Mon Oct 15 2012 - 12:07:41 PDT)
- Re: [AMBER] job failed for REMD in cluster (Mon Oct 15 2012 - 12:06:32 PDT)
- Re: [AMBER] Can not find dhfr containing 23,558 atoms in AMBER (Tue Oct 09 2012 - 01:11:59 PDT)
- Re: [AMBER] Errors in Amber12 installation (Mon Oct 08 2012 - 13:26:49 PDT)
- Re: [AMBER] Asterisks in the restart file (Mon Oct 08 2012 - 05:44:25 PDT)
Sajeewa Pemasinghe
- [AMBER] Meaning of the term "pre-equilibrated" waters (Sun Oct 21 2012 - 09:54:10 PDT)
- Re: [AMBER] How Can I modify a amino acid in Amber? (Sat Oct 13 2012 - 05:33:52 PDT)
- Re: [AMBER] How Can I modify a amino acid in Amber? (Sat Oct 13 2012 - 00:48:49 PDT)
- Re: [AMBER] Fwd: Notes and warnings in the generalized Born calculation (Fri Oct 12 2012 - 18:37:02 PDT)
- Re: [AMBER] Fwd: Notes and warnings in the generalized Born calculation (Fri Oct 12 2012 - 18:36:20 PDT)
- Re: [AMBER] Notes and warnings in the generalized Born calculation (Fri Oct 12 2012 - 18:35:39 PDT)
- [AMBER] Fwd: Notes and warnings in the generalized Born calculation (Fri Oct 12 2012 - 14:23:48 PDT)
- [AMBER] Notes and warnings in the generalized Born calculation (Fri Oct 12 2012 - 11:24:45 PDT)
- Re: [AMBER] Problems in Amber12 parallel installation (Tue Oct 09 2012 - 11:56:45 PDT)
- [AMBER] Problems in Amber12 parallel installation (Mon Oct 08 2012 - 20:38:34 PDT)
- Re: [AMBER] Errors in Amber12 installation (Mon Oct 08 2012 - 19:11:21 PDT)
- Re: [AMBER] Errors in Amber12 installation (Mon Oct 08 2012 - 19:10:58 PDT)
- Re: [AMBER] Errors in Amber12 installation (Mon Oct 08 2012 - 19:09:52 PDT)
- Re: [AMBER] Errors in Amber12 installation (Mon Oct 08 2012 - 17:30:25 PDT)
- [AMBER] Errors in Amber12 installation (Mon Oct 08 2012 - 11:28:04 PDT)
- Re: [AMBER] Meaning of setting gbsa=0 in generalized Born calculations (Fri Oct 05 2012 - 07:48:36 PDT)
- [AMBER] Meaning of setting gbsa=0 in generalized Born calculations (Thu Oct 04 2012 - 21:01:50 PDT)
- Re: [AMBER] How do I generate prmtop files with bondi radii? (Thu Oct 04 2012 - 15:52:22 PDT)
- [AMBER] How do I generate prmtop files with bondi radii? (Thu Oct 04 2012 - 15:20:36 PDT)
- [AMBER] Problem in Installing Amber12/Tools in parallel (Wed Oct 03 2012 - 23:40:55 PDT)
- Re: [AMBER] Setting the random seed in Langevin dynamics (Wed Oct 03 2012 - 08:53:53 PDT)
- Re: [AMBER] Setting the random seed in Langevin dynamics (Wed Oct 03 2012 - 06:38:18 PDT)
- Re: [AMBER] To which ensemble does generalized Born trajectory fall? (Wed Oct 03 2012 - 06:31:03 PDT)
- Re: [AMBER] Setting the random seed in Langevin dynamics (Wed Oct 03 2012 - 06:19:55 PDT)
- [AMBER] Setting the random seed in Langevin dynamics (Tue Oct 02 2012 - 20:57:37 PDT)
- [AMBER] To which ensemble does generalized Born trajectory fall? (Tue Oct 02 2012 - 20:43:44 PDT)
- [AMBER] effect neutralizing ions on value of "saltcon" in generalized Born model (Mon Oct 01 2012 - 13:36:09 PDT)
Sangeetha B
- Re: [AMBER] difference in amino94.xml (MCPB) and all_amino94.lib (leap) for CYM (Wed Oct 10 2012 - 04:27:22 PDT)
- Re: [AMBER] difference in amino94.xml (MCPB) and all_amino94.lib (leap) for CYM (Wed Oct 10 2012 - 04:14:40 PDT)
- [AMBER] difference in amino94.xml (MCPB) and all_amino94.lib (leap) for CYM (Tue Oct 09 2012 - 03:59:19 PDT)
- [AMBER] different Partial charges for CYM in amino94.xml (MCPB) and all_amino94.lib (leap) (Mon Oct 01 2012 - 00:30:48 PDT)
Sangmin Lee
- Re: [AMBER] Obtain trajectory in NAB (Thu Oct 04 2012 - 22:17:58 PDT)
- [AMBER] Obtain trajectory in NAB (Thu Oct 04 2012 - 01:13:46 PDT)
Sanjib Paul
- [AMBER] Download problem of amber12 (Tue Oct 30 2012 - 23:25:35 PDT)
- [AMBER] What does the word 'DIPGRP - 1' mean? (Thu Oct 04 2012 - 05:50:37 PDT)
Scott Le Grand
- Re: [AMBER] cuda pmemd failed (Thu Oct 18 2012 - 11:02:15 PDT)
- Re: [AMBER] job failed for REMD in cluster (Mon Oct 15 2012 - 13:47:04 PDT)
- Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU (Mon Oct 15 2012 - 10:56:46 PDT)
setyanto md
- Re: [AMBER] different between PBSA and MMPBSA ? (Mon Oct 08 2012 - 04:01:13 PDT)
- Re: [AMBER] different between PBSA and MMPBSA ? (Mon Oct 08 2012 - 01:05:34 PDT)
- Re: [AMBER] different between PBSA and MMPBSA ? (Tue Oct 02 2012 - 04:41:26 PDT)
- Re: [AMBER] different between PBSA and MMPBSA ? (Tue Oct 02 2012 - 02:59:49 PDT)
- [AMBER] different between PBSA and MMPBSA ? (Tue Oct 02 2012 - 02:00:20 PDT)
Shafinaz Chowdhury
- Re: [AMBER] Count number of frames in any trajectory file (Mon Oct 15 2012 - 13:14:39 PDT)
Shashidhar Rao
- Re: [AMBER] details of energy values for individual frames in MMPBSA.py calculations... (Mon Oct 15 2012 - 13:19:59 PDT)
- Re: [AMBER] details of energy values for individual frames in MMPBSA.py calculations... (Mon Oct 15 2012 - 13:14:13 PDT)
- Re: [AMBER] details of energy values for individual frames in MMPBSA.py calculations... (Mon Oct 15 2012 - 12:25:09 PDT)
- [AMBER] details of energy values for individual frames in MMPBSA.py calculations... (Mon Oct 15 2012 - 12:12:41 PDT)
- [AMBER] problems with the keyword "append" in trajout command... (Fri Oct 12 2012 - 11:46:24 PDT)
Sindrila Dutta banik
- [AMBER] Problem related to the radial distribution function (Wed Oct 10 2012 - 04:55:31 PDT)
- [AMBER] Basis of sander of Amber11 and Amber9 (Tue Oct 09 2012 - 13:12:27 PDT)
- [AMBER] Problem related to the Amber11 installation in user account (Tue Oct 09 2012 - 02:19:36 PDT)
- Re: [AMBER] Problem related to the Amber11 installation in user account (Tue Oct 09 2012 - 01:25:52 PDT)
- [AMBER] Problem related to the Amber11 installation in user account (Tue Oct 09 2012 - 00:59:16 PDT)
- [AMBER] Problem related to the Amber11 installation in user account (Mon Oct 08 2012 - 21:39:46 PDT)
- [AMBER] Problem related to the analysis of mdcrd (Wed Oct 03 2012 - 23:48:59 PDT)
- [AMBER] Problem related to the trajectory analysis (Wed Oct 03 2012 - 11:20:10 PDT)
- [AMBER] Difference between ntx5 and ntx 7 (Mon Oct 01 2012 - 23:01:14 PDT)
- [AMBER] Problem related to the parallel installation of Amber11 (Mon Oct 01 2012 - 13:21:16 PDT)
- [AMBER] Problem related to the parallel installation of Amber11 (Mon Oct 01 2012 - 12:57:42 PDT)
- [AMBER] Problem related to the parallel installation of Amber11 (Mon Oct 01 2012 - 11:49:35 PDT)
- Re: [AMBER] Problem related to the parallel installation of Amber11 (Mon Oct 01 2012 - 10:39:24 PDT)
- Re: [AMBER] Problem related to the parallel installation of Amber11 (Mon Oct 01 2012 - 02:11:47 PDT)
- [AMBER] Problem related to the parallel installation og Amber11 (Sun Sep 30 2012 - 09:36:23 PDT)
Soumya Lipsa Rath
- Re: [AMBER] Estimating time in AMD (Mon Oct 08 2012 - 07:19:30 PDT)
- Re: [AMBER] Estimating time in AMD (Mon Oct 08 2012 - 02:31:46 PDT)
- [AMBER] Estimating time in AMD (Sun Oct 07 2012 - 22:08:04 PDT)
steinbrt.rci.rutgers.edu
- Re: [AMBER] questions about thermodynamic integration atom name and order (Wed Oct 31 2012 - 01:35:56 PDT)
- Re: [AMBER] Nonstandard residue: phosphotyrosine (Mon Oct 29 2012 - 11:22:41 PDT)
- Re: [AMBER] short bonds in average pdb (Thu Oct 18 2012 - 07:09:54 PDT)
- Re: [AMBER] Temperature in TI run (Wed Oct 17 2012 - 00:48:13 PDT)
Steven Neumann
- [AMBER] Side chain correction for ASP (Wed Oct 17 2012 - 08:35:06 PDT)
- [AMBER] Side chain correction for Asp (Wed Oct 17 2012 - 07:43:35 PDT)
Su, Shiquan
- Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" (Sun Oct 07 2012 - 14:35:48 PDT)
- Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" (Thu Oct 04 2012 - 10:21:25 PDT)
- [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" (Wed Oct 03 2012 - 12:57:54 PDT)
subramanian boopathi
- [AMBER] Reg: error in equilibration (Mon Oct 08 2012 - 05:09:02 PDT)
Syed Tarique Moin
- Re: [AMBER] simulation box shape changed (Thu Oct 11 2012 - 02:10:47 PDT)
- [AMBER] simulation box shape changed (Wed Oct 03 2012 - 23:46:41 PDT)
Terry
- Re: [AMBER] Problem in running parallel (Tue Oct 30 2012 - 22:33:15 PDT)
Thomas Evangelidis
- [AMBER] about salt concentration (Thu Oct 11 2012 - 02:23:28 PDT)
Tomasz Borowski
- Re: [AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? (Mon Oct 29 2012 - 05:25:45 PDT)
- Re: [AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? (Tue Oct 23 2012 - 04:40:02 PDT)
- [AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? (Fri Oct 19 2012 - 01:13:38 PDT)
Tommy Yap
- Re: [AMBER] Input files for MMPBSA (Mon Oct 15 2012 - 18:59:35 PDT)
- [AMBER] Input files for MMPBSA (Sun Oct 14 2012 - 19:54:24 PDT)
Tong Zhu
- Re: [AMBER] can i strip water energy from .out ? (Sun Oct 28 2012 - 21:45:19 PDT)
- Re: [AMBER] If i strip water from the trajectory files, would it influence the analysis results? (Sun Oct 28 2012 - 21:43:06 PDT)
- [AMBER] Non-polar solvation free energy in AMBER11 MMPBSA.py (Wed Oct 10 2012 - 23:55:07 PDT)
Tru Huynh
- Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" (Mon Oct 08 2012 - 06:27:14 PDT)
- Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" (Fri Oct 05 2012 - 00:42:03 PDT)
Urszula Uciechowska
- Re: [AMBER] Fwd: Re: files for RED (Wed Oct 31 2012 - 00:55:35 PDT)
- Re: [AMBER] Fwd: Re: files for RED (Tue Oct 30 2012 - 01:54:51 PDT)
- Re: [AMBER] files for RED (Sat Oct 27 2012 - 07:30:06 PDT)
- Re: [AMBER] files for RED (Thu Oct 25 2012 - 04:10:02 PDT)
- Re: [AMBER] files for RED (Wed Oct 24 2012 - 03:23:44 PDT)
- [AMBER] files for RED (Mon Oct 22 2012 - 01:52:17 PDT)
vaibhav dixit
- Re: [AMBER] configure problem during installation (Sat Oct 20 2012 - 07:45:38 PDT)
- [AMBER] configure problem during installation (Sat Oct 20 2012 - 01:40:26 PDT)
- Re: [AMBER] short bonds in average pdb (Thu Oct 18 2012 - 07:37:44 PDT)
- Re: [AMBER] Clustering VS constant rmsd (Wed Oct 17 2012 - 10:47:02 PDT)
- [AMBER] bad atom type: cl error in MMPBSA decomp (Fri Oct 12 2012 - 02:43:39 PDT)
- [AMBER] angle between axes of two helices (Wed Oct 10 2012 - 22:24:38 PDT)
- Re: [AMBER] how to predict time for MMPBSA decomp analysis (Tue Oct 09 2012 - 23:25:06 PDT)
- Re: [AMBER] diff. between avg/rep structures & connectivity problem in PDB files (Mon Oct 08 2012 - 08:15:44 PDT)
- [AMBER] diff. between avg/rep structures & connectivity problem in PDB files (Sun Oct 07 2012 - 02:24:02 PDT)
- Re: [AMBER] PairwiseDistance file location (Fri Oct 05 2012 - 18:58:53 PDT)
- Re: [AMBER] PairwiseDistance file location (Thu Oct 04 2012 - 22:10:40 PDT)
- [AMBER] PairwiseDistance file location (Thu Oct 04 2012 - 01:28:11 PDT)
Vijay Manickam Achari
- Re: [AMBER] calculating intramolecular hydrogen bonding (Mon Oct 15 2012 - 01:19:08 PDT)
- [AMBER] calculating intramolecular hydrogen bonding (Fri Oct 05 2012 - 00:29:22 PDT)
Vlad Cojocaru
- Re: [AMBER] parallel MMPBSA: no of cores versus no of frames analyzed (Mon Oct 01 2012 - 09:39:06 PDT)
- [AMBER] parallel MMPBSA: no of cores versus no of frames analyzed (Mon Oct 01 2012 - 09:10:47 PDT)
Xioling Chuang
- [AMBER] Pairwise decoposition (MMPBSA) (Tue Oct 16 2012 - 19:34:41 PDT)
Yanyan MENG
- [AMBER] rmsd rmsf (Tue Oct 30 2012 - 00:50:10 PDT)
yanyuna
- Re: [AMBER] glyco (Mon Oct 15 2012 - 19:58:57 PDT)
- [AMBER] glyco (Mon Oct 15 2012 - 01:59:46 PDT)
- [AMBER] glycoprotein (Sun Oct 14 2012 - 19:59:01 PDT)
- [AMBER] glycoprotein (Sat Oct 13 2012 - 23:27:26 PDT)
Yi An
- [AMBER] antechamber limitation on molecule size (Wed Oct 31 2012 - 12:05:59 PDT)
Yu-Ming Huang
- [AMBER] tleap has error by applying amber ff03ua (Tue Oct 30 2012 - 17:04:29 PDT)
Yubo Fan
- [AMBER] cuda pmemd failed (Thu Oct 18 2012 - 06:37:55 PDT)
- [AMBER] cuda pmemd failed (Thu Oct 18 2012 - 06:00:05 PDT)
- [AMBER] cuda pmemd failed (Thu Oct 18 2012 - 04:51:52 PDT)
- [AMBER] cuda pmemd failed (Thu Oct 18 2012 - 00:41:11 PDT)
Yulin Huang
- Re: [AMBER] questions about thermodynamic integration atom name and order (Wed Oct 31 2012 - 19:10:16 PDT)
- Re: [AMBER] questions about thermodynamic integration atom name and order (Wed Oct 31 2012 - 09:17:59 PDT)
- Re: [AMBER] questions about thermodynamic integration atom name and order (Wed Oct 31 2012 - 08:30:36 PDT)
- Re: [AMBER] questions about thermodynamic integration atom name and order (Wed Oct 31 2012 - 08:27:49 PDT)
- [AMBER] questions about thermodynamic integration atom name and order (Mon Oct 29 2012 - 07:35:55 PDT)
- [AMBER] join amber mailing list (Fri Oct 26 2012 - 13:44:50 PDT)
Yun Shi
- Re: [AMBER] Atom-type for aromatic carbon attached by amide nitrogen (Tue Oct 16 2012 - 20:29:13 PDT)
- Re: [AMBER] Atom-type for aromatic carbon attached by amide nitrogen (Tue Oct 16 2012 - 16:07:01 PDT)
- [AMBER] Atom-type for aromatic carbon attached by amide nitrogen (Tue Oct 16 2012 - 12:39:15 PDT)
zhukk
- [AMBER] Arsenic VDW parameters (Tue Oct 09 2012 - 01:11:34 PDT)
Γιώργος Λαμπρινίδης
- Re: [AMBER] Queastions Regarding Tutorial A11 NCSU Method (Mon Oct 08 2012 - 23:43:48 PDT)
- [AMBER] Queastions Regarding Tutorial A11 NCSU Method (Mon Oct 08 2012 - 12:48:17 PDT)
Алексей Раевский
- [AMBER] Antechamber preparartion (Mon Oct 29 2012 - 04:57:10 PDT)
千语千寻
- Re: [AMBER] questions about thermodynamic integration atom name and order (Mon Oct 29 2012 - 07:59:04 PDT)
- [AMBER] If i strip water from the trajectory files, would it influence the analysis results? (Sun Oct 28 2012 - 19:17:17 PDT)
- [AMBER] can i strip water energy from .out ? (Thu Oct 25 2012 - 23:22:30 PDT)
陶晓芳
- [AMBER] Can not find dhfr containing 23,558 atoms in AMBER (Mon Oct 08 2012 - 20:18:53 PDT)
강현아
- [AMBER] space-time correlation in AMBER (Tue Oct 30 2012 - 19:38:58 PDT)

Amber Archive Oct 2012 by author