Amber Archive Mar 2011: by author

abc def
- [AMBER] RMSD Calculation (Fri Mar 18 2011 - 09:47:41 PDT)
Adrian Roitberg
- Re: [AMBER] Inconsistencies between reported lines and executed lines in source code (Thu Mar 31 2011 - 11:33:19 PDT)
- Re: [AMBER] How to get the free energy landscape from a MD simulation? (Thu Mar 24 2011 - 08:23:24 PDT)
- Re: [AMBER] how to calculate scattering trajectory (Mon Mar 21 2011 - 08:16:50 PDT)
- Re: [AMBER] how to calculate scattering trajectory (Sun Mar 20 2011 - 14:09:47 PDT)
- Re: [AMBER] strip command usage in ptraj (Sun Mar 13 2011 - 08:57:31 PDT)
- Re: [AMBER] strip command usage in ptraj (Sun Mar 13 2011 - 08:41:44 PDT)
- Re: [AMBER] strip command usage in ptraj (Sun Mar 13 2011 - 08:23:26 PDT)
- Re: [AMBER] acceptance probabilities remd (Tue Mar 08 2011 - 03:17:58 PST)
Albert Lee
- Re: [AMBER] Inconsistencies between reported lines and executed lines in source code (Thu Mar 31 2011 - 12:39:13 PDT)
- Re: [AMBER] Inconsistencies between reported lines and executed lines in source code (Thu Mar 31 2011 - 11:56:06 PDT)
- [AMBER] Inconsistencies between reported lines and executed lines in source code (Thu Mar 31 2011 - 11:12:23 PDT)
Alessio Atzori
- [AMBER] R: Exchange Acceptance Ratio (Wed Mar 30 2011 - 06:21:48 PDT)
- [AMBER] Exchange Acceptance Ratio (Wed Mar 30 2011 - 03:57:36 PDT)
- [AMBER] R: Flags of secstruct (Thu Mar 24 2011 - 17:21:59 PDT)
- [AMBER] Flags of secstruct (Tue Mar 22 2011 - 08:14:11 PDT)
Alexander Metz
- [AMBER] ptraj minimum rmsd in presence of homotopic atoms (Tue Mar 29 2011 - 02:21:21 PDT)
Ali M. Naserian-Nik
- Re: [AMBER] Restart Problem: The results of an integrated simulation and restarted simulations are not equal! (Tue Mar 01 2011 - 00:42:52 PST)
amit dong
- Re: [AMBER] nmode calculations (Fri Mar 25 2011 - 11:39:40 PDT)
- [AMBER] nmode calculations (Fri Mar 25 2011 - 11:12:24 PDT)
- [AMBER] nmode memory issue (Mon Mar 21 2011 - 10:01:05 PDT)
Andre Serobian
- Re: [AMBER] nmropt modes for GPU accelerated pmemd 11 (Wed Mar 30 2011 - 13:09:43 PDT)
- Re: [AMBER] nmropt modes for GPU accelerated pmemd 11 (Wed Mar 30 2011 - 12:43:10 PDT)
- [AMBER] nmropt modes for GPU accelerated pmemd 11 (Wed Mar 30 2011 - 00:24:04 PDT)
- Re: [AMBER] Assertion failed: nat < 5000, file makeDIST_RST (Wed Mar 16 2011 - 17:51:37 PDT)
- Re: [AMBER] Assertion failed: nat < 5000, file makeDIST_RST (Tue Mar 15 2011 - 18:44:02 PDT)
- [AMBER] Assertion failed: nat < 5000, file makeDIST_RST (Tue Mar 15 2011 - 13:20:47 PDT)
Andreas Goetz
- [AMBER] AMBER Workshop in Shanghai, China, August 22-26 2011 (Tue Mar 15 2011 - 13:29:25 PDT)
Andrew Jewett
- Re: [AMBER] Pressure regulation and position restraints (Thu Mar 10 2011 - 18:51:55 PST)
- Re: [AMBER] missing AMBER features for simulating surfaces and linear assemblies (Wed Mar 09 2011 - 13:08:31 PST)
- Re: [AMBER] missing AMBER features for simulating surfaces and linear assemblies (Wed Mar 09 2011 - 13:00:22 PST)
- [AMBER] Pressure regulation and position restraints (Mon Mar 07 2011 - 04:33:36 PST)
- [AMBER] missing AMBER features for simulating surfaces and linear assemblies (Mon Mar 07 2011 - 02:18:31 PST)
Anselm Horn
- Re: [AMBER] non standard Alanine (Fri Mar 04 2011 - 07:55:01 PST)
Antje Wolf
- Re: [AMBER] NPT simulation crash using a GPU CARD for a simulation carried out in a organic explicit solvent (Tue Mar 01 2011 - 23:44:39 PST)
asakiayumikio.gmail.com
- Re: [AMBER] how to calculate the B-factor of crystal pdb (Mon Mar 14 2011 - 07:59:10 PDT)
- [AMBER] how to calculate the B-factor of crystal pdb (Sun Mar 13 2011 - 23:58:43 PDT)
- Re: [AMBER] strip command usage in ptraj (Sun Mar 13 2011 - 18:48:41 PDT)
- Re: [AMBER] strip command usage in ptraj (Sun Mar 13 2011 - 09:05:00 PDT)
- Re: [AMBER] strip command usage in ptraj (Sun Mar 13 2011 - 08:47:13 PDT)
- Re: [AMBER] strip command usage in ptraj (Sun Mar 13 2011 - 08:30:26 PDT)
- [AMBER] strip command usage in ptraj (Sun Mar 13 2011 - 08:14:46 PDT)
- Re: [AMBER] questions about the input file of MD process (Sun Mar 13 2011 - 08:07:19 PDT)
- Re: [AMBER] questions about the input file of MD process (Sun Mar 13 2011 - 08:04:28 PDT)
- Re: [AMBER] questions about the input file of MD process (Sun Mar 13 2011 - 07:34:15 PDT)
- [AMBER] questions about the input file of MD process (Sun Mar 13 2011 - 00:45:44 PST)
- [AMBER] question about the distance of pronton transfer and acetylation (Tue Mar 08 2011 - 18:19:42 PST)
- Re: [AMBER] forefile of acetyl coenzyme A (Mon Mar 07 2011 - 06:30:06 PST)
- Re: [AMBER] how to deal with flexibility of peptide during prod. process (Mon Mar 07 2011 - 06:28:24 PST)
- Re: [AMBER] forefile of acetyl coenzyme A (Mon Mar 07 2011 - 06:16:54 PST)
- [AMBER] forefile of acetyl coenzyme A (Mon Mar 07 2011 - 06:07:27 PST)
- [AMBER] how to deal with flexibility of peptide during prod. process (Mon Mar 07 2011 - 05:57:37 PST)
aseal.klyuniv.ac.in
- [AMBER] Request for a quotation of AMBER (Mon Mar 07 2011 - 23:38:14 PST)
Astrid Maaß
- Re: [AMBER] protein charge (Mon Mar 21 2011 - 07:23:04 PDT)
Aust, Susanne
- Re: [AMBER] interaction energy (Mon Mar 14 2011 - 06:32:01 PDT)
- Re: [AMBER] interaction energy (Thu Mar 10 2011 - 03:24:16 PST)
- [AMBER] interaction energy (Thu Mar 10 2011 - 00:34:28 PST)
Azat Mukhametov
- [AMBER] Compatibility Question (Mon Mar 14 2011 - 17:57:09 PDT)
Bala subramanian
- [AMBER] checking interaction between periodic images (Tue Mar 01 2011 - 02:37:04 PST)
Baptiste Legrand
- Re: [AMBER] Generating an average structure from a rst/pdb list? (Fri Mar 04 2011 - 02:06:25 PST)
- Re: [AMBER] Generating an average structure from a rst/pdb list? (Thu Mar 03 2011 - 13:02:04 PST)
- [AMBER] Generating an average structure from a rst/pdb list? (Thu Mar 03 2011 - 09:21:14 PST)
- Re: [AMBER] To fix dihedral angles during a simulation. (Wed Mar 02 2011 - 02:08:37 PST)
Beale, John
- [AMBER] hydrogen bonding facility in ptraj (Fri Mar 04 2011 - 05:38:11 PST)
Ben Roberts
- Re: [AMBER] Loading .mol2 file in sleap (Wed Mar 30 2011 - 20:16:59 PDT)
- Re: [AMBER] Loading .mol2 file in sleap (Wed Mar 30 2011 - 13:19:21 PDT)
- Re: [AMBER] Loading .mol2 file in sleap (Wed Mar 30 2011 - 12:16:20 PDT)
- Re: [AMBER] Loading .mol2 file in sleap (Wed Mar 30 2011 - 07:43:00 PDT)
- Re: [AMBER] Sander was terminating in the midddle (Thu Mar 24 2011 - 10:54:56 PDT)
- Re: [AMBER] error installing AmberTools-1.2 in ubuntu 10.10 (Thu Mar 17 2011 - 12:52:26 PDT)
- Re: [AMBER] error in creating prmtop and inpcrd files (Sun Mar 13 2011 - 14:34:48 PDT)
- Re: [AMBER] error in creating prmtop and inpcrd files (Sun Mar 13 2011 - 11:42:29 PDT)
- Re: [AMBER] Problem installing Amber11/Ambertools1.4 on Ubuntu10.10 (Tue Mar 08 2011 - 10:09:15 PST)
- Re: [AMBER] xleap not installed (Tue Mar 08 2011 - 09:13:47 PST)
- Re: [AMBER] a question about using oplsaa ff in amber (Tue Mar 08 2011 - 08:44:05 PST)
Bill Miller III
- Re: [AMBER] nmode calculations (Fri Mar 25 2011 - 12:00:42 PDT)
- Re: [AMBER] nmode calculations (Fri Mar 25 2011 - 11:23:33 PDT)
- Re: [AMBER] Error with MM-PBSA perl file for pairwise residue decomposition (Fri Mar 25 2011 - 04:07:45 PDT)
- Re: [AMBER] number of frames read in mmpbsa.py (Wed Mar 23 2011 - 09:59:00 PDT)
- Re: [AMBER] number of frames read in mmpbsa.py (Wed Mar 23 2011 - 09:52:44 PDT)
- Re: [AMBER] scientific question on decomposition analysis in pbsa calculation (Wed Mar 23 2011 - 07:37:59 PDT)
- Re: [AMBER] Doubts in MM-PBSA (Wed Mar 23 2011 - 06:57:05 PDT)
- Re: [AMBER] Perl Vs Python in MMPBSA calculations in Amber 10 (Wed Mar 23 2011 - 06:53:43 PDT)
- Re: [AMBER] MM-PBSA Error (Mon Mar 21 2011 - 04:30:33 PDT)
- Re: [AMBER] changing maximum number of frames for mmpbsa.py (Sat Mar 19 2011 - 09:40:39 PDT)
- Re: [AMBER] trouble with mmpbsa.py (Fri Mar 18 2011 - 09:50:17 PDT)
- Re: [AMBER] Energy Decomposition using mmpbsa script (Sat Mar 12 2011 - 07:47:56 PST)
- Re: [AMBER] Bad magic number ? (Sat Mar 12 2011 - 07:02:56 PST)
- Re: [AMBER] Energy Decomposition using mmpbsa script (Sat Mar 12 2011 - 05:31:16 PST)
- Re: [AMBER] Query regarding mmpbsa output file (Sat Mar 12 2011 - 04:26:48 PST)
- Re: [AMBER] Query regarding mmpbsa output file (Fri Mar 11 2011 - 06:44:32 PST)
- Re: [AMBER] interaction energy (Thu Mar 10 2011 - 03:38:51 PST)
- [AMBER] Nab PB focusing error (Wed Mar 09 2011 - 12:07:22 PST)
- Re: [AMBER] Splitting the interaction energy (Wed Mar 09 2011 - 06:44:06 PST)
- Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. (Mon Mar 07 2011 - 05:41:02 PST)
- Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. (Mon Mar 07 2011 - 04:57:26 PST)
- Re: [AMBER] is it possible to identify each mode in Nmode calculation? (Mon Mar 07 2011 - 04:54:57 PST)
- Re: [AMBER] xleap not installed (Tue Mar 01 2011 - 06:12:09 PST)
Bill Ross
- Re: [AMBER] Keep getting LINMIN error. Not sure how to progress. (Mon Mar 28 2011 - 11:39:39 PDT)
- Re: [AMBER] deleting protein atoms from prmtop topology files using rdparm (Fri Mar 25 2011 - 10:38:19 PDT)
- Re: [AMBER] Differences in the periodic box dimensions (Tue Mar 22 2011 - 10:07:37 PDT)
- Re: [AMBER] how to calculate scattering trajectory (Sun Mar 20 2011 - 14:06:52 PDT)
- Re: [AMBER] Amber archive mailing list is not working (Sat Mar 12 2011 - 23:50:21 PST)
- Re: [AMBER] How to save a restart file (Fri Mar 11 2011 - 10:52:24 PST)
- Re: [AMBER] Partial Charges for Atom Types (Wed Mar 09 2011 - 09:51:45 PST)
- Re: [AMBER] Blowing array; too many frames!! (Fri Mar 04 2011 - 15:30:14 PST)
- Re: [AMBER] randomly place counterions (Wed Mar 02 2011 - 12:02:27 PST)
- Re: [AMBER] water mediated H-Bond (Wed Mar 02 2011 - 11:45:34 PST)
- Re: [AMBER] CHAMBER prmtop (Tue Mar 01 2011 - 20:05:29 PST)
- Re: [AMBER] CHAMBER prmtop (Tue Mar 01 2011 - 19:51:11 PST)
- Re: [AMBER] water mediated H-Bond (Tue Mar 01 2011 - 12:02:28 PST)
- Re: [AMBER] water mediated H-Bond (Tue Mar 01 2011 - 10:09:20 PST)
Bingwu Yu
- [AMBER] How do I plot the angle population distribution (Thu Mar 24 2011 - 06:42:36 PDT)
- [AMBER] average structure pdb file looks wrong (Tue Mar 22 2011 - 13:39:03 PDT)
- [AMBER] calculation of population of each conformers (Mon Mar 21 2011 - 14:45:22 PDT)
- Re: [AMBER] Dihedral angles does not match VMD vs ptraj (Fri Mar 18 2011 - 21:08:04 PDT)
- Re: [AMBER] Dihedral angles does not match VMD vs ptraj (Fri Mar 18 2011 - 14:24:12 PDT)
- [AMBER] Dihedral angles does not match VMD vs ptraj (Fri Mar 18 2011 - 13:30:42 PDT)
- Re: [AMBER] Is rst file the last frame of output crd file? (Fri Mar 18 2011 - 11:24:40 PDT)
- Re: [AMBER] Is rst file the last frame of output crd file? (Fri Mar 18 2011 - 11:10:14 PDT)
- [AMBER] Is rst file the last frame of output crd file? (Fri Mar 18 2011 - 10:07:04 PDT)
Bongkeun Kim
- [AMBER] Using Intel compilers on AMD CPU (Thu Mar 17 2011 - 20:10:48 PDT)
Burcu Aykac Fas
- [AMBER] irest (Wed Mar 09 2011 - 06:38:38 PST)
Carlos Simmerling
- Re: [AMBER] The validity of a per-residue decomposition in amber (Wed Mar 30 2011 - 06:47:34 PDT)
- Re: [AMBER] R: Exchange Acceptance Ratio (Wed Mar 30 2011 - 06:44:25 PDT)
- Re: [AMBER] Keep getting LINMIN error. Not sure how to progress. (Mon Mar 28 2011 - 05:39:07 PDT)
- Re: [AMBER] AmberTools1.4 question (Sat Mar 26 2011 - 10:46:24 PDT)
- Re: [AMBER] How to analysis radius of gyration? (Thu Mar 24 2011 - 07:56:14 PDT)
- Re: [AMBER] odd output from rms measurement (Wed Mar 23 2011 - 17:24:58 PDT)
- Re: [AMBER] odd output from rms measurement (Wed Mar 23 2011 - 15:15:58 PDT)
- Re: [AMBER] how to choose the biasing potential based on the coarsefree energy curve (Tue Mar 15 2011 - 07:24:17 PDT)
- Re: [AMBER] no answer so far - free energy profile for water slab (Tue Mar 15 2011 - 04:02:44 PDT)
- Re: [AMBER] how to calculate the B-factor of crystal pdb (Mon Mar 14 2011 - 04:23:49 PDT)
- Re: [AMBER] questions about the input file of MD process (Sun Mar 13 2011 - 07:38:53 PDT)
- Re: [AMBER] the output of REMD simulations (Fri Mar 11 2011 - 09:42:42 PST)
- Re: [AMBER] the output of REMD simulations (Fri Mar 11 2011 - 09:36:09 PST)
- Re: [AMBER] Umbrella sampling coordinate question (Thu Mar 10 2011 - 09:47:45 PST)
- Re: [AMBER] Umbrella sampling coordinate question (Thu Mar 10 2011 - 06:45:41 PST)
- Re: [AMBER] continuum solvation with low viscosity (Wed Mar 09 2011 - 04:19:58 PST)
- Re: [AMBER] Umbrella sampling coordinate question (Wed Mar 09 2011 - 04:04:24 PST)
- Re: [AMBER] acceptance probabilities remd (Tue Mar 08 2011 - 04:00:14 PST)
- Re: [AMBER] acceptance probabilities remd (Tue Mar 08 2011 - 03:49:14 PST)
- Re: [AMBER] Fwd: Implicit solvent GB calculation (Mon Mar 07 2011 - 07:10:41 PST)
- Re: [AMBER] how to deal with flexibility of peptide during prod. process (Mon Mar 07 2011 - 06:18:39 PST)
- Re: [AMBER] Showing torsion energy as a function of angle (Sun Mar 06 2011 - 15:23:11 PST)
- [AMBER] ACS COMP division awards for Fall 2011 meeting (Sat Mar 05 2011 - 07:44:30 PST)
case
- Re: [AMBER] Loading .mol2 file in sleap (Wed Mar 30 2011 - 18:52:36 PDT)
- Re: [AMBER] Atom name convention/conversion in antechamber (Sat Mar 26 2011 - 17:32:53 PDT)
- Re: [AMBER] ff10 (Sat Mar 26 2011 - 14:26:17 PDT)
- Re: [AMBER] can I calculate binding energy with some restraints (Mon Mar 21 2011 - 10:23:35 PDT)
- Re: [AMBER] TI minimizations cannot be performed with > 2 CPUs (Sun Mar 20 2011 - 06:26:04 PDT)
- Re: [AMBER] Missing Parameters (Sat Mar 19 2011 - 07:14:43 PDT)
- Re: [AMBER] Amber11 on osx using port and gcc4.5 (Fri Mar 18 2011 - 14:31:17 PDT)
- Re: [AMBER] Assertion failed: nat < 5000, file makeDIST_RST (Thu Mar 17 2011 - 05:34:51 PDT)
- Re: [AMBER] Assertion failed: nat < 5000, file makeDIST_RST (Wed Mar 16 2011 - 04:47:37 PDT)
- Re: [AMBER] amber11 Installation Test Failures (Tue Mar 15 2011 - 18:58:06 PDT)
- Re: [AMBER] Assertion failed: nat < 5000, file makeDIST_RST (Tue Mar 15 2011 - 17:51:21 PDT)
- Re: [AMBER] AmberTools 1.4 possible bug for secstruct (test case attached) (Sat Mar 12 2011 - 05:54:02 PST)
- Re: [AMBER] Problems with tleap (Mon Mar 07 2011 - 10:56:58 PST)
- Re: [AMBER] h-bond donor acceptor definition confusion (Mon Mar 07 2011 - 06:13:48 PST)
- Re: [AMBER] using NMR restraints within LMOD (Mon Mar 07 2011 - 05:06:45 PST)
- Re: [AMBER] Diffusion coefficient (Mon Mar 07 2011 - 04:58:38 PST)
- Re: [AMBER] Zn Bond Length solvatebox (Fri Mar 04 2011 - 04:40:29 PST)
- Re: [AMBER] xleap not installed (Thu Mar 03 2011 - 04:20:26 PST)
- Re: [AMBER] To fix dihedral angles during a simulation. (Wed Mar 02 2011 - 06:39:37 PST)
- Re: [AMBER] Restart Problem: The results of an integrated simulation and restarted simulations are not equal! (Tue Mar 01 2011 - 04:47:41 PST)
Catein Catherine
- [AMBER] How to use perl to replace number to txt? (Thu Mar 31 2011 - 02:48:48 PDT)
- [AMBER] Tools to calculate free energies landscape from the MD simulation without doing PMF? (Fri Mar 25 2011 - 01:13:33 PDT)
- Re: [AMBER] Any manual for python or perl to transform a matrix for data analysis? (Fri Mar 25 2011 - 01:06:14 PDT)
- [AMBER] Any manual for python or perl to transform a matrix for data analysis? (Fri Mar 25 2011 - 00:46:53 PDT)
- [AMBER] How to get the free energy landscape from a MD simulation? (Thu Mar 24 2011 - 07:55:19 PDT)
- [AMBER] How to analysis radius of gyration? (Thu Mar 24 2011 - 07:50:34 PDT)
Cenk \(Jenk\) Andac
- Re: [AMBER] irest (Wed Mar 09 2011 - 07:07:05 PST)
CHAMI F.
- Re: [AMBER] HEME parameters (Wed Mar 02 2011 - 03:53:54 PST)
chandan patel
- Re: [AMBER] Reimaging Problem (Thu Mar 17 2011 - 02:40:02 PDT)
- [AMBER] Reimaging Problem (Wed Mar 16 2011 - 03:43:39 PDT)
Chih-Ying Lin
- [AMBER] Diffusion coefficient (Fri Mar 04 2011 - 09:41:42 PST)
Chris Bryant
- Re: [AMBER] error in creating prmtop and inpcrd files (Sun Mar 13 2011 - 15:47:45 PDT)
- Re: [AMBER] error in creating prmtop and inpcrd files (Sun Mar 13 2011 - 13:55:51 PDT)
- [AMBER] error in creating prmtop and inpcrd files (Sun Mar 13 2011 - 10:48:56 PDT)
Chris Chris
- Re: [AMBER] How to use perl to replace number to txt? (Thu Mar 31 2011 - 05:17:14 PDT)
- [AMBER] segmentation fault when using mmpbsa.py (Wed Mar 30 2011 - 15:03:46 PDT)
- Re: [AMBER] deleting protein atoms from prmtop topology files using rdparm (Thu Mar 24 2011 - 14:29:25 PDT)
- Re: [AMBER] odd output from rms measurement (Wed Mar 23 2011 - 18:33:52 PDT)
- Re: [AMBER] odd output from rms measurement (Wed Mar 23 2011 - 16:50:11 PDT)
- [AMBER] odd output from rms measurement (Wed Mar 23 2011 - 14:55:44 PDT)
- [AMBER] number of frames read in mmpbsa.py (Wed Mar 23 2011 - 09:44:41 PDT)
- [AMBER] changing maximum number of frames for mmpbsa.py (Sat Mar 19 2011 - 09:27:03 PDT)
- Re: [AMBER] trouble with mmpbsa.py (Fri Mar 18 2011 - 10:30:59 PDT)
- [AMBER] trouble with mmpbsa.py (Fri Mar 18 2011 - 09:44:08 PDT)
Christoph Malisi
- [AMBER] ptraj problems (Thu Mar 24 2011 - 07:05:42 PDT)
cieplak.cgl.ucsf.edu
- Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. (Wed Mar 09 2011 - 23:32:56 PST)
colvin
- Re: [AMBER] sander.MPI running on 8 nodes or 1?? (Tue Mar 08 2011 - 22:13:57 PST)
- [AMBER] sander.MPI running on 8 nodes or 1?? (Tue Mar 08 2011 - 01:11:03 PST)
- Re: [AMBER] chamber (Thu Mar 03 2011 - 01:24:53 PST)
- Re: [AMBER] CHAMBER prmtop (Thu Mar 03 2011 - 01:22:39 PST)
- Re: [AMBER] CHAMBER prmtop (Tue Mar 01 2011 - 22:36:36 PST)
- Re: [AMBER] CHAMBER prmtop (Tue Mar 01 2011 - 19:58:06 PST)
- [AMBER] CHAMBER prmtop (Tue Mar 01 2011 - 19:46:50 PST)
Crowley, Michael
- Re: [AMBER] AmberTools 1.4 possible bug for secstruct (test case attached) (Sun Mar 13 2011 - 12:55:31 PDT)
Daniel Chipman
- [AMBER] new residue with amoeba (Wed Mar 30 2011 - 12:54:11 PDT)
Daniel Roe
- Re: [AMBER] Help: Clustering trajectories based on dihedral angle? (Fri Mar 25 2011 - 18:43:59 PDT)
- Re: [AMBER] odd output from rms measurement (Thu Mar 24 2011 - 00:02:13 PDT)
- Re: [AMBER] Ptraj crashes and Hbond analysis (Wed Mar 23 2011 - 06:45:14 PDT)
- Re: [AMBER] Flags of secstruct (Tue Mar 22 2011 - 10:46:46 PDT)
- Re: [AMBER] distance cutoff of closest command (Wed Mar 16 2011 - 06:02:12 PDT)
- Re: [AMBER] distance cutoff of closest command (Wed Mar 16 2011 - 05:59:43 PDT)
- Re: [AMBER] amber11 Installation Test Failures (Tue Mar 15 2011 - 16:55:28 PDT)
- Re: [AMBER] angle in h-bond analysis (Mon Mar 14 2011 - 05:58:22 PDT)
- Re: [AMBER] amber11 Installation Test Failures (Sun Mar 13 2011 - 19:21:21 PDT)
- Re: [AMBER] Fwd: Implicit solvent GB calculation (Mon Mar 07 2011 - 07:42:19 PST)
- Re: [AMBER] Fwd: Implicit solvent GB calculation (Mon Mar 07 2011 - 07:40:34 PST)
- Re: [AMBER] Generating an average structure from a rst/pdb list? (Thu Mar 03 2011 - 10:54:31 PST)
- Re: [AMBER] Blowing array; too many frames!! (Thu Mar 03 2011 - 10:48:15 PST)
- Re: [AMBER] Blowing array; too many frames!! (Thu Mar 03 2011 - 08:31:29 PST)
- Re: [AMBER] Blowing array; too many frames!! (Thu Mar 03 2011 - 08:06:05 PST)
- Re: [AMBER] Blowing array; too many frames!! (Thu Mar 03 2011 - 06:38:50 PST)
- Re: [AMBER] checking interaction between periodic images (Tue Mar 01 2011 - 06:54:42 PST)
Daniel Sindhikara
- Re: [AMBER] Exchange Acceptance Ratio (Wed Mar 30 2011 - 05:00:02 PDT)
- Re: [AMBER] Thermostat (Thu Mar 17 2011 - 00:27:17 PDT)
- Re: [AMBER] how to choose the biasing potential based on the coarsefree energy curve (Tue Mar 15 2011 - 07:48:55 PDT)
- Re: [AMBER] how to choose the biasing potential based on the coarse free energy curve (Mon Mar 14 2011 - 23:03:15 PDT)
- Re: [AMBER] Would liek to plot GBTOT vs Time (Sun Mar 13 2011 - 23:40:13 PDT)
David A Case
- Re: [AMBER] The validity of a per-residue decomposition in amber (Thu Mar 31 2011 - 05:53:02 PDT)
- Re: [AMBER] Atom name convention/conversion in antechamber (Tue Mar 29 2011 - 04:54:04 PDT)
- Re: [AMBER] problem with peptide simulations (Mon Mar 28 2011 - 13:04:33 PDT)
- Re: [AMBER] pmemd and nmr restraint (Fri Mar 25 2011 - 12:18:16 PDT)
- Re: [AMBER] How to get the free energy landscape from a MD simulation? (Thu Mar 24 2011 - 08:44:16 PDT)
- Re: [AMBER] Amber (Thu Mar 24 2011 - 08:34:47 PDT)
- Re: [AMBER] Atom name convention/conversion in antechamber (Thu Mar 24 2011 - 06:24:11 PDT)
- Re: [AMBER] Creating distaint restaint in Amber (Thu Mar 24 2011 - 06:18:14 PDT)
- Re: [AMBER] solvation free energy (Tue Mar 22 2011 - 11:42:32 PDT)
- Re: [AMBER] AMBER 10 serial compile problem (Tue Mar 15 2011 - 10:24:19 PDT)
- Re: [AMBER] how to obtain 4x4x1.1nm water; how to add polarizable models (Mon Mar 14 2011 - 08:16:30 PDT)
- Re: [AMBER] how to run PIMD (Fri Mar 11 2011 - 10:31:03 PST)
- Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. (Thu Mar 10 2011 - 09:43:47 PST)
- Re: [AMBER] Creating distaint restaint in Amber (Thu Mar 10 2011 - 05:56:18 PST)
- Re: [AMBER] Pressure regulation and position restraints (Wed Mar 09 2011 - 08:57:49 PST)
- Re: [AMBER] missing AMBER features for simulating surfaces and linear assemblies (Wed Mar 09 2011 - 08:54:27 PST)
- Re: [AMBER] Partial Charges for Atom Types (Wed Mar 09 2011 - 08:44:52 PST)
- Re: [AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE (Wed Mar 09 2011 - 07:35:32 PST)
- Re: [AMBER] Request for a quotation of AMBER (Tue Mar 08 2011 - 05:06:22 PST)
- Re: [AMBER] igb=1 and gbsa=0 (Tue Mar 08 2011 - 05:00:11 PST)
David Cantu
- Re: [AMBER] Parallel amber11 Installation FAIL (Mon Mar 21 2011 - 19:07:21 PDT)
- Re: [AMBER] Amber11 make test FAILURE and ERROR (Mon Mar 21 2011 - 18:57:02 PDT)
- [AMBER] Parallel amber11 Installation FAIL (Mon Mar 21 2011 - 16:49:23 PDT)
- [AMBER] Amber11 make test FAILURE and ERROR (Sun Mar 20 2011 - 01:45:34 PDT)
- [AMBER] AmberTools 1.4 make test Error (Sun Mar 20 2011 - 01:39:50 PDT)
- Re: [AMBER] amber11 Installation Test Failures (Sun Mar 20 2011 - 01:34:55 PDT)
- Re: [AMBER] amber11 Installation Test Failures (Sat Mar 19 2011 - 23:39:08 PDT)
- Re: [AMBER] amber11 Installation Test Failures (Sat Mar 19 2011 - 23:16:27 PDT)
- [AMBER] NCSU (Tue Mar 15 2011 - 20:44:00 PDT)
- Re: [AMBER] amber11 Installation Test Failures (Tue Mar 15 2011 - 19:08:04 PDT)
- Re: [AMBER] amber11 Installation Test Failures (Tue Mar 15 2011 - 18:40:15 PDT)
- Re: [AMBER] amber11 Installation Test Failures (Tue Mar 15 2011 - 16:58:06 PDT)
- Re: [AMBER] amber11 Installation Test Failures (Tue Mar 15 2011 - 16:16:02 PDT)
- Re: [AMBER] amber11 Installation Test Failures (Tue Mar 15 2011 - 14:31:24 PDT)
- Re: [AMBER] amber11 Installation Test Failures (Mon Mar 14 2011 - 00:16:41 PDT)
- [AMBER] amber11 Installation Test Failures (Sun Mar 13 2011 - 18:11:59 PDT)
David Case
- Re: [AMBER] using thermodynamic integration, how to deal with absolute pka and conformation change (Wed Mar 16 2011 - 06:25:26 PDT)
- Re: [AMBER] docking evaluation using amber (Fri Mar 11 2011 - 18:18:26 PST)
david condon
- Re: [AMBER] How to save a restart file (Fri Mar 11 2011 - 09:14:43 PST)
- Re: [AMBER] How to save a restart file (Fri Mar 11 2011 - 08:56:14 PST)
- [AMBER] Showing torsion energy as a function of angle (Sun Mar 06 2011 - 14:46:50 PST)
David Watson
- Re: [AMBER] AMBER 10 serial compile problem (Tue Mar 15 2011 - 09:53:41 PDT)
- Re: [AMBER] Amber archive mailing list is not working (Mon Mar 14 2011 - 10:37:50 PDT)
dhilip kumar ramalingam
- [AMBER] regarding anal function (Fri Mar 25 2011 - 04:08:02 PDT)
- [AMBER] regrding the anal working (Thu Mar 24 2011 - 22:28:32 PDT)
Dian Jiao
- [AMBER] TI minimizations cannot be performed with > 2 CPUs (Fri Mar 18 2011 - 22:43:29 PDT)
- Re: [AMBER] free energy calculation with TI (Tue Mar 15 2011 - 20:17:44 PDT)
- Re: [AMBER] free energy calculation with TI (Tue Mar 15 2011 - 15:12:19 PDT)
- [AMBER] free energy calculation with TI (Tue Mar 15 2011 - 13:55:04 PDT)
Diego Javier Alonso de Armiño
- [AMBER] Thermostat (Wed Mar 16 2011 - 19:50:05 PDT)
Dima A Sabbah
- Re: [AMBER] nmode memory issue (Mon Mar 21 2011 - 10:50:34 PDT)
Dmitry Mukha
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 12:24:15 PDT)
Dmitry Nilov
- Re: [AMBER] Add Residue at N-terminal (Thu Mar 31 2011 - 07:09:54 PDT)
- Re: [AMBER] positional restraint on crystal water (Wed Mar 30 2011 - 02:56:27 PDT)
- Re: [AMBER] positional restraint on crystal water (Wed Mar 30 2011 - 02:18:17 PDT)
- Re: [AMBER] positional restraint on crystal water (Wed Mar 30 2011 - 02:03:18 PDT)
- Re: [AMBER] positional restraint on crystal water (Wed Mar 30 2011 - 01:26:37 PDT)
- Re: [AMBER] water box deforms during MD (Mon Mar 28 2011 - 07:17:22 PDT)
- Re: [AMBER] enzyme MD trajectory looks funny (Mon Mar 28 2011 - 06:20:53 PDT)
- Re: [AMBER] PMF calculations in Amber 10 (Wed Mar 23 2011 - 22:11:02 PDT)
- Re: [AMBER] Restraints on equilibration of solvated complexes (Wed Mar 16 2011 - 12:05:22 PDT)
- Re: [AMBER] Restraints on equilibration of solvated complexes (Wed Mar 16 2011 - 08:47:28 PDT)
- Re: [AMBER] Restraints on equilibration of solvated complexes (Wed Mar 16 2011 - 08:10:32 PDT)
- Re: [AMBER] docking evaluation using amber (Mon Mar 14 2011 - 06:32:02 PDT)
- Re: [AMBER] question about the distance of pronton transfer and acetylation (Wed Mar 09 2011 - 02:06:46 PST)
- Re: [AMBER] MD simulation of protein with Calcium ion (Wed Mar 02 2011 - 03:02:46 PST)
Dmitry Osolodkin
- Re: [AMBER] AMBER 10 serial compile problem (Tue Mar 15 2011 - 13:22:01 PDT)
- Re: [AMBER] AMBER 10 serial compile problem (Tue Mar 15 2011 - 10:45:07 PDT)
- Re: [AMBER] AMBER 10 serial compile problem (Tue Mar 15 2011 - 10:29:59 PDT)
- Re: [AMBER] AMBER 10 serial compile problem (Tue Mar 15 2011 - 09:52:50 PDT)
- [AMBER] AMBER 10 serial compile problem (Tue Mar 15 2011 - 09:35:37 PDT)
Dwight McGee
- Re: [AMBER] Extract binding free energy for each snapshot (Fri Mar 25 2011 - 07:39:05 PDT)
- Re: [AMBER] number of frames read in mmpbsa.py (Wed Mar 23 2011 - 10:29:09 PDT)
- Re: [AMBER] Nmode error of MMPBSA.py (Wed Mar 23 2011 - 06:17:03 PDT)
- Re: [AMBER] MM/PBSA (Problem in snapshot generation) (Mon Mar 21 2011 - 12:14:00 PDT)
- Re: [AMBER] MM/PBSA (Problem in snapshot generation) (Mon Mar 21 2011 - 10:43:56 PDT)
- Re: [AMBER] Calculation with CUTCAP (Mon Mar 14 2011 - 20:28:35 PDT)
Eliac Brown
- Re: [AMBER] mmpbsa.pl energy decompistion stopped (Mon Mar 21 2011 - 19:37:26 PDT)
- [AMBER] mmpbsa.pl energy decompistion stopped (Mon Mar 21 2011 - 16:41:36 PDT)
- Re: [AMBER] MMPBSA question (Sat Mar 19 2011 - 17:57:52 PDT)
- [AMBER] MMPBSA question (Sat Mar 19 2011 - 16:35:42 PDT)
- [AMBER] Explicit and implicit n-octanol solvent (Tue Mar 15 2011 - 07:03:47 PDT)
- [AMBER] GB parameters for Octane (Sat Mar 12 2011 - 10:10:49 PST)
- Re: [AMBER] Energy Decomposition using mmpbsa script (Sat Mar 12 2011 - 10:05:47 PST)
- Re: [AMBER] Energy Decomposition using mmpbsa script (Sat Mar 12 2011 - 07:32:36 PST)
- [AMBER] Energy Decomposition using mmpbsa script (Sat Mar 12 2011 - 05:05:20 PST)
- [AMBER] Splitting the interaction energy (Wed Mar 09 2011 - 06:26:58 PST)
Elisa Frezza
- Re: [AMBER] Implicit simulation (Wed Mar 30 2011 - 10:17:12 PDT)
- [AMBER] Implicit simulation (Wed Mar 30 2011 - 10:03:30 PDT)
erik zuiderweg
- Re: [AMBER] docking evaluation using amber (Sat Mar 12 2011 - 08:17:07 PST)
- [AMBER] docking evaluation using amber (Fri Mar 11 2011 - 17:33:00 PST)
filip fratev
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 16:17:34 PDT)
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 15:16:54 PDT)
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 08:29:13 PDT)
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 08:26:29 PDT)
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 05:08:35 PDT)
- Re: [AMBER] docking evaluation using amber (Fri Mar 11 2011 - 21:15:23 PST)
- [AMBER] CUDA 4.0 RC (Mon Mar 07 2011 - 18:35:28 PST)
Francesco Oteri
- [AMBER] Atom distribution in PMEMD.cuda (Wed Mar 30 2011 - 07:02:31 PDT)
- [AMBER] AmberTools and GROMACS (Sat Mar 19 2011 - 11:31:04 PDT)
- Re: [AMBER] questions about the input file of MD process (Sun Mar 13 2011 - 08:09:23 PDT)
- Re: [AMBER] questions about the input file of MD process (Sun Mar 13 2011 - 07:41:04 PDT)
- Re: [AMBER] questions about the input file of MD process (Sun Mar 13 2011 - 07:27:39 PDT)
- [AMBER] igb=1 and gbsa=0 (Mon Mar 07 2011 - 15:38:43 PST)
- [AMBER] implicit solvent with cuda (Thu Mar 03 2011 - 04:44:07 PST)
- [AMBER] generalized Born question (Tue Mar 01 2011 - 10:21:00 PST)
Francesco Pietra
- Re: [AMBER] Atom name convention/conversion in antechamber (Sun Mar 27 2011 - 02:11:56 PDT)
- [AMBER] charmmgen issues (Mon Mar 21 2011 - 04:04:03 PDT)
FyD
- Re: [AMBER] RESP: optimized charges not reasonable (Tue Mar 29 2011 - 04:54:03 PDT)
- Re: [AMBER] RESP: optimized charges not reasonable (Tue Mar 29 2011 - 01:36:54 PDT)
- Re: [AMBER] parameters for metal site (Thu Mar 17 2011 - 11:30:37 PDT)
- Re: [AMBER] parameters for metal site (Thu Mar 17 2011 - 07:03:21 PDT)
- Re: [AMBER] Regarding: Adding New Multi-atom Residue (Ligand) including partial charges (Mon Mar 14 2011 - 23:55:22 PDT)
- Re: [AMBER] non standard Alanine (Fri Mar 04 2011 - 07:50:50 PST)
g t
- Re: [AMBER] positional restraint on crystal water (Wed Mar 30 2011 - 09:35:18 PDT)
- Re: [AMBER] deleting protein atoms from prmtop topology files using rdparm (Wed Mar 30 2011 - 08:14:59 PDT)
- Re: [AMBER] The validity of a per-residue decomposition in amber (Wed Mar 30 2011 - 08:13:26 PDT)
- [AMBER] The validity of a per-residue decomposition in amber (Wed Mar 30 2011 - 06:36:33 PDT)
- Re: [AMBER] deleting protein atoms from prmtop topology files using rdparm (Fri Mar 25 2011 - 03:41:55 PDT)
- [AMBER] deleting protein atoms from prmtop topology files using rdparm (Thu Mar 24 2011 - 12:01:36 PDT)
- Re: [AMBER] reference for per-residue decomposition using TI Calculation (Thu Mar 24 2011 - 09:54:12 PDT)
- Re: [AMBER] TI minimizations cannot be performed with > 2 CPUs (Sat Mar 19 2011 - 11:56:38 PDT)
- [AMBER] reference for per-residue decomposition using TI Calculation (Sat Mar 19 2011 - 11:49:00 PDT)
Ganesh Kamath
- [AMBER] Spatial distribution function (Fri Mar 25 2011 - 11:19:24 PDT)
- Re: [AMBER] forefile of acetyl coenzyme A (Mon Mar 07 2011 - 06:19:03 PST)
- Re: [AMBER] forefile of acetyl coenzyme A (Mon Mar 07 2011 - 06:11:37 PST)
- [AMBER] AMBER parameters for lead (Fri Mar 04 2011 - 12:24:48 PST)
George Tzotzos
- Re: [AMBER] Restraints on equilibration of solvated complexes (Wed Mar 16 2011 - 10:52:00 PDT)
- Re: [AMBER] Restraints on equilibration of solvated complexes (Wed Mar 16 2011 - 08:25:28 PDT)
- [AMBER] Restraints on equilibration of solvated complexes (Wed Mar 16 2011 - 07:37:17 PDT)
- Re: [AMBER] docking evaluation using amber (Mon Mar 14 2011 - 11:57:20 PDT)
Gould, Ian R
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 06:09:19 PDT)
gromacs
- [AMBER] how to obtain 4x4x1.1nm water; how to add polarizable models (Mon Mar 14 2011 - 05:44:42 PDT)
Gustavo Seabra
- Re: [AMBER] Tools to calculate free energies landscape from the MD simulation without doing PMF? (Fri Mar 25 2011 - 05:33:18 PDT)
- Re: [AMBER] Is rst file the last frame of output crd file? (Fri Mar 18 2011 - 11:20:01 PDT)
- Re: [AMBER] MD- the enzyme bouncing (Mon Mar 14 2011 - 17:19:47 PDT)
- Re: [AMBER] Amber archive mailing list is not working (Sat Mar 12 2011 - 03:56:02 PST)
- Re: [AMBER] Amber archive mailing list is not working (Sat Mar 12 2011 - 03:53:53 PST)
Haipeng Wei
- Re: [AMBER] how to run amber on mutli-gpu/muti-nodes (Tue Mar 15 2011 - 17:04:52 PDT)
- [AMBER] how to run amber on mutli-gpu/muti-nodes (Tue Mar 15 2011 - 15:08:40 PDT)
Haldoupis I.
- Re: [AMBER] how to minimize a protein-ligand system with the protein constrained (Wed Mar 23 2011 - 14:28:41 PDT)
Hannes Loeffler
- Re: [AMBER] How to use perl to replace number to txt? (Thu Mar 31 2011 - 03:19:11 PDT)
- Re: [AMBER] checking interaction between periodic images (Tue Mar 01 2011 - 08:29:18 PST)
hari krishna
- [AMBER] stacking energy calculation (Wed Mar 16 2011 - 03:06:36 PDT)
- Re: [AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE (Wed Mar 09 2011 - 20:20:11 PST)
- [AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE (Wed Mar 09 2011 - 06:28:55 PST)
- Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. (Mon Mar 07 2011 - 20:14:43 PST)
- Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. (Mon Mar 07 2011 - 05:33:14 PST)
- Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. (Thu Mar 03 2011 - 08:47:54 PST)
- [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. (Thu Mar 03 2011 - 03:07:36 PST)
Hashem Taha
- Re: [AMBER] problem with peptide simulations (Mon Mar 28 2011 - 13:00:58 PDT)
- [AMBER] problem with peptide simulations (Mon Mar 28 2011 - 12:05:55 PDT)
Hector A. Baldoni
- [AMBER] Bad magic number ? (Sat Mar 12 2011 - 06:41:19 PST)
Hirdesh Kumar
- [AMBER] Amber Installation error (Fri Mar 25 2011 - 05:22:25 PDT)
- [AMBER] Query regarding mmpbsa run (Mon Mar 14 2011 - 03:59:38 PDT)
- Re: [AMBER] Amber archive mailing list is not working (Sun Mar 13 2011 - 22:04:51 PDT)
- Re: [AMBER] Amber archive mailing list is not working (Fri Mar 11 2011 - 23:07:13 PST)
- [AMBER] Amber archive mailing list is not working (Fri Mar 11 2011 - 22:50:55 PST)
- Re: [AMBER] Query regarding mmpbsa output file (Fri Mar 11 2011 - 21:58:04 PST)
- [AMBER] Query regarding mmpbsa output file (Fri Mar 11 2011 - 06:24:33 PST)
- Re: [AMBER] water mediated H-Bond (Wed Mar 02 2011 - 01:25:31 PST)
Hopkins, Robert
- Re: [AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file (Mon Mar 28 2011 - 12:16:33 PDT)
Hoshin Kim
- [AMBER] positive GBtot value (Thu Mar 24 2011 - 18:02:30 PDT)
Hugh Heldenbrand
- Re: [AMBER] Keep getting LINMIN error. Not sure how to progress. (Mon Mar 28 2011 - 05:40:50 PDT)
- Re: [AMBER] randomly place counterions (Wed Mar 02 2011 - 07:16:29 PST)
- Re: [AMBER] randomly place counterions (Wed Mar 02 2011 - 04:56:01 PST)
I.Haldoupis
- Re: [AMBER] Keep getting LINMIN error. Not sure how to progress. (Tue Mar 29 2011 - 03:15:15 PDT)
- [AMBER] Keep getting LINMIN error. Not sure how to progress. (Mon Mar 28 2011 - 05:27:00 PDT)
- [AMBER] how to minimize a protein-ligand system with the protein constrained (Wed Mar 23 2011 - 13:09:13 PDT)
Ignacio Faustino Plo
- Re: [AMBER] RESP: optimized charges not reasonable (Tue Mar 29 2011 - 03:46:12 PDT)
- [AMBER] RESP: optimized charges not reasonable (Mon Mar 28 2011 - 09:59:52 PDT)
Ignacio J. General
- Re: [AMBER] ptraj: box information for truncated octahedron (Thu Mar 24 2011 - 10:24:08 PDT)
- [AMBER] tleap strange behavior (Wed Mar 23 2011 - 08:45:29 PDT)
- Re: [AMBER] Thermodynamic Integration (Thu Mar 17 2011 - 08:22:56 PDT)
- Re: [AMBER] Thermodynamic Integration (Thu Mar 17 2011 - 07:09:19 PDT)
- [AMBER] Thermodynamic Integration (Wed Mar 16 2011 - 14:22:07 PDT)
Ilyas Yildirim
- [AMBER] AMD Opteron system - compiling pmemd with intel or gfortran? (Fri Mar 25 2011 - 13:54:22 PDT)
- Re: [AMBER] How to get the free energy landscape from a MD simulation? (Thu Mar 24 2011 - 11:33:28 PDT)
- Re: [AMBER] How to get the free energy landscape from a MD simulation? (Thu Mar 24 2011 - 09:25:00 PDT)
- Re: [AMBER] pmemd and generalized NMR torsional restraints in AMBER10 (Wed Mar 23 2011 - 17:24:11 PDT)
- Re: [AMBER] pmemd and generalized NMR torsional restraints in AMBER10 (Wed Mar 23 2011 - 17:16:04 PDT)
- Re: [AMBER] pmemd and generalized NMR torsional restraints in AMBER10 (Wed Mar 23 2011 - 17:14:03 PDT)
- [AMBER] pmemd and generalized NMR torsional restraints in AMBER10 (Wed Mar 23 2011 - 16:48:27 PDT)
- Re: [AMBER] Missing Parameters (Fri Mar 18 2011 - 22:39:11 PDT)
- Re: [AMBER] Missing Parameters (Fri Mar 18 2011 - 21:31:00 PDT)
- Re: [AMBER] Missing Parameters (Thu Mar 17 2011 - 12:59:00 PDT)
- Re: [AMBER] Missing Parameters (Tue Mar 15 2011 - 11:18:49 PDT)
- Re: [AMBER] Amber archive mailing list is not working (Fri Mar 11 2011 - 23:29:31 PST)
Jack Lee
- [AMBER] clustering MD results (Wed Mar 30 2011 - 01:34:06 PDT)
Jack Lei
- [AMBER] unsubscribe (Wed Mar 23 2011 - 22:29:20 PDT)
Jacopo Sgrignani
- Re: [AMBER] compiling with cuda (Fri Mar 25 2011 - 08:21:44 PDT)
- [AMBER] compiling with cuda (Fri Mar 25 2011 - 01:47:49 PDT)
Jagur Lambix
- [AMBER] parameter for CNTs (Thu Mar 31 2011 - 16:02:14 PDT)
Jason Swails
- Re: [AMBER] parameter for CNTs (Thu Mar 31 2011 - 16:54:03 PDT)
- Re: [AMBER] Inconsistencies between reported lines and executed lines in source code (Thu Mar 31 2011 - 12:22:01 PDT)
- Re: [AMBER] segmentation fault when using mmpbsa.py (Wed Mar 30 2011 - 16:23:43 PDT)
- Re: [AMBER] nmropt modes for GPU accelerated pmemd 11 (Wed Mar 30 2011 - 12:59:03 PDT)
- Re: [AMBER] Implicit simulation (Wed Mar 30 2011 - 10:13:40 PDT)
- Re: [AMBER] script problem (Tue Mar 29 2011 - 14:15:22 PDT)
- Re: [AMBER] Atom name convention/conversion in antechamber (Tue Mar 29 2011 - 08:46:23 PDT)
- Re: [AMBER] Neutral Lysine (LYN) not calculated in MM_PBSA (Tue Mar 29 2011 - 08:16:53 PDT)
- Re: [AMBER] problem with peptide simulations (Mon Mar 28 2011 - 13:27:15 PDT)
- Re: [AMBER] problem with peptide simulations (Mon Mar 28 2011 - 12:29:07 PDT)
- Re: [AMBER] enzyme MD trajectory looks funny (Mon Mar 28 2011 - 08:34:23 PDT)
- Re: [AMBER] Keep getting LINMIN error. Not sure how to progress. (Mon Mar 28 2011 - 08:32:14 PDT)
- Re: [AMBER] ff10 (Sun Mar 27 2011 - 01:45:06 PDT)
- Re: [AMBER] ff10 (Sun Mar 27 2011 - 01:32:19 PDT)
- Re: [AMBER] AMD Opteron system - compiling pmemd with intel or gfortran? (Fri Mar 25 2011 - 22:44:48 PDT)
- Re: [AMBER] AMD Opteron system - compiling pmemd with intel or gfortran? (Fri Mar 25 2011 - 19:21:07 PDT)
- Re: [AMBER] how critical charge neutralization of a system (Fri Mar 25 2011 - 15:39:52 PDT)
- Re: [AMBER] QM/MM error in amber 10 (Fri Mar 25 2011 - 15:32:25 PDT)
- Re: [AMBER] Neutral Lysine (LYN) not calculated in MM_PBSA (Fri Mar 25 2011 - 14:01:19 PDT)
- Re: [AMBER] Any manual for python or perl to transform a matrix for data analysis? (Fri Mar 25 2011 - 08:23:50 PDT)
- Re: [AMBER] compiling with cuda (Fri Mar 25 2011 - 08:16:04 PDT)
- Re: [AMBER] Amber Installation error (Fri Mar 25 2011 - 08:12:38 PDT)
- Re: [AMBER] Error: vlimit exceeded for step (Fri Mar 25 2011 - 08:09:43 PDT)
- Re: [AMBER] Extract binding free energy for each snapshot (Fri Mar 25 2011 - 07:56:36 PDT)
- Re: [AMBER] Extract binding free energy for each snapshot (Fri Mar 25 2011 - 07:54:57 PDT)
- Re: [AMBER] Error with MM-PBSA perl file for pairwise residue decomposition (Thu Mar 24 2011 - 20:31:44 PDT)
- Re: [AMBER] positive GBtot value (Thu Mar 24 2011 - 18:33:23 PDT)
- Re: [AMBER] deleting protein atoms from prmtop topology files using rdparm (Thu Mar 24 2011 - 13:05:58 PDT)
- Re: [AMBER] Sander was terminating in the midddle (Thu Mar 24 2011 - 10:56:05 PDT)
- Re: [AMBER] odd output from rms measurement (Thu Mar 24 2011 - 08:41:54 PDT)
- Re: [AMBER] ptraj problems (Thu Mar 24 2011 - 08:35:14 PDT)
- Re: [AMBER] How do I plot the angle population distribution (Thu Mar 24 2011 - 08:31:21 PDT)
- Re: [AMBER] Amber (Thu Mar 24 2011 - 08:21:56 PDT)
- Re: [AMBER] odd output from rms measurement (Wed Mar 23 2011 - 18:43:12 PDT)
- Re: [AMBER] extract vdw energy (Wed Mar 23 2011 - 18:35:31 PDT)
- Re: [AMBER] how to minimize a protein-ligand system with the protein constrained (Wed Mar 23 2011 - 17:40:46 PDT)
- Re: [AMBER] odd output from rms measurement (Wed Mar 23 2011 - 17:35:00 PDT)
- Re: [AMBER] pmemd and generalized NMR torsional restraints in AMBER10 (Wed Mar 23 2011 - 17:18:52 PDT)
- Re: [AMBER] pmemd and generalized NMR torsional restraints in AMBER10 (Wed Mar 23 2011 - 17:08:15 PDT)
- Re: [AMBER] pmemd and generalized NMR torsional restraints in AMBER10 (Wed Mar 23 2011 - 17:10:28 PDT)
- Re: [AMBER] PMF calculations in Amber 10 (Wed Mar 23 2011 - 16:32:03 PDT)
- Re: [AMBER] error on atom parameters (Wed Mar 23 2011 - 12:03:56 PDT)
- Re: [AMBER] number of frames read in mmpbsa.py (Wed Mar 23 2011 - 11:55:04 PDT)
- Re: [AMBER] Doubts in MM-PBSA (Tue Mar 22 2011 - 18:23:29 PDT)
- Re: [AMBER] compiling AmberTools1.4 with -cuda flag (Tue Mar 22 2011 - 16:06:36 PDT)
- Re: [AMBER] Doubts in MM-PBSA (Tue Mar 22 2011 - 16:05:02 PDT)
- Re: [AMBER] mmpbsa.pl energy decompistion stopped (Mon Mar 21 2011 - 18:24:01 PDT)
- Re: [AMBER] Parallel amber11 Installation FAIL (Mon Mar 21 2011 - 18:13:12 PDT)
- Re: [AMBER] amber11 Installation Test Failures (Sun Mar 20 2011 - 07:36:09 PDT)
- Re: [AMBER] Amber11 make test FAILURE and ERROR (Sun Mar 20 2011 - 07:33:14 PDT)
- Re: [AMBER] MMPBSA question (Sat Mar 19 2011 - 19:11:16 PDT)
- Re: [AMBER] MMPBSA question (Sat Mar 19 2011 - 17:31:02 PDT)
- Re: [AMBER] Differences in the periodic box dimensions (Sat Mar 19 2011 - 16:39:15 PDT)
- Re: [AMBER] problem with gas-phase MD simulation in Amber8. (Fri Mar 18 2011 - 12:12:54 PDT)
- Re: [AMBER] trouble with mmpbsa.py (Fri Mar 18 2011 - 10:47:20 PDT)
- Re: [AMBER] Is rst file the last frame of output crd file? (Fri Mar 18 2011 - 10:36:07 PDT)
- Re: [AMBER] error installing AmberTools-1.2 in ubuntu 10.10 (Fri Mar 18 2011 - 01:58:34 PDT)
- Re: [AMBER] error installing AmberTools-1.2 in ubuntu 10.10 (Thu Mar 17 2011 - 14:21:25 PDT)
- Re: [AMBER] Segmentation fault (Thu Mar 17 2011 - 09:55:19 PDT)
- Re: [AMBER] Segmentation fault (Thu Mar 17 2011 - 09:53:44 PDT)
- Re: [AMBER] NVT Vs NPT (Thu Mar 17 2011 - 08:49:57 PDT)
- Re: [AMBER] MMPBSA energy contribution (Thu Mar 17 2011 - 08:40:34 PDT)
- Re: [AMBER] Thermostat (Thu Mar 17 2011 - 00:05:01 PDT)
- Re: [AMBER] NVT Vs NPT (Wed Mar 16 2011 - 09:49:39 PDT)
- Re: [AMBER] how to run amber on mutli-gpu/muti-nodes (Tue Mar 15 2011 - 17:23:29 PDT)
- Re: [AMBER] amber11 Installation Test Failures (Tue Mar 15 2011 - 17:14:05 PDT)
- Re: [AMBER] AMBER 10 serial compile problem (Tue Mar 15 2011 - 11:09:46 PDT)
- Re: [AMBER] AMBER 10 serial compile problem (Tue Mar 15 2011 - 10:41:28 PDT)
- Re: [AMBER] AMBER 10 serial compile problem (Tue Mar 15 2011 - 10:06:17 PDT)
- Re: [AMBER] AMBER 10 serial compile problem (Tue Mar 15 2011 - 09:57:54 PDT)
- Re: [AMBER] Calculation with CUTCAP (Tue Mar 15 2011 - 07:43:50 PDT)
- Re: [AMBER] amber11 intel mpi compile on altix 450 problem (Tue Mar 15 2011 - 07:38:03 PDT)
- Re: [AMBER] MD- the enzyme bouncing (Mon Mar 14 2011 - 15:07:40 PDT)
- Re: [AMBER] amber11 Installation Test Failures (Mon Mar 14 2011 - 07:08:52 PDT)
- Re: [AMBER] Would liek to plot GBTOT vs Time (Mon Mar 14 2011 - 00:02:28 PDT)
- Re: [AMBER] error in creating prmtop and inpcrd files (Sun Mar 13 2011 - 14:55:13 PDT)
- Re: [AMBER] Bad magic number ? (Sat Mar 12 2011 - 08:20:59 PST)
- Re: [AMBER] Amber archive mailing list is not working (Fri Mar 11 2011 - 23:18:58 PST)
- Re: [AMBER] Amber archive mailing list is not working (Fri Mar 11 2011 - 22:55:01 PST)
- Re: [AMBER] How to save a restart file (Fri Mar 11 2011 - 12:13:04 PST)
- Re: [AMBER] How to save a restart file (Fri Mar 11 2011 - 09:52:29 PST)
- Re: [AMBER] interaction energy (Thu Mar 10 2011 - 07:24:40 PST)
- Re: [AMBER] sander.MPI running on 8 nodes or 1?? (Tue Mar 08 2011 - 11:27:13 PST)
- Re: [AMBER] Is the neutralization necessary for the GB model? (Mon Mar 07 2011 - 13:42:07 PST)
- Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. (Mon Mar 07 2011 - 09:07:43 PST)
- Re: [AMBER] xleap not installed (Sat Mar 05 2011 - 07:02:28 PST)
- Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. (Thu Mar 03 2011 - 04:26:35 PST)
- Re: [AMBER] xleap not installed (Wed Mar 02 2011 - 22:49:13 PST)
- Re: [AMBER] error reading NMR restraints (Wed Mar 02 2011 - 16:25:59 PST)
- Re: [AMBER] xleap not installed (Tue Mar 01 2011 - 06:36:42 PST)
- Re: [AMBER] How to defining a bond between the Cβ of the substrate and the Cα of the catalytic serine (Tue Mar 01 2011 - 05:41:15 PST)
- Re: [AMBER] checking interaction between periodic images (Tue Mar 01 2011 - 05:29:33 PST)
Jio M
- [AMBER] h-bond donor acceptor definition confusion (Mon Mar 07 2011 - 06:06:51 PST)
Jiri Sponer
- Re: [AMBER] stacking energy calculation (Wed Mar 16 2011 - 04:02:39 PDT)
Joachim Reichelt
- [AMBER] Amber11 on osx using port and gcc4.5 (Fri Mar 18 2011 - 05:42:58 PDT)
John Khan
- [AMBER] Problem installing Amber11/Ambertools1.4 on Ubuntu10.10 (Tue Mar 08 2011 - 10:01:59 PST)
John S
- [AMBER] usage of 2drms (Thu Mar 24 2011 - 10:12:36 PDT)
- [AMBER] error on atom parameters (Wed Mar 23 2011 - 11:07:47 PDT)
- [AMBER] MMPBSA energy contribution (Thu Mar 17 2011 - 08:05:12 PDT)
Jojart_Balazs
- [AMBER] discrepancy after sieve in ptraj (Thu Mar 17 2011 - 05:24:46 PDT)
- Re: [AMBER] no answer so far - free energy profile for water slab (Wed Mar 16 2011 - 07:38:35 PDT)
Jorgen Simonsen
- Re: [AMBER] ff10 (Sun Mar 27 2011 - 01:47:53 PDT)
- Re: [AMBER] ff10 (Sun Mar 27 2011 - 01:40:55 PDT)
- Re: [AMBER] ff10 (Sun Mar 27 2011 - 00:30:28 PDT)
- [AMBER] ff10 (Sat Mar 26 2011 - 11:39:44 PDT)
- [AMBER] solvation free energy (Tue Mar 22 2011 - 11:08:57 PDT)
- Re: [AMBER] parameters for metal site (Thu Mar 17 2011 - 07:39:14 PDT)
- [AMBER] parameters for metal site (Thu Mar 17 2011 - 02:24:16 PDT)
- Re: [AMBER] acceptance probabilities remd (Tue Mar 08 2011 - 03:58:18 PST)
- [AMBER] acceptance probabilities remd (Tue Mar 08 2011 - 02:02:59 PST)
juan zeng
- [AMBER] about Nmod in amber11 (Tue Mar 08 2011 - 23:25:11 PST)
Junjian Miao
- Re: [AMBER] using thermodynamic integration, how to deal with absolute pka and conformation change (Thu Mar 17 2011 - 20:32:55 PDT)
- [AMBER] using thermodynamic integration, how to deal with absolute pka and conformation change (Wed Mar 16 2011 - 05:58:58 PDT)
- Re: [AMBER] a question about using oplsaa ff in amber (Tue Mar 08 2011 - 17:13:58 PST)
- [AMBER] a question about using oplsaa ff in amber (Mon Mar 07 2011 - 20:12:35 PST)
- [AMBER] how to create periodic box similar to TIP3PBOX? (Thu Mar 03 2011 - 17:32:35 PST)
juzer stationwala
- Re: [AMBER] error installing AmberTools-1.2 in ubuntu 10.10 (Fri Mar 18 2011 - 02:02:50 PDT)
kala
- [AMBER] Zn active site parameterization (Sun Mar 06 2011 - 11:59:04 PST)
Kamali Sripathi
- Re: [AMBER] Ptraj crashes and Hbond analysis (Thu Mar 24 2011 - 06:36:28 PDT)
- Re: [AMBER] Ptraj crashes and Hbond analysis (Wed Mar 23 2011 - 11:44:45 PDT)
- Re: [AMBER] Ptraj crashes and Hbond analysis (Wed Mar 23 2011 - 11:16:15 PDT)
- Re: [AMBER] Ptraj crashes and Hbond analysis (Wed Mar 23 2011 - 06:01:05 PDT)
- [AMBER] Ptraj crashes and Hbond analysis (Tue Mar 22 2011 - 09:43:37 PDT)
- Re: [AMBER] Ptraj: Hbond and Bfactor analyses (Thu Mar 17 2011 - 18:49:21 PDT)
Kevin Hauser
- Re: [AMBER] randomly place counterions (Wed Mar 02 2011 - 08:52:10 PST)
- Re: [AMBER] randomly place counterions (Wed Mar 02 2011 - 06:59:18 PST)
kurisaki.ncube.human.nagoya-u.ac.jp
- [AMBER] Can we relax protein and ligand separately? (Wed Mar 09 2011 - 17:34:38 PST)
- Re: [AMBER] Will no implementation of feupdateenv cause serious problems? (Tue Mar 01 2011 - 22:29:52 PST)
- [AMBER] Will no implementation of feupdateenv cause serious problems? (Tue Mar 01 2011 - 21:55:51 PST)
Lachele Foley (Lists)
- Re: [AMBER] Dihedral angles does not match VMD vs ptraj (Fri Mar 18 2011 - 14:42:04 PDT)
- Re: [AMBER] Dihedral angles does not match VMD vs ptraj (Fri Mar 18 2011 - 14:40:48 PDT)
- Re: [AMBER] Dihedral angles does not match VMD vs ptraj (Fri Mar 18 2011 - 14:08:33 PDT)
- [AMBER] Important Notice Re Sleap (especially with Glycam) (Mon Mar 14 2011 - 07:27:12 PDT)
leila karami
- [AMBER] ptraj / water-mediated hydrogen bonds (Thu Mar 03 2011 - 05:11:39 PST)
- [AMBER] ptraj / water-medited hydrogen bonds (Thu Mar 03 2011 - 04:26:41 PST)
Lihua Wang
- [AMBER] mm_pbsa input for energy decomposition (Mon Mar 14 2011 - 16:23:06 PDT)
Lisa Perez
- Re: [AMBER] amber11 intel mpi compile on altix 450 problem (Wed Mar 16 2011 - 09:45:03 PDT)
- [AMBER] amber11 intel mpi compile on altix 450 problem (Mon Mar 14 2011 - 22:09:01 PDT)
Lorenzo Gontrani
- [AMBER] Force Field question - DLPOLY to AMBER (Tue Mar 22 2011 - 10:09:51 PDT)
Lowe, Ben (Ext)
- Re: [AMBER] Zn Bond Length solvatebox (Fri Mar 04 2011 - 04:58:37 PST)
- [AMBER] Zn Bond Length solvatebox (Fri Mar 04 2011 - 02:25:53 PST)
Lucio Ferella
- [AMBER] solvatecap (Fri Mar 25 2011 - 11:07:51 PDT)
M. L. Dodson
- Re: [AMBER] How to use perl to replace number to txt? (Thu Mar 31 2011 - 07:31:36 PDT)
M. Shahid
- Re: [AMBER] Any manual for python or perl to transform a matrix for data analysis? (Fri Mar 25 2011 - 13:57:33 PDT)
Madhurima Jana
- [AMBER] building HA8 (hyaluronic acid 8-mer) using amber leap (Fri Mar 04 2011 - 21:36:04 PST)
Mahmoud Soliman
- Re: [AMBER] script problem (Tue Mar 29 2011 - 14:44:46 PDT)
- [AMBER] script problem (Tue Mar 29 2011 - 14:16:15 PDT)
- Re: [AMBER] water box deforms during MD (Mon Mar 28 2011 - 08:49:06 PDT)
- [AMBER] water box deforms during MD (Mon Mar 28 2011 - 07:02:20 PDT)
- Re: [AMBER] enzyme MD trajectory looks funny (Mon Mar 28 2011 - 06:37:21 PDT)
- Re: [AMBER] enzyme MD trajectory looks funny (Mon Mar 28 2011 - 06:34:35 PDT)
- [AMBER] enzyme MD trajectory looks funny (Mon Mar 28 2011 - 06:10:38 PDT)
- Re: [AMBER] QM/MM error in amber 10 (Sun Mar 27 2011 - 22:46:47 PDT)
- [AMBER] QM/MM error in amber 10 (Fri Mar 25 2011 - 15:21:16 PDT)
- [AMBER] how critical charge neutralization of a system (Fri Mar 25 2011 - 14:02:35 PDT)
- Re: [AMBER] How to get the free energy landscape from a MD simulation? (Thu Mar 24 2011 - 12:08:30 PDT)
- Re: [AMBER] How to get the free energy landscape from a MD simulation? (Thu Mar 24 2011 - 10:50:19 PDT)
- Re: [AMBER] Atom name convention/conversion in antechamber (Thu Mar 24 2011 - 09:12:47 PDT)
- Re: [AMBER] How to get the free energy landscape from a MD simulation? (Thu Mar 24 2011 - 09:06:25 PDT)
- Re: [AMBER] How to get the free energy landscape from a MD simulation? (Thu Mar 24 2011 - 08:23:10 PDT)
- [AMBER] PMF calculations in Amber 10 (Wed Mar 23 2011 - 16:17:28 PDT)
- Re: [AMBER] scientific question on decomposition analysis in pbsa calculation (Wed Mar 23 2011 - 08:11:47 PDT)
- Re: [AMBER] scientific question on decomposition analysis in pbsa calculation (Wed Mar 23 2011 - 07:38:56 PDT)
- Re: [AMBER] Perl Vs Python in MMPBSA calculations in Amber 10 (Wed Mar 23 2011 - 07:23:49 PDT)
- [AMBER] scientific question on decomposition analysis in pbsa calculation (Wed Mar 23 2011 - 07:20:37 PDT)
- [AMBER] Perl Vs Python in MMPBSA calculations in Amber 10 (Wed Mar 23 2011 - 06:52:04 PDT)
- Re: [AMBER] can I calculate binding energy with some restraints (Mon Mar 21 2011 - 10:40:24 PDT)
- [AMBER] can I calculate binding energy with some restraints (Mon Mar 21 2011 - 08:06:17 PDT)
- Re: [AMBER] NVT Vs NPT (Wed Mar 16 2011 - 12:36:43 PDT)
- Re: [AMBER] NVT Vs NPT MD simulations (Wed Mar 16 2011 - 08:00:46 PDT)
- [AMBER] NVT Vs NPT (Wed Mar 16 2011 - 00:31:07 PDT)
- [AMBER] MD- the enzyme bouncing (Mon Mar 14 2011 - 13:44:41 PDT)
- [AMBER] MD- the enzyme bouncing (Mon Mar 14 2011 - 13:44:11 PDT)
- Re: [AMBER] continuum solvation with low viscosity (Wed Mar 09 2011 - 06:17:36 PST)
- [AMBER] continuum solvation with low viscosity (Tue Mar 08 2011 - 12:28:05 PST)
manikanthan bhavaraju
- [AMBER] GBSA calculations using mm_pbsa.pl (Sat Mar 26 2011 - 17:59:38 PDT)
- Re: [AMBER] Reimaging Problem (Wed Mar 16 2011 - 09:34:05 PDT)
Mannan
- Re: [AMBER] Would liek to plot GBTOT vs Time (Sun Mar 13 2011 - 22:59:39 PDT)
marc gueroult
- Re: [AMBER] pmemd and nmr restraint (Thu Mar 31 2011 - 08:56:16 PDT)
- [AMBER] pmemd and nmr restraint (Fri Mar 25 2011 - 10:53:21 PDT)
Marek Maly
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Thu Mar 31 2011 - 02:34:38 PDT)
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 12:26:50 PDT)
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 11:59:20 PDT)
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 08:24:07 PDT)
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 06:48:35 PDT)
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 05:34:30 PDT)
- [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 02:39:41 PDT)
- Re: [AMBER] Missing Parameters (Thu Mar 17 2011 - 13:05:02 PDT)
- Re: [AMBER] NVT Vs NPT (Thu Mar 17 2011 - 10:03:08 PDT)
- Re: [AMBER] NVT Vs NPT (Thu Mar 17 2011 - 09:10:17 PDT)
- Re: [AMBER] NVT Vs NPT (Thu Mar 17 2011 - 06:25:27 PDT)
- Re: [AMBER] PB Bomb in pb_aaradi ? (Thu Mar 17 2011 - 03:43:28 PDT)
- [AMBER] PB Bomb in pb_aaradi ? (Tue Mar 15 2011 - 20:49:14 PDT)
- [AMBER] PB Bomb in pb_aaradi ? (Tue Mar 15 2011 - 18:45:06 PDT)
Mariano Rech
- [AMBER] Ptraj analyze crankshaft (Thu Mar 10 2011 - 08:12:25 PST)
Mark Williamson
- Re: [AMBER] Is rst file the last frame of output crd file? (Fri Mar 18 2011 - 10:21:15 PDT)
- Re: [AMBER] chamber (Thu Mar 03 2011 - 01:53:24 PST)
- Re: [AMBER] CHAMBER prmtop (Wed Mar 02 2011 - 09:48:02 PST)
- Re: [AMBER] chamber (Wed Mar 02 2011 - 08:18:27 PST)
markus metz
- [AMBER] AmberTools1.4 question (Sat Mar 26 2011 - 10:40:56 PDT)
marta wiśniewska.
- Re: [AMBER] problem with gas-phase MD simulation in Amber8. (Fri Mar 18 2011 - 12:20:17 PDT)
- Re: [AMBER] problem with gas-phase MD simulation in Amber8. (Fri Mar 18 2011 - 12:08:36 PDT)
- Re: [AMBER] problem with gas-phase MD simulation in Amber8. (Fri Mar 18 2011 - 10:13:03 PDT)
- [AMBER] problem with gas-phase MD simulation in Amber8. (Fri Mar 18 2011 - 04:37:09 PDT)
Martina Roeselova
- Re: [AMBER] no answer so far - free energy profile for water slab (Tue Mar 15 2011 - 07:57:16 PDT)
- [AMBER] no answer so far - free energy profile for water slab (Tue Mar 15 2011 - 02:20:09 PDT)
- [AMBER] free energy profile for water slab (Fri Mar 11 2011 - 10:24:04 PST)
MASLYK, MACIEJ MARCIN
- [AMBER] ODP: Segmentation fault (Tue Mar 22 2011 - 04:10:55 PDT)
- [AMBER] Segmentation fault (Wed Mar 16 2011 - 08:50:36 PDT)
Massimiliano Porrini
- [AMBER] non standard Alanine (Fri Mar 04 2011 - 06:41:59 PST)
Melanie
- Re: [AMBER] Missing Parameters (Fri Mar 18 2011 - 21:05:47 PDT)
- Re: [AMBER] Missing Parameters (Thu Mar 17 2011 - 12:27:35 PDT)
- [AMBER] Missing Parameters (Tue Mar 15 2011 - 10:29:32 PDT)
Mengjuei Hsieh
- Re: [AMBER] problem with gas-phase MD simulation in Amber8. (Fri Mar 18 2011 - 05:19:49 PDT)
- Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. (Thu Mar 10 2011 - 11:47:15 PST)
- Re: [AMBER] xleap not installed (Sat Mar 05 2011 - 07:29:29 PST)
mirage .
- Re: [AMBER] angle in h-bond analysis (Mon Mar 14 2011 - 00:40:47 PDT)
- [AMBER] angle in h-bond analysis (Fri Mar 11 2011 - 06:10:20 PST)
mish
- Re: [AMBER] MM/PBSA (Problem in snapshot generation) (Mon Mar 21 2011 - 11:06:34 PDT)
- [AMBER] MM/PBSA (Problem in snapshot generation) (Mon Mar 21 2011 - 10:00:37 PDT)
- [AMBER] How to calculate water density around the certain residue or ligand (Tue Mar 15 2011 - 07:47:54 PDT)
- [AMBER] grid action command in ptraj (Wed Mar 09 2011 - 04:41:06 PST)
Monika Sharma
- Re: [AMBER] Error with MM-PBSA perl file for pairwise residue decomposition (Fri Mar 25 2011 - 03:18:59 PDT)
- [AMBER] Error with MM-PBSA perl file for pairwise residue decomposition (Thu Mar 24 2011 - 20:09:16 PDT)
Muriel Jourdan
- Re: [AMBER] probleme with "reference" using ptraj (Mon Mar 21 2011 - 08:48:59 PDT)
- [AMBER] probleme with "reference" using ptraj (Mon Mar 21 2011 - 07:28:09 PDT)
N.R. Jena
- Re: [AMBER] MM-PBSA Error (Mon Mar 21 2011 - 04:38:59 PDT)
- [AMBER] MM-PBSA Error (Mon Mar 21 2011 - 04:25:31 PDT)
Naveen Samala
- [AMBER] Regarding: Adding New Multi-atom Residue (Ligand) including partial charges (Mon Mar 14 2011 - 11:30:32 PDT)
- [AMBER] Atom Types involved in Carbon monoxide and Cyanide bonds (Wed Mar 09 2011 - 12:45:39 PST)
- [AMBER] Partial Charges for Atom Types (Wed Mar 09 2011 - 08:17:37 PST)
Nitu Bansal
- [AMBER] Nitu Bansal wants to chat (Fri Mar 11 2011 - 09:17:44 PST)
Osman, Roman
- Re: [AMBER] Calculation with CUTCAP (Tue Mar 15 2011 - 06:34:22 PDT)
Ouaray Z.
- [AMBER] protein charge (Mon Mar 21 2011 - 06:52:23 PDT)
pankhuri arora
- [AMBER] Error: vlimit exceeded for step (Fri Mar 25 2011 - 04:38:11 PDT)
Pegado Luis
- Re: [AMBER] Problems with tleap (Tue Mar 08 2011 - 02:04:34 PST)
- [AMBER] Problems with tleap (Mon Mar 07 2011 - 10:42:55 PST)
Per Jr. Greisen
- Re: [AMBER] enzyme MD trajectory looks funny (Mon Mar 28 2011 - 06:07:55 PDT)
- Re: [AMBER] Any manual for python or perl to transform a matrix for data analysis? (Fri Mar 25 2011 - 00:55:13 PDT)
- Re: [AMBER] how to minimize a protein-ligand system with the protein constrained (Wed Mar 23 2011 - 13:14:44 PDT)
- Re: [AMBER] Partial Charges for Atom Types (Wed Mar 09 2011 - 08:42:07 PST)
- Re: [AMBER] Zn active site parameterization (Mon Mar 07 2011 - 05:12:30 PST)
Pooja Khurana
- [AMBER] symmetry corrected RMSD calculation (Sat Mar 19 2011 - 19:38:21 PDT)
py
- Re: [AMBER] How to defining a bond between the Cβ of the substrate and the Cα of the catalytic serine (Tue Mar 01 2011 - 06:28:17 PST)
r smith
- Re: [AMBER] Loading .mol2 file in sleap (Wed Mar 30 2011 - 12:30:46 PDT)
- Re: [AMBER] Loading .mol2 file in sleap (Wed Mar 30 2011 - 09:19:21 PDT)
- Re: [AMBER] Loading .mol2 file in sleap (Wed Mar 30 2011 - 09:08:07 PDT)
- [AMBER] Loading .mol2 file in sleap (Wed Mar 30 2011 - 06:12:15 PDT)
Rahul Banerjee
- Re: [AMBER] probleme with "reference" using ptraj (Mon Mar 21 2011 - 07:30:27 PDT)
- Re: [AMBER] How to save a restart file (Fri Mar 11 2011 - 09:04:58 PST)
- [AMBER] How to save a restart file (Fri Mar 11 2011 - 08:51:50 PST)
Rajesh Raju
- Re: [AMBER] Umbrella sampling coordinate question (Thu Mar 10 2011 - 09:59:19 PST)
- Re: [AMBER] Umbrella sampling coordinate question (Thu Mar 10 2011 - 09:45:22 PST)
- Re: [AMBER] Umbrella sampling coordinate question (Wed Mar 09 2011 - 10:55:38 PST)
- [AMBER] Umbrella sampling coordinate question (Tue Mar 08 2011 - 15:21:36 PST)
Rajeswari A.
- Re: [AMBER] enzyme MD trajectory looks funny (Mon Mar 28 2011 - 06:19:02 PDT)
- Re: [AMBER] Help: Clustering trajectories based on dihedral angle? (Mon Mar 28 2011 - 05:40:37 PDT)
- [AMBER] Help: Clustering trajectories based on dihedral angle? (Fri Mar 25 2011 - 01:38:00 PDT)
Ray Luo, Ph.D.
- Re: [AMBER] scientific question on decomposition analysis in pbsa calculation (Wed Mar 23 2011 - 07:24:52 PDT)
- Re: [AMBER] PB Bomb in pb_aaradi ? (Thu Mar 17 2011 - 10:33:54 PDT)
- Re: [AMBER] PB Bomb in pb_aaradi ? (Tue Mar 15 2011 - 21:43:46 PDT)
- Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. (Thu Mar 10 2011 - 10:26:02 PST)
- Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. (Thu Mar 10 2011 - 09:48:43 PST)
- Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. (Thu Mar 10 2011 - 09:16:05 PST)
- Re: [AMBER] Nab PB focusing error (Wed Mar 09 2011 - 12:23:12 PST)
- Re: [AMBER] Unresolved problem about MM/PBSA (Thu Mar 03 2011 - 19:04:02 PST)
- Re: [AMBER] total charge of NPRO in amber03 force field (Thu Mar 03 2011 - 08:20:59 PST)
- Re: [AMBER] Unresolved problem about MM/PBSA (Thu Mar 03 2011 - 08:09:06 PST)
Robert Wohlhueter
- [AMBER] compiling AmberTools1.4 with -cuda flag (Tue Mar 22 2011 - 15:46:56 PDT)
Roman Osman
- Re: [AMBER] Calculation with CUTCAP (Tue Mar 15 2011 - 07:51:16 PDT)
- [AMBER] Calculation with CUTCAP (Mon Mar 14 2011 - 20:20:43 PDT)
ros
- [AMBER] CUDA Installation URL (Fri Mar 25 2011 - 09:40:22 PDT)
- [AMBER] Specially For You (Thu Mar 10 2011 - 05:55:29 PST)
Ross Walker
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Thu Mar 31 2011 - 11:23:31 PDT)
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 15:48:37 PDT)
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 12:21:54 PDT)
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 11:29:58 PDT)
- Re: [AMBER] nmropt modes for GPU accelerated pmemd 11 (Wed Mar 30 2011 - 11:27:10 PDT)
- Re: [AMBER] compiling AmberTools1.4 with -cuda flag (Tue Mar 22 2011 - 16:09:24 PDT)
- Re: [AMBER] problem with gas-phase MD simulation in Amber8. (Fri Mar 18 2011 - 10:54:00 PDT)
- Re: [AMBER] Using Intel compilers on AMD CPU (Fri Mar 18 2011 - 09:09:43 PDT)
- Re: [AMBER] NVT Vs NPT (Thu Mar 17 2011 - 09:31:23 PDT)
- Re: [AMBER] Problem with link atom in QM/MM (Wed Mar 16 2011 - 09:39:41 PDT)
- Re: [AMBER] how to run amber on mutli-gpu/muti-nodes (Tue Mar 15 2011 - 15:13:44 PDT)
- Re: [AMBER] Compatibility Question (Mon Mar 14 2011 - 18:44:29 PDT)
- Re: [AMBER] Amber archive mailing list is not working (Mon Mar 14 2011 - 09:57:23 PDT)
- Re: [AMBER] Amber archive mailing list is not working (Sat Mar 12 2011 - 10:50:07 PST)
- [AMBER] Amber Training Workshop Announcement - Barcelona, Spain. 3-6 May 2011 (Fri Mar 11 2011 - 10:24:53 PST)
- Re: [AMBER] CUDA 4.0 RC (Mon Mar 07 2011 - 20:53:14 PST)
- Re: [AMBER] implicit solvent with cuda (Thu Mar 03 2011 - 06:21:56 PST)
- Re: [AMBER] Will no implementation of feupdateenv cause serious problems? (Tue Mar 01 2011 - 22:18:00 PST)
- Re: [AMBER] CHAMBER prmtop (Tue Mar 01 2011 - 20:30:08 PST)
Rubben Torella
- Re: [AMBER] Neutral Lysine (LYN) not calculated in MM_PBSA (Tue Mar 29 2011 - 03:50:57 PDT)
- [AMBER] Neutral Lysine (LYN) not calculated in MM_PBSA (Fri Mar 25 2011 - 10:34:17 PDT)
- Re: [AMBER] Fwd: Implicit solvent GB calculation (Mon Mar 07 2011 - 08:03:16 PST)
- Re: [AMBER] Fwd: Implicit solvent GB calculation (Mon Mar 07 2011 - 07:17:59 PST)
- [AMBER] Fwd: Implicit solvent GB calculation (Mon Mar 07 2011 - 07:04:35 PST)
Sangita Kachhap
- Re: [AMBER] positional restraint on crystal water (Wed Mar 30 2011 - 03:14:44 PDT)
- Re: [AMBER] positional restraint on crystal water (Wed Mar 30 2011 - 02:40:00 PDT)
- Re: [AMBER] positional restraint on crystal water (Wed Mar 30 2011 - 02:31:53 PDT)
- Re: [AMBER] positional restraint on crystal water (Wed Mar 30 2011 - 01:45:42 PDT)
- [AMBER] positional restraint on crystal water (Wed Mar 30 2011 - 00:30:16 PDT)
- Re: [AMBER] Sander was terminating in the midddle (Fri Mar 25 2011 - 07:05:56 PDT)
- Re: [AMBER] Sander was terminating in the midddle (Thu Mar 24 2011 - 11:28:15 PDT)
- Re: [AMBER] odd output from rms measurement (Thu Mar 24 2011 - 02:54:29 PDT)
- Re: [AMBER] distance cutoff of closest command (Wed Mar 16 2011 - 11:05:50 PDT)
- Re: [AMBER] distance cutoff of closest command (Wed Mar 16 2011 - 10:24:38 PDT)
- [AMBER] distance cutoff of closest command (Wed Mar 16 2011 - 03:07:36 PDT)
- Re: [AMBER] how to run PIMD (Fri Mar 11 2011 - 11:15:35 PST)
- [AMBER] how to run PIMD (Fri Mar 11 2011 - 09:29:20 PST)
- Re: [AMBER] Blowing array; too many frames!! (Fri Mar 04 2011 - 11:24:04 PST)
- Re: [AMBER] Blowing array; too many frames!! (Thu Mar 03 2011 - 20:37:48 PST)
- Re: [AMBER] Blowing array; too many frames!! (Thu Mar 03 2011 - 19:56:52 PST)
- Re: [AMBER] Blowing array; too many frames!! (Thu Mar 03 2011 - 09:00:18 PST)
- Re: [AMBER] Blowing array; too many frames!! (Thu Mar 03 2011 - 08:25:01 PST)
- Re: [AMBER] Blowing array; too many frames!! (Thu Mar 03 2011 - 07:59:50 PST)
- [AMBER] Blowing array; too many frames!! (Thu Mar 03 2011 - 04:33:30 PST)
- Re: [AMBER] water mediated H-Bond (Wed Mar 02 2011 - 19:56:52 PST)
- Re: [AMBER] water mediated H-Bond (Wed Mar 02 2011 - 01:52:31 PST)
- Re: [AMBER] water mediated H-Bond (Wed Mar 02 2011 - 00:41:36 PST)
- Re: [AMBER] water mediated H-Bond (Tue Mar 01 2011 - 10:17:14 PST)
- [AMBER] water mediated H-Bond (Tue Mar 01 2011 - 09:37:31 PST)
Sasha Buzko
- Re: [AMBER] pmemd.cuda issues on Tesla S2050 (Wed Mar 02 2011 - 09:54:08 PST)
Scott Brozell
- Re: [AMBER] HEME parameters (Thu Mar 03 2011 - 19:10:11 PST)
Scott Le Grand
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Thu Mar 31 2011 - 12:33:49 PDT)
- Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? (Wed Mar 30 2011 - 11:37:21 PDT)
- Re: [AMBER] compiling with cuda (Fri Mar 25 2011 - 08:53:55 PDT)
- Re: [AMBER] CUDA 4.0 RC (Tue Mar 08 2011 - 20:04:31 PST)
Sergio R Aragon
- Re: [AMBER] AMD Opteron system - compiling pmemd with intel or gfortran? (Fri Mar 25 2011 - 22:21:39 PDT)
- Re: [AMBER] AMD Opteron system - compiling pmemd with intel or gfortran? (Fri Mar 25 2011 - 16:42:19 PDT)
setyanto md
- Re: [AMBER] Add Residue at N-terminal (Thu Mar 31 2011 - 07:17:59 PDT)
- [AMBER] Add Residue at N-terminal (Thu Mar 31 2011 - 06:57:17 PDT)
- Re: [AMBER] Diffusion coefficient (Tue Mar 08 2011 - 20:33:40 PST)
Seungyeul Yoo
- [AMBER] Residuegen Usage (Tue Mar 22 2011 - 15:26:03 PDT)
Sidney Elmer
- [AMBER] how to print out frames from conflib and lmod_traj arrays in NAB (Tue Mar 22 2011 - 18:10:43 PDT)
sonali dhindwal
- Re: [AMBER] xleap not installed (Tue Mar 08 2011 - 04:00:31 PST)
- Re: [AMBER] xleap not installed (Sun Mar 06 2011 - 22:15:04 PST)
- Re: [AMBER] xleap not installed (Sat Mar 05 2011 - 04:54:59 PST)
- Re: [AMBER] xleap not installed (Thu Mar 03 2011 - 02:19:48 PST)
- Re: [AMBER] xleap not installed (Wed Mar 02 2011 - 20:26:17 PST)
- Re: [AMBER] xleap not installed (Tue Mar 01 2011 - 20:54:11 PST)
- Re: [AMBER] xleap not installed (Tue Mar 01 2011 - 06:24:57 PST)
- [AMBER] xleap not installed (Tue Mar 01 2011 - 05:56:24 PST)
steinbrt.rci.rutgers.edu
- Re: [AMBER] water box deforms during MD (Mon Mar 28 2011 - 07:05:23 PDT)
- Re: [AMBER] Any manual for python or perl to transform a matrix for data analysis? (Fri Mar 25 2011 - 01:31:02 PDT)
- Re: [AMBER] Tools to calculate free energies landscape from the MD simulation without doing PMF? (Fri Mar 25 2011 - 01:25:37 PDT)
- Re: [AMBER] How to get the free energy landscape from a MD simulation? (Thu Mar 24 2011 - 08:27:48 PDT)
- Re: [AMBER] How to get the free energy landscape from a MD simulation? (Thu Mar 24 2011 - 08:04:03 PDT)
- Re: [AMBER] problem with gas-phase MD simulation in Amber8. (Fri Mar 18 2011 - 05:22:50 PDT)
- Re: [AMBER] Thermodynamic Integration (Fri Mar 18 2011 - 02:11:50 PDT)
- Re: [AMBER] Thermodynamic Integration (Thu Mar 17 2011 - 08:06:03 PDT)
- Re: [AMBER] Thermodynamic Integration (Thu Mar 17 2011 - 02:10:20 PDT)
- Re: [AMBER] free energy calculation with TI (Wed Mar 16 2011 - 02:25:15 PDT)
- Re: [AMBER] free energy calculation with TI (Wed Mar 16 2011 - 02:21:52 PDT)
- Re: [AMBER] free energy calculation with TI (Tue Mar 15 2011 - 14:31:38 PDT)
- Re: [AMBER] interaction energy (Thu Mar 10 2011 - 03:42:48 PST)
- Re: [AMBER] interaction energy (Thu Mar 10 2011 - 01:39:43 PST)
- Re: [AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE (Thu Mar 10 2011 - 00:03:05 PST)
- Re: [AMBER] randomly place counterions (Wed Mar 02 2011 - 04:42:17 PST)
Steven Cox
- [AMBER] PMEMD on the Open Science Grid (Thu Mar 31 2011 - 07:19:42 PDT)
subrata paul
- [AMBER] rdf plot (Fri Mar 11 2011 - 19:54:29 PST)
Sushil Mishra
- Re: [AMBER] nmode memory issue (Mon Mar 21 2011 - 10:14:52 PDT)
Thomas Cheatham III
- Re: [AMBER] clustering MD results (Wed Mar 30 2011 - 14:28:39 PDT)
- Re: [AMBER] Help: Clustering trajectories based on dihedral angle? (Fri Mar 25 2011 - 15:35:25 PDT)
- Re: [AMBER] Ptraj crashes and Hbond analysis (Tue Mar 22 2011 - 16:33:37 PDT)
- Re: [AMBER] average structure pdb file looks wrong (Tue Mar 22 2011 - 16:19:03 PDT)
thomas.fox.boehringer-ingelheim.com
- Re: [AMBER] Atom name convention/conversion in antechamber (Mon Mar 28 2011 - 23:45:09 PDT)
- Re: [AMBER] ptraj: box information for truncated octahedron (Thu Mar 24 2011 - 11:25:24 PDT)
- [AMBER] ptraj: box information for truncated octahedron (Thu Mar 24 2011 - 10:10:35 PDT)
- Re: [AMBER] Atom name convention/conversion in antechamber (Thu Mar 24 2011 - 08:42:50 PDT)
- [AMBER] Atom name convention/conversion in antechamber (Wed Mar 23 2011 - 03:47:26 PDT)
- Re: [AMBER] randomly place counterions (Wed Mar 02 2011 - 08:25:48 PST)
- Re: [AMBER] randomly place counterions (Wed Mar 02 2011 - 08:07:02 PST)
- [AMBER] randomly place counterions (Wed Mar 02 2011 - 02:55:55 PST)
Tru Huynh
- Re: [AMBER] amber11 Installation Test Failures (Sat Mar 19 2011 - 17:30:40 PDT)
- Re: [AMBER] AmberTools 1.4 possible bug for secstruct (test case attached) (Mon Mar 14 2011 - 10:46:34 PDT)
- [AMBER] AmberTools 1.4 possible bug for secstruct (test case attached) (Fri Mar 11 2011 - 16:30:57 PST)
vani panguluri
- Re: [AMBER] Sander was terminating in the midddle (Thu Mar 24 2011 - 23:08:39 PDT)
- Re: [AMBER] Sander was terminating in the midddle (Thu Mar 24 2011 - 11:09:13 PDT)
- Re: [AMBER] Sander was terminating in the midddle (Thu Mar 24 2011 - 11:02:06 PDT)
- [AMBER] Sander was terminating in the midddle (Thu Mar 24 2011 - 10:47:10 PDT)
- Re: [AMBER] Doubts in MM-PBSA (Tue Mar 22 2011 - 21:44:52 PDT)
- Re: [AMBER] Doubts in MM-PBSA (Tue Mar 22 2011 - 18:01:30 PDT)
- [AMBER] Doubts in MM-PBSA (Tue Mar 22 2011 - 14:52:00 PDT)
Vijay Manickam Achari
- [AMBER] Differences in the periodic box dimensions (Sat Mar 19 2011 - 14:38:25 PDT)
- [AMBER] changing X Y Z orientation (Fri Mar 18 2011 - 03:47:21 PDT)
- Re: [AMBER] error installing AmberTools-1.2 in ubuntu 10.10 (Thu Mar 17 2011 - 19:57:11 PDT)
- [AMBER] error installing AmberTools-1.2 in ubuntu 10.10 (Thu Mar 17 2011 - 12:24:46 PDT)
Vivien Landre
- Re: [AMBER] Creating distaint restaint in Amber (Wed Mar 23 2011 - 00:26:30 PDT)
- [AMBER] Creating distaint restaint in Amber (Wed Mar 09 2011 - 19:40:37 PST)
Vlastimil Zíma
- [AMBER] Add residue copied from other unit (Tue Mar 15 2011 - 08:24:14 PDT)
Wei Huang
- Re: [AMBER] Extract binding free energy for each snapshot (Fri Mar 25 2011 - 08:17:07 PDT)
- [AMBER] Extract binding free energy for each snapshot (Fri Mar 25 2011 - 07:18:07 PDT)
Wen Xu
- Re: [AMBER] how to calculate scattering trajectory (Mon Mar 21 2011 - 08:11:41 PDT)
- [AMBER] how to calculate scattering trajectory (Sun Mar 20 2011 - 12:51:01 PDT)
Wong, Sergio E.
- Re: [AMBER] using NMR restraints within LMOD (Wed Mar 09 2011 - 10:52:59 PST)
- [AMBER] using NMR restraints within LMOD (Fri Mar 04 2011 - 13:45:12 PST)
- [AMBER] error reading NMR restraints (Wed Mar 02 2011 - 15:59:56 PST)
Wook Lee
- Re: [AMBER] Problem with link atom in QM/MM (Thu Mar 17 2011 - 06:29:45 PDT)
- Re: [AMBER] Problem with link atom in QM/MM (Thu Mar 17 2011 - 01:39:47 PDT)
- [AMBER] Problem with link atom in QM/MM (Wed Mar 16 2011 - 08:01:31 PDT)
Ye MEI
- Re: [AMBER] how to choose the biasing potential based on thecoarsefree energy curve (Tue Mar 15 2011 - 20:28:05 PDT)
- Re: [AMBER] how to choose the biasing potential based on the coarsefree energy curve (Tue Mar 15 2011 - 06:41:53 PDT)
- [AMBER] how to choose the biasing potential based on the coarse free energy curve (Mon Mar 14 2011 - 21:21:12 PDT)
- Re: [AMBER] total charge of NPRO in amber03 force field (Thu Mar 03 2011 - 03:00:21 PST)
- [AMBER] total charge of NPRO in amber03 force field (Thu Mar 03 2011 - 02:52:23 PST)
Yuan Ding
- Re: [AMBER] extract vdw energy (Wed Mar 23 2011 - 18:41:07 PDT)
- [AMBER] extract vdw energy (Wed Mar 23 2011 - 17:41:33 PDT)
Yuan Yao
- Re: [AMBER] QM/MM error in amber 10 (Fri Mar 25 2011 - 15:20:04 PDT)
- Re: [AMBER] QM/MM error in amber 10 (Fri Mar 25 2011 - 15:16:29 PDT)
zhihong ke
- [AMBER] convert the atomic b factor to residual b factor (Fri Mar 18 2011 - 14:27:45 PDT)
- Re: [AMBER] the output of REMD simulations (Fri Mar 11 2011 - 09:39:59 PST)
- [AMBER] the output of REMD simulations (Fri Mar 11 2011 - 09:35:00 PST)
- Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. (Thu Mar 10 2011 - 10:06:29 PST)
- Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. (Thu Mar 10 2011 - 09:48:11 PST)
- Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. (Thu Mar 10 2011 - 09:13:02 PST)
- [AMBER] the charge of NPRO in FF03 is equal to 0.9. (Wed Mar 09 2011 - 12:46:40 PST)
- Re: [AMBER] Is the neutralization necessary for the GB model? (Mon Mar 07 2011 - 13:51:00 PST)
- [AMBER] Is the neutralization necessary for the GB model? (Mon Mar 07 2011 - 13:24:19 PST)
- [AMBER] is it possible to identify each mode in Nmode calculation? (Fri Mar 04 2011 - 12:44:28 PST)
ÏéÇ« ¿×
- Re: [AMBER] Unresolved problem about MM/PBSA (Thu Mar 03 2011 - 17:25:17 PST)
姜笑楠
- Re: [AMBER] odd output from rms measurement (Thu Mar 24 2011 - 00:31:34 PDT)
- [AMBER] Amber (Wed Mar 23 2011 - 23:50:08 PDT)
祥谦孔
- [AMBER] Unresolved problem about MM/PBSA (Thu Mar 03 2011 - 08:01:07 PST)
陳昭同
- [AMBER] Nmode error of MMPBSA.py (Wed Mar 23 2011 - 02:30:36 PDT)

Amber Archive Mar 2011 by author