Amber Archive Oct 2013 by author
503 messages
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Starting
Mon Sep 30 2013 - 11:00:04 PDT,
Ending
Thu Oct 31 2013 - 15:00:03 PDT
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Adrian Roitberg
Re: [AMBER] About foundations of T-REMD
(Fri Oct 25 2013 - 07:39:28 PDT)
Re: [AMBER] Doubt regarding the metadynamics simulation
(Thu Oct 17 2013 - 09:10:55 PDT)
Re: [AMBER] Doubt regarding the metadynamics simulation
(Thu Oct 17 2013 - 08:01:42 PDT)
Ahmed Ayoub
[AMBER] QM/MM interfacing Gaussian
(Sat Oct 26 2013 - 04:21:45 PDT)
Alan
Re: [AMBER] AmberTools13 and Amber11
(Fri Oct 11 2013 - 09:16:23 PDT)
[AMBER] AmberTools13 and Amber11
(Fri Oct 11 2013 - 08:07:10 PDT)
Aldo Segura
Re: [AMBER] NAB : Orienting a molecule
(Fri Oct 04 2013 - 12:53:09 PDT)
Alessandra Lacetera
[AMBER] High Temperature at NSTEP = 0
(Tue Oct 22 2013 - 08:41:12 PDT)
Andreas Goetz
Re: [AMBER] Terachem tests with trial version
(Wed Oct 23 2013 - 10:38:40 PDT)
[AMBER] Update 21 for Amber 12: EXTERN QM/MM interface
(Tue Oct 22 2013 - 15:44:03 PDT)
Re: [AMBER] About the Mg charge in AMBER FF
(Fri Oct 04 2013 - 19:20:35 PDT)
anu chandra
Re: [AMBER] Difference between the .crd file format in AMBER-7 and AMBER-12
(Sun Oct 27 2013 - 21:50:49 PDT)
[AMBER] Difference between the .crd file format in AMBER-7 and AMBER-12
(Sat Oct 26 2013 - 00:40:19 PDT)
Re: [AMBER] PTRAJ - Problem with inserting TER card
(Thu Oct 17 2013 - 21:19:32 PDT)
Re: [AMBER] PTRAJ - Problem with inserting TER card
(Wed Oct 16 2013 - 22:19:16 PDT)
[AMBER] PTRAJ - Problem with inserting TER card
(Wed Oct 16 2013 - 00:56:09 PDT)
[AMBER] High energy in per-residue MMPBSA calculation
(Thu Oct 10 2013 - 05:22:50 PDT)
[AMBER] Predicting druggable hotspots
(Wed Oct 02 2013 - 03:36:15 PDT)
Asmit Bhowmick
[AMBER] Hydrogen Bond Term in Amber ff99SB forcefield
(Sun Oct 06 2013 - 18:48:52 PDT)
Bajarang Kumbhar
[AMBER] optimization using gaussian and RESP using antechamber
(Mon Oct 21 2013 - 04:29:16 PDT)
[AMBER] problem using the R.E.D server output
(Mon Oct 21 2013 - 01:58:30 PDT)
[AMBER] problem for prmtop and inpcrd file generation
(Thu Oct 17 2013 - 22:44:42 PDT)
[AMBER] RESP charge calculation problem for SO4 -2 group
(Wed Oct 16 2013 - 05:00:00 PDT)
Baptiste Legrand
Re: [AMBER] Distributions of the phi and psi torsion angles during MD simulations
(Thu Oct 10 2013 - 14:50:31 PDT)
[AMBER] Distributions of the phi and psi torsion angles during MD simulations
(Thu Oct 10 2013 - 00:51:54 PDT)
Beale, John
[AMBER] Script?
(Tue Oct 22 2013 - 10:30:30 PDT)
Biao Ma
Re: [AMBER] The Error when I run MdoutAnalysizer.py
(Thu Oct 03 2013 - 22:36:48 PDT)
[AMBER] The Error when I run MdoutAnalysizer.py
(Wed Oct 02 2013 - 23:41:37 PDT)
Re: [AMBER] about error with "Must have more residues than processors!"
(Wed Oct 02 2013 - 20:47:49 PDT)
[AMBER] about error with "Must have more residues than processors!"
(Tue Oct 01 2013 - 09:00:20 PDT)
Bill Miller III
Re: [AMBER] MMPBSA problem with CHAMBER generated topology file
(Mon Oct 21 2013 - 20:22:53 PDT)
Re: [AMBER] PMEMD trajectory and MMPBSA
(Mon Oct 14 2013 - 05:33:07 PDT)
Brian Radak
Re: [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible?
(Tue Oct 29 2013 - 14:24:52 PDT)
Re: [AMBER] Making Au surface using xleap
(Fri Oct 25 2013 - 11:23:25 PDT)
Re: [AMBER] About foundations of T-REMD
(Fri Oct 25 2013 - 07:42:28 PDT)
Re: [AMBER] parmed.py bug when using the "parmout" command ?
(Thu Oct 24 2013 - 08:06:28 PDT)
Re: [AMBER] High Temperature at NSTEP = 0
(Tue Oct 22 2013 - 08:57:03 PDT)
[AMBER] Error message from pmemd.cuda
(Wed Oct 16 2013 - 13:30:00 PDT)
Re: [AMBER] PMF for 2 Arginines
(Wed Oct 16 2013 - 10:23:21 PDT)
Re: [AMBER] PMF for 2 Arginines
(Wed Oct 16 2013 - 07:30:21 PDT)
Re: [AMBER] How to calculate the free energy change of a chemical reaction by the thermodynamic integration approach?
(Fri Oct 11 2013 - 06:30:45 PDT)
Re: [AMBER] ERROR in DISTANCE RESTRAINT
(Tue Oct 08 2013 - 10:30:38 PDT)
Re: [AMBER] Generation of melting curves
(Mon Oct 07 2013 - 06:39:08 PDT)
Carlos Simmerling
Re: [AMBER] High Temperature at NSTEP = 0
(Tue Oct 22 2013 - 10:27:11 PDT)
Re: [AMBER] PMF for 2 Arginines
(Wed Oct 16 2013 - 10:50:25 PDT)
Re: [AMBER] Amber99SB force field
(Tue Oct 08 2013 - 11:18:07 PDT)
Re: [AMBER] Generation of melting curves
(Mon Oct 07 2013 - 07:49:43 PDT)
case
Re: [AMBER] DNA with NAB
(Sat Oct 26 2013 - 06:07:45 PDT)
Re: [AMBER] Single quotes in AMBER manual
(Sat Oct 26 2013 - 06:02:27 PDT)
Re: [AMBER] QM/MM interfacing Gaussian
(Sat Oct 26 2013 - 06:01:05 PDT)
Re: [AMBER] Difference between the .crd file format in AMBER-7 and AMBER-12
(Sat Oct 26 2013 - 05:58:46 PDT)
Re: [AMBER] How to use TIP4P/2005 water model
(Sat Oct 26 2013 - 05:54:23 PDT)
Re: [AMBER] why are pres_X, pres_Y, and pres_Z different?
(Fri Oct 25 2013 - 15:23:17 PDT)
Re: [AMBER] Problem about water Cap with igb=10
(Thu Oct 24 2013 - 16:52:16 PDT)
Re: [AMBER] DNA with NAB
(Thu Oct 24 2013 - 16:50:25 PDT)
Re: [AMBER] problem with heme parameters bound to HIS
(Thu Oct 24 2013 - 13:17:54 PDT)
Re: [AMBER] Leap ff10 and Sodium ion
(Thu Oct 24 2013 - 04:25:08 PDT)
Re: [AMBER] namelist input > 80 columns
(Wed Oct 23 2013 - 11:18:34 PDT)
Re: [AMBER] problem with heme parameters bound to HIS
(Fri Oct 18 2013 - 08:10:42 PDT)
Re: [AMBER] unique atoms in TI softcore
(Fri Oct 18 2013 - 08:07:47 PDT)
Re: [AMBER] Segmentation fault in tleap
(Fri Oct 11 2013 - 17:57:04 PDT)
Re: [AMBER] MPI install with openmpi
(Sat Oct 05 2013 - 09:50:18 PDT)
Re: [AMBER] MPI install with openmpi
(Sat Oct 05 2013 - 06:28:20 PDT)
Re: [AMBER] NAB : Orienting a molecule
(Sat Oct 05 2013 - 06:19:57 PDT)
CHAMI F.
[AMBER] changeLJ14Pair
(Fri Oct 04 2013 - 04:52:24 PDT)
Concha, Monica
Re: [AMBER] Sander error (AmberTools 13 & Amber10)
(Thu Oct 31 2013 - 14:40:54 PDT)
Re: [AMBER] Sander error (AmberTools 13 & Amber10)
(Thu Oct 31 2013 - 09:51:12 PDT)
[AMBER] Sander error (AmberTools 13 & Amber10)
(Thu Oct 31 2013 - 08:24:39 PDT)
Re: [AMBER] Sander error
(Tue Oct 29 2013 - 13:39:09 PDT)
[AMBER] Sander error
(Tue Oct 29 2013 - 13:09:24 PDT)
Re: [AMBER] AmberTools13
(Fri Oct 25 2013 - 14:37:43 PDT)
[AMBER] AmberTools13
(Fri Oct 25 2013 - 13:42:29 PDT)
cwt
[AMBER] How to calculate the free energy change of a chemical reaction by the thermodynamic integration approach?
(Thu Oct 10 2013 - 23:18:00 PDT)
Daniel Roe
Re: [AMBER] Sander error (AmberTools 13 & Amber10)
(Thu Oct 31 2013 - 14:56:44 PDT)
Re: [AMBER] Sander error (AmberTools 13 & Amber10)
(Thu Oct 31 2013 - 12:23:43 PDT)
Re: [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible?
(Thu Oct 31 2013 - 08:59:24 PDT)
Re: [AMBER] Sander error (AmberTools 13 & Amber10)
(Thu Oct 31 2013 - 08:38:57 PDT)
Re: [AMBER] mdcrd to dcd
(Thu Oct 31 2013 - 06:42:45 PDT)
Re: [AMBER] Hbond analysis
(Wed Oct 30 2013 - 13:36:51 PDT)
Re: [AMBER] Hbond analysis
(Wed Oct 30 2013 - 13:12:25 PDT)
Re: [AMBER] Hbond analysis
(Wed Oct 30 2013 - 12:01:25 PDT)
Re: [AMBER] acclerated molecular dynamics alphaP
(Tue Oct 29 2013 - 08:19:58 PDT)
Re: [AMBER] huge values for the vibrational entropy from ptraj
(Tue Oct 29 2013 - 08:12:40 PDT)
Re: [AMBER] problem in saving prmtop file in ff12SB force field
(Mon Oct 28 2013 - 07:04:09 PDT)
Re: [AMBER] Error - PMEMD.MPI cannot understand line in rst file
(Mon Oct 28 2013 - 06:57:39 PDT)
Re: [AMBER] ptraj - loading list of frames
(Sat Oct 26 2013 - 13:48:57 PDT)
Re: [AMBER] AmberTools13
(Fri Oct 25 2013 - 14:05:11 PDT)
Re: [AMBER] Constant pH with enzyme and substrate
(Fri Oct 25 2013 - 13:06:23 PDT)
Re: [AMBER] Regarding radial distribution function
(Thu Oct 24 2013 - 06:43:44 PDT)
Re: [AMBER] Script?
(Tue Oct 22 2013 - 12:25:03 PDT)
Re: [AMBER] example of MTKpp on Ambertools 13
(Mon Oct 21 2013 - 07:58:43 PDT)
Re: [AMBER] output of diffusion data doesn't show two columns for big number values
(Sat Oct 19 2013 - 09:32:09 PDT)
Re: [AMBER] How to deal with duplicate frames during MD?
(Fri Oct 18 2013 - 06:59:42 PDT)
Re: [AMBER] PTRAJ - Problem with inserting TER card
(Fri Oct 18 2013 - 06:54:10 PDT)
Re: [AMBER] PTRAJ - Problem with inserting TER card
(Thu Oct 17 2013 - 11:04:33 PDT)
Re: [AMBER] PTRAJ - Problem with inserting TER card
(Wed Oct 16 2013 - 08:10:02 PDT)
Re: [AMBER] Fwd: Shifting molecules by a box length
(Thu Oct 10 2013 - 08:17:44 PDT)
Re: [AMBER] Reading NetCDF file
(Mon Oct 07 2013 - 13:25:15 PDT)
Re: [AMBER] Generation of melting curves
(Mon Oct 07 2013 - 07:39:04 PDT)
Re: [AMBER] NAB : Orienting a molecule
(Fri Oct 04 2013 - 13:38:00 PDT)
Re: [AMBER] rotational diffusion error
(Fri Oct 04 2013 - 07:11:19 PDT)
Re: [AMBER] Reading NetCDF file
(Fri Oct 04 2013 - 07:05:46 PDT)
Re: [AMBER] Temperature based trajectory in REMD
(Wed Oct 02 2013 - 10:22:15 PDT)
Re: [AMBER] PROBLEM USING ANTECHAMBER
(Wed Oct 02 2013 - 08:50:26 PDT)
Re: [AMBER] Problem in antechamber execution Problem in antechamber execution problem in antechamber execution
(Tue Oct 01 2013 - 09:08:48 PDT)
David A Case
Re: [AMBER] Installation error
(Thu Oct 31 2013 - 06:45:06 PDT)
Re: [AMBER] Monte Carlo Method/Simulation in AMBER 12
(Thu Oct 31 2013 - 04:44:53 PDT)
Re: [AMBER] huge values for the vibrational entropy from ptraj
(Thu Oct 31 2013 - 04:44:22 PDT)
Re: [AMBER] Installation error
(Wed Oct 30 2013 - 04:52:45 PDT)
Re: [AMBER] huge values for the vibrational entropy from ptraj
(Tue Oct 29 2013 - 06:21:25 PDT)
Re: [AMBER] huge values for the vibrational entropy from ptraj
(Tue Oct 29 2013 - 04:45:24 PDT)
Re: [AMBER] why are pres_X, pres_Y, and pres_Z different?
(Mon Oct 28 2013 - 08:40:00 PDT)
Re: [AMBER] problem after minimization of pure DMF
(Mon Oct 28 2013 - 04:44:36 PDT)
Re: [AMBER] DNA with NAB
(Mon Oct 14 2013 - 04:46:57 PDT)
Re: [AMBER] Segmentation fault in tleap
(Fri Oct 11 2013 - 10:27:12 PDT)
Re: [AMBER] Protein-DNA covalent bond
(Fri Oct 11 2013 - 07:39:12 PDT)
Re: [AMBER] Segmentation fault in tleap
(Fri Oct 11 2013 - 07:21:59 PDT)
Re: [AMBER] Questions about softcore part
(Thu Oct 10 2013 - 04:43:30 PDT)
Re: [AMBER] Problem in creating .mol2 and .frcmod files
(Wed Oct 09 2013 - 07:22:02 PDT)
Re: [AMBER] ERROR in DISTANCE RESTRAINT
(Tue Oct 08 2013 - 12:29:50 PDT)
Re: [AMBER] Soft-core questions for TI method
(Mon Oct 07 2013 - 05:21:19 PDT)
Re: [AMBER] Hydrogen Bond Term in Amber ff99SB forcefield
(Mon Oct 07 2013 - 05:16:28 PDT)
Re: [AMBER] MPI install with openmpi
(Mon Oct 07 2013 - 05:14:12 PDT)
Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"
(Thu Oct 03 2013 - 09:08:47 PDT)
Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"
(Wed Oct 02 2013 - 04:39:31 PDT)
Re: [AMBER] rotational diffusion error
(Wed Oct 02 2013 - 04:34:36 PDT)
Re: [AMBER] problem with addIons in tleap
(Tue Oct 01 2013 - 04:44:03 PDT)
Re: [AMBER] Generating topology files for two proteins in a single input pdb
(Tue Oct 01 2013 - 04:43:07 PDT)
Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"
(Tue Oct 01 2013 - 04:37:25 PDT)
Re: [AMBER] Use of Langevin Thermostat with Amoeba force field
(Tue Oct 01 2013 - 04:34:24 PDT)
David Case
Re: [AMBER] unique atoms in TI softcore
(Thu Oct 17 2013 - 04:45:04 PDT)
Re: [AMBER] Questions regarding AMBER
(Sat Oct 12 2013 - 08:39:09 PDT)
Debayan Chakraborty
[AMBER] I/O errors while using CHARMM psf with CHAMBER
(Thu Oct 10 2013 - 16:23:01 PDT)
Deborah Howe
Re: [AMBER] How to use TIP4P/2005 water model
(Sat Oct 26 2013 - 08:20:01 PDT)
[AMBER] How to use TIP4P/2005 water model
(Fri Oct 25 2013 - 19:57:22 PDT)
Devlina Chakravarty
[AMBER] Modified Cysteine
(Tue Oct 01 2013 - 04:36:09 PDT)
Dhananjay
Re: [AMBER] Installation error
(Thu Oct 31 2013 - 04:41:38 PDT)
Re: [AMBER] Installation error
(Thu Oct 31 2013 - 04:33:37 PDT)
Re: [AMBER] Installation error
(Thu Oct 31 2013 - 04:07:43 PDT)
[AMBER] Installation error
(Wed Oct 30 2013 - 01:41:49 PDT)
Dickson, Callum
Re: [AMBER] FW: Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
(Mon Oct 28 2013 - 05:33:20 PDT)
Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
(Wed Oct 09 2013 - 05:44:06 PDT)
Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
(Wed Oct 09 2013 - 01:07:35 PDT)
Dongshan Wei
Re: [AMBER] How to run npt simulation if IFBOX=0 in .prmtop file?
(Thu Oct 10 2013 - 06:58:37 PDT)
[AMBER] How to run npt simulation if IFBOX=0 in .prmtop file?
(Thu Oct 10 2013 - 05:43:30 PDT)
Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file
(Wed Oct 09 2013 - 05:50:33 PDT)
Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file
(Tue Oct 08 2013 - 20:35:42 PDT)
Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file
(Tue Oct 08 2013 - 08:37:10 PDT)
Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file
(Mon Sep 30 2013 - 19:05:43 PDT)
[AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file
(Mon Sep 30 2013 - 10:56:42 PDT)
Emmanuel Oluwatobi SALAWU
[AMBER] Monte Carlo Method/Simulation in AMBER 12
(Thu Oct 31 2013 - 03:38:15 PDT)
Eugene Yedvabny
Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD
(Sun Oct 06 2013 - 21:58:04 PDT)
Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD
(Fri Oct 04 2013 - 17:34:32 PDT)
[AMBER] Generating reservoirs for non-Boltzmann T-RREMD
(Fri Oct 04 2013 - 12:50:42 PDT)
Fabrício Bracht
Re: [AMBER] Hbond analysis
(Wed Oct 30 2013 - 13:31:25 PDT)
Re: [AMBER] Hbond analysis
(Wed Oct 30 2013 - 13:28:36 PDT)
Re: [AMBER] Hbond analysis
(Wed Oct 30 2013 - 13:02:10 PDT)
[AMBER] Hbond analysis
(Wed Oct 30 2013 - 11:34:26 PDT)
Re: [AMBER] Terachem tests with trial version
(Thu Oct 24 2013 - 00:12:26 PDT)
Re: [AMBER] Terachem tests with trial version
(Wed Oct 23 2013 - 13:24:41 PDT)
[AMBER] Terachem tests with trial version
(Wed Oct 23 2013 - 00:21:47 PDT)
Re: [AMBER] Replica exchange umbrella sampling
(Sat Oct 05 2013 - 00:29:29 PDT)
[AMBER] Replica exchange umbrella sampling
(Fri Oct 04 2013 - 00:00:52 PDT)
filip fratev
[AMBER] Python script to reweight aMD simulations
(Wed Oct 16 2013 - 21:02:59 PDT)
Francesco Pietra
[AMBER] About foundations of T-REMD
(Fri Oct 25 2013 - 07:28:51 PDT)
FyD
Re: [AMBER] problem after minimization of pure DMF
(Wed Oct 30 2013 - 04:59:20 PDT)
Re: [AMBER] CYM residue problem(MCPB)
(Fri Oct 18 2013 - 12:16:31 PDT)
Re: [AMBER] CYM residue problem(MCPB)
(Thu Oct 17 2013 - 11:53:19 PDT)
Re: [AMBER] RESP charge calculation problem for SO4 -2 group
(Wed Oct 16 2013 - 07:58:37 PDT)
Re: [AMBER] Constant pH with ligand
(Tue Oct 15 2013 - 22:25:53 PDT)
Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools
(Tue Oct 15 2013 - 22:21:40 PDT)
Re: [AMBER] Questions regarding AMBER
(Sun Oct 13 2013 - 09:44:11 PDT)
Re: [AMBER] Questions regarding AMBER
(Sun Oct 13 2013 - 07:05:20 PDT)
Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools
(Sun Oct 13 2013 - 07:02:23 PDT)
Re: [AMBER] Iron(III)Hydroxide complexing with Enterobactin (quantum chemistry calculations?)
(Sun Oct 13 2013 - 01:45:33 PDT)
Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools
(Sun Oct 13 2013 - 00:45:40 PDT)
Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file
(Thu Oct 10 2013 - 02:01:25 PDT)
Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file
(Thu Oct 10 2013 - 01:04:30 PDT)
Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file
(Wed Oct 09 2013 - 00:09:44 PDT)
Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file
(Wed Oct 09 2013 - 00:03:20 PDT)
Re: [AMBER] About the Mg charge in AMBER FF
(Fri Oct 04 2013 - 05:07:43 PDT)
Re: [AMBER] Modified Cysteine
(Tue Oct 01 2013 - 08:17:42 PDT)
Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file
(Mon Sep 30 2013 - 22:35:43 PDT)
Gargi Borgohai
[AMBER] Generation of melting curves
(Sun Oct 06 2013 - 20:59:11 PDT)
Re: [AMBER] Temperature based trajectory in REMD
(Wed Oct 02 2013 - 02:05:13 PDT)
George Green
Re: [AMBER] Generating topology files for two proteins in a single input pdb
(Tue Oct 01 2013 - 11:13:49 PDT)
Re: [AMBER] Generating topology files for two proteins in a single input pdb
(Tue Oct 01 2013 - 04:55:11 PDT)
Re: [AMBER] Generating topology files for two proteins in a single input pdb
(Tue Oct 01 2013 - 04:52:54 PDT)
Re: [AMBER] Generating topology files for two proteins in a single input pdb
(Tue Oct 01 2013 - 04:49:59 PDT)
Re: [AMBER] Generating topology files for two proteins in a single input pdb
(Tue Oct 01 2013 - 04:48:42 PDT)
George Patargias
Re: [AMBER] About the Mg charge in AMBER FF
(Fri Oct 04 2013 - 05:36:32 PDT)
[AMBER] About the Mg charge in AMBER FF
(Fri Oct 04 2013 - 02:28:36 PDT)
Gustavo Seabra
Re: [AMBER] PROBLEM IN QM/MM RUN
(Sat Oct 19 2013 - 08:49:11 PDT)
Hai Nguyen
Re: [AMBER] MMGBSA, Generalized Born, protein-nucleic acid complex
(Thu Oct 24 2013 - 11:37:21 PDT)
Hamed S. Hayatshahi
[AMBER] TI soft-core parameters
(Thu Oct 31 2013 - 13:13:54 PDT)
Hannes Loeffler
Re: [AMBER] About calculating entropy
(Thu Oct 31 2013 - 07:03:28 PDT)
Re: [AMBER] unique atoms in TI softcore
(Thu Oct 17 2013 - 07:42:58 PDT)
[AMBER] unique atoms in TI softcore
(Thu Oct 17 2013 - 03:01:11 PDT)
[AMBER] tleap cannot handle dummies in the middle?
(Fri Oct 11 2013 - 09:18:43 PDT)
Heribert Reis
[AMBER] Fwd: Shifting molecules by a box length
(Thu Oct 10 2013 - 07:41:11 PDT)
[AMBER] Shifting molecules by a box length
(Wed Oct 09 2013 - 07:53:29 PDT)
HIMANSHU JOSHI
[AMBER] NAB : Orienting a molecule
(Fri Oct 04 2013 - 11:33:48 PDT)
Hiromasa WATANABE
Re: [AMBER] About INP in case of MS=1
(Tue Oct 08 2013 - 23:03:58 PDT)
[AMBER] About INP in case of MS=1
(Wed Oct 02 2013 - 22:55:00 PDT)
Hoshin Kim
[AMBER] Making Au surface using xleap
(Fri Oct 25 2013 - 08:39:30 PDT)
houcemeddine
Re: [AMBER] CYM residue problem(MCPB)
(Fri Oct 18 2013 - 06:11:14 PDT)
[AMBER] CYM residue problem(MCPB)
(Thu Oct 17 2013 - 08:29:17 PDT)
[AMBER] strange behavior of MCPB
(Wed Oct 16 2013 - 08:50:03 PDT)
Igor Marques
[AMBER] GAFF angle term constants with phosphor or sulphur
(Tue Oct 08 2013 - 06:30:49 PDT)
Indrajit Deb
[AMBER] MMPBSA.py problem
(Thu Oct 24 2013 - 05:31:01 PDT)
Jacopo Sgrignani
Re: [AMBER] QM/MM MMPBSA
(Fri Oct 04 2013 - 06:33:58 PDT)
Re: [AMBER] QM/MM MMPBSA
(Fri Oct 04 2013 - 05:15:39 PDT)
Re: [AMBER] About the Mg charge in AMBER FF
(Fri Oct 04 2013 - 03:01:43 PDT)
[AMBER] QM/MM MMPBSA
(Fri Oct 04 2013 - 01:18:10 PDT)
James Maier
Re: [AMBER] How to use TIP4P/2005 water model
(Sat Oct 26 2013 - 08:56:02 PDT)
James Murdock
Re: [AMBER] GAFF angle term constants with phosphor or sulphur
(Mon Oct 14 2013 - 06:13:16 PDT)
Jan-Philip Gehrcke
Re: [AMBER] parmed.py bug when using the "parmout" command ?
(Thu Oct 24 2013 - 10:30:22 PDT)
Re: [AMBER] Running simultaneously AMBER jobs in CPU and GPU
(Fri Oct 18 2013 - 06:29:24 PDT)
Jason Swails
Re: [AMBER] Installation error
(Thu Oct 31 2013 - 11:36:14 PDT)
Re: [AMBER] Installation error
(Thu Oct 31 2013 - 06:27:25 PDT)
Re: [AMBER] About calculating entropy
(Thu Oct 31 2013 - 06:14:59 PDT)
Re: [AMBER] Installation error
(Thu Oct 31 2013 - 04:36:13 PDT)
Re: [AMBER] Monte Carlo Method/Simulation in AMBER 12
(Thu Oct 31 2013 - 04:24:59 PDT)
Re: [AMBER] Installation error
(Thu Oct 31 2013 - 04:22:25 PDT)
Re: [AMBER] Free binding energy calculations for Zinc dependent ligands
(Wed Oct 30 2013 - 05:52:10 PDT)
Re: [AMBER] Installation error
(Wed Oct 30 2013 - 04:43:58 PDT)
Re: [AMBER] Amber 12 Updater error on Arch linux
(Wed Oct 30 2013 - 04:20:18 PDT)
Re: [AMBER] Sander error
(Tue Oct 29 2013 - 13:55:36 PDT)
Re: [AMBER] Sander error
(Tue Oct 29 2013 - 13:19:41 PDT)
Re: [AMBER] huge values for the vibrational entropy from ptraj
(Tue Oct 29 2013 - 08:05:29 PDT)
Re: [AMBER] huge values for the vibrational entropy from ptraj
(Tue Oct 29 2013 - 08:00:50 PDT)
Re: [AMBER] idecomp does not work for canonical-residues
(Mon Oct 28 2013 - 03:22:13 PDT)
Re: [AMBER] idecomp does not work for canonical-residues
(Sun Oct 27 2013 - 09:05:54 PDT)
Re: [AMBER] idecomp does not work for canonical-residues
(Sun Oct 27 2013 - 05:23:58 PDT)
Re: [AMBER] AmberTools13
(Fri Oct 25 2013 - 14:05:06 PDT)
Re: [AMBER] ionic strength conversion between MMPBSA.py and PBSA
(Fri Oct 25 2013 - 08:59:31 PDT)
Re: [AMBER] ionic strength conversion between MMPBSA.py and PBSA
(Fri Oct 25 2013 - 08:08:13 PDT)
Re: [AMBER] MMPBSA, ligand sequence
(Fri Oct 25 2013 - 04:22:32 PDT)
Re: [AMBER] parmed.py bug when using the "parmout" command ?
(Thu Oct 24 2013 - 10:43:54 PDT)
Re: [AMBER] parmed.py bug when using the "parmout" command ?
(Thu Oct 24 2013 - 10:35:42 PDT)
Re: [AMBER] parmed.py bug when using the "parmout" command ?
(Thu Oct 24 2013 - 10:09:27 PDT)
Re: [AMBER] parmed.py bug when using the "parmout" command ?
(Thu Oct 24 2013 - 08:42:54 PDT)
Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB
(Thu Oct 24 2013 - 07:52:44 PDT)
Re: [AMBER] MMPBSA.py error
(Thu Oct 24 2013 - 07:40:23 PDT)
Re: [AMBER] MMPBSA.py problem
(Thu Oct 24 2013 - 07:22:03 PDT)
Re: [AMBER] MMPBSA.py error
(Thu Oct 24 2013 - 07:08:57 PDT)
Re: [AMBER] AMBERTOOLS13 test error: 01_Generalized_Born and 03_Alanine_Scanning
(Thu Oct 24 2013 - 05:21:53 PDT)
Re: [AMBER] MMPBSA.py error
(Wed Oct 23 2013 - 04:40:09 PDT)
Re: [AMBER] PCA analysis and amber prmtop file
(Tue Oct 22 2013 - 04:58:07 PDT)
Re: [AMBER] MMPBSA problem with CHAMBER generated topology file
(Tue Oct 22 2013 - 04:56:44 PDT)
Re: [AMBER] Exceed character limit in bellyrestraint mask selection
(Tue Oct 22 2013 - 04:52:24 PDT)
Re: [AMBER] example of MTKpp on Ambertools 13
(Mon Oct 21 2013 - 08:03:23 PDT)
Re: [AMBER] problem using the R.E.D server output
(Mon Oct 21 2013 - 04:46:02 PDT)
Re: [AMBER] How to deal with duplicate frames during MD?
(Sat Oct 19 2013 - 06:13:56 PDT)
Re: [AMBER] Exceed character limit in bellyrestraint mask selection
(Fri Oct 18 2013 - 11:05:47 PDT)
Re: [AMBER] CYM residue problem(MCPB)
(Fri Oct 18 2013 - 07:11:00 PDT)
Re: [AMBER] parmchk doesn't recognize the changes made in leaprc.ff99SB and parm.99
(Fri Oct 18 2013 - 06:55:07 PDT)
Re: [AMBER] Doubt regarding the metadynamics simulation
(Thu Oct 17 2013 - 09:21:20 PDT)
Re: [AMBER] CYM residue problem(MCPB)
(Thu Oct 17 2013 - 08:49:08 PDT)
Re: [AMBER] Constant pH with ligand
(Tue Oct 15 2013 - 17:33:04 PDT)
Re: [AMBER] Exceed character limit in bellyrestraint mask selection
(Tue Oct 15 2013 - 09:34:01 PDT)
Re: [AMBER] How do I use MMPBSA.py for namd .dcd file?
(Mon Oct 14 2013 - 06:16:30 PDT)
Re: [AMBER] How do I use MMPBSA.py for namd .dcd file?
(Sat Oct 12 2013 - 17:06:05 PDT)
Re: [AMBER] running MMPBSA.py on an NMR ensemble
(Sat Oct 12 2013 - 07:51:25 PDT)
Re: [AMBER] AmberTools13 and Amber11
(Fri Oct 11 2013 - 08:45:26 PDT)
Re: [AMBER] Stuck on AmberTools12 bug fix.23
(Fri Oct 11 2013 - 04:20:11 PDT)
Re: [AMBER] Segmentation fault in tleap
(Thu Oct 10 2013 - 17:19:34 PDT)
Re: [AMBER] SHAKE flucatuation
(Thu Oct 10 2013 - 12:23:05 PDT)
Re: [AMBER] solvate box
(Thu Oct 10 2013 - 09:08:55 PDT)
Re: [AMBER] Distributions of the phi and psi torsion angles during MD simulations
(Thu Oct 10 2013 - 06:45:17 PDT)
Re: [AMBER] How to run npt simulation if IFBOX=0 in .prmtop file?
(Thu Oct 10 2013 - 05:56:41 PDT)
Re: [AMBER] AMBER ff99Sbildn
(Wed Oct 09 2013 - 08:45:01 PDT)
Re: [AMBER] AMBER ff99Sbildn
(Wed Oct 09 2013 - 08:20:26 PDT)
Re: [AMBER] Shifting molecules by a box length
(Wed Oct 09 2013 - 08:06:46 PDT)
Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD
(Tue Oct 08 2013 - 05:01:24 PDT)
Re: [AMBER] Parameter Discrepancy in Walker Tutorial B1?
(Tue Oct 08 2013 - 04:50:06 PDT)
Re: [AMBER] ambertools patch 19 fails
(Mon Oct 07 2013 - 08:58:53 PDT)
Re: [AMBER] problem in creating .mol2 and .frcmod files
(Mon Oct 07 2013 - 07:40:27 PDT)
Re: [AMBER] MPI install with openmpi
(Sun Oct 06 2013 - 07:17:30 PDT)
Re: [AMBER] Error in antechamber Installation
(Sun Oct 06 2013 - 05:04:47 PDT)
Re: [AMBER] Regarding addition of DL_Poly Inversion potential in Amber
(Sat Oct 05 2013 - 17:52:17 PDT)
Re: [AMBER] changeLJ14Pair
(Fri Oct 04 2013 - 07:04:45 PDT)
Re: [AMBER] QM/MM MMPBSA
(Fri Oct 04 2013 - 06:59:18 PDT)
Re: [AMBER] QM/MM MMPBSA
(Fri Oct 04 2013 - 06:53:58 PDT)
Re: [AMBER] Reading NetCDF file
(Fri Oct 04 2013 - 06:18:12 PDT)
Re: [AMBER] About the Mg charge in AMBER FF
(Fri Oct 04 2013 - 05:38:02 PDT)
Re: [AMBER] QM/MM MMPBSA
(Fri Oct 04 2013 - 05:34:34 PDT)
Re: [AMBER] Replica exchange umbrella sampling
(Fri Oct 04 2013 - 04:17:12 PDT)
Re: [AMBER] QM/MM MMPBSA
(Fri Oct 04 2013 - 04:07:07 PDT)
Re: [AMBER] The Error when I run MdoutAnalysizer.py
(Thu Oct 03 2013 - 07:36:21 PDT)
Re: [AMBER] The Error when I run MdoutAnalysizer.py
(Thu Oct 03 2013 - 04:33:41 PDT)
Re: [AMBER] about error with "Must have more residues than processors!"
(Tue Oct 01 2013 - 09:26:01 PDT)
Re: [AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle
(Tue Oct 01 2013 - 09:20:29 PDT)
Re: [AMBER] Generating topology files for two proteins in a single input pdb
(Tue Oct 01 2013 - 04:54:21 PDT)
Re: [AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle
(Tue Oct 01 2013 - 04:50:01 PDT)
Re: [AMBER] MMPBSA.py MPI problem on TACC Stampede
(Tue Oct 01 2013 - 04:36:10 PDT)
Jeremy Hallum
[AMBER] A problem with a specific input in pmemd.cuda.MPI. 4 GPU fails, 2 GPU works fine.
(Fri Oct 04 2013 - 11:26:52 PDT)
Jia Xu
Re: [AMBER] strange behavior of MCPB
(Wed Oct 16 2013 - 09:51:36 PDT)
Jio M
Re: [AMBER] DNA with NAB
(Fri Oct 25 2013 - 07:14:34 PDT)
Re: [AMBER] DNA with NAB
(Thu Oct 24 2013 - 12:23:39 PDT)
Re: [AMBER] DNA with NAB
(Tue Oct 22 2013 - 08:42:21 PDT)
[AMBER] DNA with NAB
(Sun Oct 13 2013 - 15:47:52 PDT)
Jiri Sponer
Re: [AMBER] Questions regarding AMBER
(Sat Oct 12 2013 - 07:39:15 PDT)
Johannes Zuegg
[AMBER] Leap ff10 and Sodium ion
(Wed Oct 23 2013 - 17:05:56 PDT)
John Gehman
Re: [AMBER] Protein-DNA covalent bond
(Sat Oct 12 2013 - 00:53:12 PDT)
[AMBER] Protein-DNA covalent bond
(Thu Oct 10 2013 - 17:51:55 PDT)
Jonathan Saboury
[AMBER] Iron(III)Hydroxide complexing with Enterobactin (quantum chemistry calculations?)
(Sat Oct 12 2013 - 21:43:07 PDT)
Jonathan Sheehan
[AMBER] Single quotes in AMBER manual
(Fri Oct 25 2013 - 12:40:34 PDT)
Jose Borreguero
Re: [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible?
(Thu Oct 31 2013 - 08:45:43 PDT)
Re: [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible?
(Wed Oct 30 2013 - 05:56:27 PDT)
[AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible?
(Tue Oct 29 2013 - 13:37:07 PDT)
Re: [AMBER] why are pres_X, pres_Y, and pres_Z different?
(Mon Oct 28 2013 - 08:53:01 PDT)
Re: [AMBER] why are pres_X, pres_Y, and pres_Z different?
(Mon Oct 28 2013 - 08:07:57 PDT)
[AMBER] why are pres_X, pres_Y, and pres_Z different?
(Fri Oct 25 2013 - 08:42:02 PDT)
Kamali Sripathi
Re: [AMBER] Questions regarding AMBER
(Sun Oct 13 2013 - 15:04:04 PDT)
Re: [AMBER] Questions regarding AMBER
(Sun Oct 13 2013 - 07:31:04 PDT)
Re: [AMBER] Questions regarding AMBER
(Sun Oct 13 2013 - 06:01:20 PDT)
[AMBER] Questions regarding AMBER
(Sat Oct 12 2013 - 07:22:10 PDT)
kurisaki
Re: [AMBER] mdcrd to dcd
(Thu Oct 31 2013 - 04:49:45 PDT)
Re: [AMBER] idecomp does not work for canonical-residues
(Mon Oct 28 2013 - 04:00:53 PDT)
Re: [AMBER] idecomp does not work for canonical-residues
(Sun Oct 27 2013 - 18:26:49 PDT)
Re: [AMBER] idecomp does not work for canonical-residues
(Sun Oct 27 2013 - 06:01:56 PDT)
[AMBER] idecomp does not work for canonical-residues
(Sat Oct 26 2013 - 23:43:00 PDT)
M. Reza Ganjalikhany
[AMBER] Amber 12 Updater error on Arch linux
(Wed Oct 30 2013 - 02:52:16 PDT)
maghtar
Re: [AMBER] MMPBSA, ligand sequence
(Fri Oct 25 2013 - 07:17:32 PDT)
[AMBER] MMPBSA, ligand sequence
(Fri Oct 25 2013 - 03:29:28 PDT)
Makoto Chikira
Re: [AMBER] MPI install with openmpi
(Sun Oct 06 2013 - 06:36:27 PDT)
Re: [AMBER] MPI install with openmpi
(Sat Oct 05 2013 - 18:23:43 PDT)
Re: [AMBER] MPI install with openmpi
(Sat Oct 05 2013 - 08:37:08 PDT)
[AMBER] MPI install with openmpi
(Sat Oct 05 2013 - 00:33:21 PDT)
marco.molinari
Re: [AMBER] AMBERTOOLS13 test error: 01_Generalized_Born and, 03_Alanine_Scanning (Jason Swails)
(Fri Oct 25 2013 - 05:42:27 PDT)
[AMBER] AMBERTOOLS13 test error: 01_Generalized_Born and 03_Alanine_Scanning
(Thu Oct 24 2013 - 03:55:11 PDT)
Mark Healey
[AMBER] ptraj - loading list of frames
(Sat Oct 26 2013 - 13:24:06 PDT)
Mary Varughese
[AMBER] MMPBSA calculation
(Tue Oct 22 2013 - 15:57:59 PDT)
Mathias Gruber
[AMBER] Block Averaging of Trajectory
(Tue Oct 08 2013 - 06:03:23 PDT)
Matthew Wampole
[AMBER] ambertools patch 19 fails
(Mon Oct 07 2013 - 07:57:46 PDT)
Mike Limb
Re: [AMBER] Exceed character limit in bellyrestraint mask selection
(Tue Oct 22 2013 - 03:39:32 PDT)
Re: [AMBER] Exceed character limit in bellyrestraint mask selection
(Fri Oct 18 2013 - 10:35:44 PDT)
[AMBER] Exceed character limit in bellyrestraint mask selection
(Tue Oct 15 2013 - 08:29:18 PDT)
mmalett.nmt.edu
Re: [AMBER] Segmentation fault in tleap
(Fri Oct 11 2013 - 13:19:17 PDT)
Re: [AMBER] Segmentation fault in tleap
(Fri Oct 11 2013 - 09:15:15 PDT)
Re: [AMBER] Segmentation fault in tleap
(Thu Oct 10 2013 - 17:26:00 PDT)
[AMBER] Segmentation fault in tleap
(Thu Oct 10 2013 - 16:53:58 PDT)
Mohan Pradhan
Re: [AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle
(Tue Oct 01 2013 - 06:11:22 PDT)
[AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle
(Tue Oct 01 2013 - 04:11:32 PDT)
MOHD HOMAIDUR RAHMAN
[AMBER] Regarding radial distribution function
(Thu Oct 24 2013 - 04:46:48 PDT)
[AMBER] Regarding addition of DL_Poly Inversion and three body potential in Amber
(Fri Oct 04 2013 - 10:09:02 PDT)
[AMBER] Regarding addition of DL_Poly Inversion potential in Amber
(Fri Oct 04 2013 - 05:17:33 PDT)
moitrayee.mbu.iisc.ernet.in
Re: [AMBER] problem with heme parameters bound to HIS
(Fri Oct 18 2013 - 09:37:15 PDT)
[AMBER] problem with heme parameters bound to HIS
(Fri Oct 18 2013 - 02:05:48 PDT)
Muthukumaran R
[AMBER] Running simultaneously AMBER jobs in CPU and GPU
(Fri Oct 18 2013 - 04:24:54 PDT)
Neha Gandhi
[AMBER] PCA analysis and amber prmtop file
(Tue Oct 22 2013 - 01:29:37 PDT)
Nicole Ippolito
[AMBER] acclerated molecular dynamics alphaP
(Tue Oct 29 2013 - 07:59:22 PDT)
Re: [AMBER] Constant pH with enzyme and substrate
(Fri Oct 25 2013 - 14:51:58 PDT)
[AMBER] Constant pH with enzyme and substrate
(Fri Oct 25 2013 - 11:00:28 PDT)
Re: [AMBER] Constant pH with ligand
(Wed Oct 16 2013 - 04:37:49 PDT)
[AMBER] Constant pH with ligand
(Tue Oct 15 2013 - 14:55:52 PDT)
Niel Henriksen
Re: [AMBER] Error message from pmemd.cuda
(Wed Oct 16 2013 - 13:46:33 PDT)
Re: [AMBER] Error message from pmemd.cuda
(Wed Oct 16 2013 - 13:44:43 PDT)
Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD
(Mon Oct 07 2013 - 11:27:56 PDT)
Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD
(Sun Oct 06 2013 - 21:18:00 PDT)
Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD
(Fri Oct 04 2013 - 13:25:18 PDT)
Nihal Korkmaz
Re: [AMBER] PMF for 2 Arginines
(Wed Oct 16 2013 - 09:38:32 PDT)
[AMBER] PMF for 2 Arginines
(Tue Oct 15 2013 - 20:44:52 PDT)
Olayide Arodola
[AMBER] About calculating entropy
(Thu Oct 31 2013 - 04:26:52 PDT)
Paolo Ruggerone
[AMBER] ITN Marie Curie positions available for early-stage researchers
(Fri Oct 04 2013 - 02:25:08 PDT)
Pawel
Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much!
(Wed Oct 30 2013 - 06:12:50 PDT)
Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much!
(Tue Oct 15 2013 - 16:26:42 PDT)
Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much!
(Mon Oct 14 2013 - 09:04:40 PDT)
peter.stauffert.boehringer-ingelheim.com
[AMBER] Scaling of multi GPU runs
(Tue Oct 08 2013 - 10:55:29 PDT)
psu4.uic.edu
Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...
(Fri Oct 11 2013 - 10:39:56 PDT)
Rasha Alqus
Re: [AMBER] MMPBSA.py error
(Thu Oct 24 2013 - 07:31:44 PDT)
Re: [AMBER] MMPBSA.py error
(Thu Oct 24 2013 - 06:02:32 PDT)
Re: [AMBER] MMPBSA.py error
(Wed Oct 23 2013 - 03:18:54 PDT)
[AMBER] MMPBSA.py error
(Wed Oct 23 2013 - 03:11:53 PDT)
[AMBER] solvate box
(Thu Oct 10 2013 - 08:35:50 PDT)
Ravi Tripathi
Re: [AMBER] Doubt regarding the metadynamics simulation
(Thu Oct 17 2013 - 09:08:18 PDT)
[AMBER] Doubt regarding the metadynamics simulation
(Thu Oct 17 2013 - 07:59:31 PDT)
Ray Luo, Ph.D.
Re: [AMBER] mmpbsa_py_energy and PBSA options
(Fri Oct 25 2013 - 11:54:27 PDT)
Re: [AMBER] mmpbsa_py_energy and PBSA options
(Fri Oct 25 2013 - 10:52:56 PDT)
Re: [AMBER] mmpbsa_py_energy and PBSA options
(Fri Oct 25 2013 - 09:56:01 PDT)
Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...
(Fri Oct 11 2013 - 10:59:11 PDT)
Re: [AMBER] MMPBSA error
(Thu Oct 10 2013 - 14:30:35 PDT)
Re: [AMBER] About INP in case of MS=1
(Wed Oct 09 2013 - 09:53:43 PDT)
Re: [AMBER] About INP in case of MS=1
(Thu Oct 03 2013 - 10:00:53 PDT)
Robert Molt
Re: [AMBER] Doubt regarding the metadynamics simulation
(Thu Oct 17 2013 - 09:14:17 PDT)
[AMBER] Parameter Discrepancy in Walker Tutorial B1?
(Mon Oct 07 2013 - 18:58:12 PDT)
rohitarora10.gmail.com
[AMBER] Error - PMEMD.MPI cannot understand line in rst file
(Mon Oct 28 2013 - 04:34:22 PDT)
Re: [AMBER] How to deal with duplicate frames during MD?
(Fri Oct 18 2013 - 16:23:21 PDT)
Re: [AMBER] How to deal with duplicate frames during MD?
(Fri Oct 18 2013 - 07:20:10 PDT)
[AMBER] How to deal with duplicate frames during MD?
(Fri Oct 18 2013 - 01:34:38 PDT)
Ross Walker
Re: [AMBER] Terachem tests with trial version
(Wed Oct 23 2013 - 16:38:03 PDT)
Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
(Wed Oct 09 2013 - 05:19:35 PDT)
Re: [AMBER] Scaling of multi GPU runs
(Tue Oct 08 2013 - 11:13:40 PDT)
Re: [AMBER] Scaling of multi GPU runs
(Tue Oct 08 2013 - 11:02:45 PDT)
Re: [AMBER] ERROR in DISTANCE RESTRAINT
(Tue Oct 08 2013 - 10:45:13 PDT)
Re: [AMBER] A problem with a specific input in pmemd.cuda.MPI. 4 GPU fails, 2 GPU works fine.
(Fri Oct 04 2013 - 11:41:17 PDT)
Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
(Tue Oct 01 2013 - 09:04:27 PDT)
Sajeewa Pemasinghe
Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools
(Sun Oct 20 2013 - 08:35:31 PDT)
Re: [AMBER] parmchk doesn't recognize the changes made in leaprc.ff99SB and parm.99
(Sat Oct 19 2013 - 12:50:50 PDT)
[AMBER] parmchk doesn't recognize the changes made in leaprc.ff99SB and parm.99
(Fri Oct 18 2013 - 06:06:36 PDT)
Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools
(Tue Oct 15 2013 - 16:47:16 PDT)
Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools
(Tue Oct 15 2013 - 14:19:12 PDT)
Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools
(Sun Oct 13 2013 - 05:41:00 PDT)
[AMBER] Problem in deriving RESP charges with RED-3.52 tools
(Sat Oct 12 2013 - 23:12:39 PDT)
Sangita Kachhap
Re: [AMBER] PMEMD trajectory and MMPBSA
(Mon Oct 14 2013 - 08:20:07 PDT)
[AMBER] PMEMD trajectory and MMPBSA
(Sun Oct 13 2013 - 22:46:51 PDT)
Scott Le Grand
Re: [AMBER] Scaling of multi GPU runs
(Tue Oct 08 2013 - 11:20:07 PDT)
Re: [AMBER] Scaling of multi GPU runs
(Tue Oct 08 2013 - 11:13:14 PDT)
setyanto md
Re: [AMBER] example of MTKpp on Ambertools 13
(Mon Oct 21 2013 - 23:31:25 PDT)
[AMBER] example of MTKpp on Ambertools 13
(Mon Oct 21 2013 - 07:18:30 PDT)
Shomesankar Bhunia
Re: [AMBER] AMBER ff99Sbildn
(Wed Oct 09 2013 - 08:59:56 PDT)
Re: [AMBER] AMBER ff99Sbildn
(Wed Oct 09 2013 - 08:34:38 PDT)
[AMBER] AMBER ff99Sbildn
(Wed Oct 09 2013 - 07:20:48 PDT)
Re: [AMBER] Amber99SB force field
(Tue Oct 08 2013 - 18:46:55 PDT)
Re: [AMBER] Amber99SB force field
(Tue Oct 08 2013 - 12:01:35 PDT)
[AMBER] Amber99SB force field
(Tue Oct 08 2013 - 11:13:52 PDT)
Sohag Biswas
Re: [AMBER] AMBER Digest, Vol 659, Issue 1
(Wed Oct 30 2013 - 23:23:10 PDT)
[AMBER] problem after minimization of pure DMF
(Sun Oct 27 2013 - 21:09:31 PDT)
Sorensen, Jesper
Re: [AMBER] MMPBSA.py MPI problem on TACC Stampede
(Tue Oct 01 2013 - 10:19:11 PDT)
[AMBER] MMPBSA.py MPI problem on TACC Stampede
(Mon Sep 30 2013 - 17:55:49 PDT)
Soumya Lipsa Rath
[AMBER] Fwd: requesting in executing CHAMBER
(Mon Oct 21 2013 - 22:57:30 PDT)
Sourav Purohit
[AMBER] ERROR in DISTANCE RESTRAINT
(Tue Oct 08 2013 - 10:21:26 PDT)
Subbarao Kanchi
Re: [AMBER] FW: Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
(Sun Oct 27 2013 - 17:39:15 PDT)
[AMBER] Fwd: FW: Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
(Fri Oct 18 2013 - 07:21:36 PDT)
Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
(Wed Oct 09 2013 - 01:44:46 PDT)
Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
(Sun Oct 06 2013 - 22:05:57 PDT)
Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
(Tue Oct 01 2013 - 19:25:11 PDT)
Subrata Paul
Re: [AMBER] problem in saving prmtop file in ff12SB force field
(Mon Oct 28 2013 - 07:37:55 PDT)
[AMBER] problem in saving prmtop file in ff12SB force field
(Mon Oct 28 2013 - 06:58:09 PDT)
sudipta
Re: [AMBER] How do I use MMPBSA.py for namd .dcd file?
(Mon Oct 14 2013 - 06:08:01 PDT)
Re: [AMBER] How do I use MMPBSA.py for namd .dcd file?
(Sat Oct 12 2013 - 10:31:35 PDT)
sumit.saurav.jain.gmail.com
[AMBER] sumit.saurav.jain.gmail.com has indicated you're a friend. Accept?
(Sat Oct 05 2013 - 16:31:25 PDT)
Symon Gathiaka
[AMBER] MMPBSA error
(Thu Oct 10 2013 - 12:36:02 PDT)
Tanmoy Paul
Re: [AMBER] optimization using gaussian and RESP using antechamber
(Wed Oct 30 2013 - 06:15:32 PDT)
[AMBER] PROBLEM IN QM/MM RUN
(Sat Oct 19 2013 - 00:17:48 PDT)
[AMBER] PROBLEM USING ANTECHAMBER
(Wed Oct 02 2013 - 05:36:47 PDT)
[AMBER] Problem in antechamber execution Problem in antechamber execution problem in antechamber execution
(Tue Oct 01 2013 - 08:15:21 PDT)
Terry M. Gray
[AMBER] Stuck on AmberTools12 bug fix.23
(Thu Oct 10 2013 - 20:25:48 PDT)
[AMBER] Stuck on AmberTools bugfix.23
(Thu Oct 10 2013 - 14:52:14 PDT)
Thomas Cheatham
Re: [AMBER] SHAKE flucatuation
(Thu Oct 10 2013 - 13:37:40 PDT)
Re: [AMBER] SHAKE flucatuation
(Thu Oct 10 2013 - 12:19:09 PDT)
Thomas Evangelidis
[AMBER] ratio between frames for MM/PBSA and frames for normal mode calculations
(Wed Oct 16 2013 - 16:10:54 PDT)
[AMBER] running MMPBSA.py on an NMR ensemble
(Sat Oct 12 2013 - 06:50:54 PDT)
thomas.fox.boehringer-ingelheim.com
Re: [AMBER] namelist input > 80 columns
(Tue Oct 22 2013 - 04:43:07 PDT)
[AMBER] namelist input > 80 columns
(Tue Oct 22 2013 - 02:41:32 PDT)
Tivani Mashamba
Re: [AMBER] About calculating entropy
(Thu Oct 31 2013 - 08:39:54 PDT)
Re: [AMBER] About calculating entropy
(Thu Oct 31 2013 - 06:47:21 PDT)
[AMBER] Free binding energy calculations for Zinc dependent ligands
(Wed Oct 30 2013 - 02:09:05 PDT)
Tong ZHU
[AMBER] Problem about water Cap with igb=10
(Sun Oct 13 2013 - 07:11:39 PDT)
Uday Midya
[AMBER] MMPBSA problem with CHAMBER generated topology file
(Mon Oct 21 2013 - 20:15:06 PDT)
Re: [AMBER] Reading NetCDF file
(Fri Oct 04 2013 - 22:33:12 PDT)
[AMBER] Reading NetCDF file
(Fri Oct 04 2013 - 05:46:46 PDT)
Vaibhav Dixit
Re: [AMBER] inquiry
(Mon Oct 14 2013 - 02:43:03 PDT)
Vijay Manickam Achari
[AMBER] output of diffusion data doesn't show two columns for big number values
(Sat Oct 19 2013 - 04:01:58 PDT)
Re: [AMBER] rotational diffusion error
(Wed Oct 02 2013 - 19:06:38 PDT)
Re: [AMBER] rotational diffusion error
(Tue Oct 01 2013 - 21:09:34 PDT)
Re: [AMBER] rotational diffusion error
(Tue Oct 01 2013 - 19:49:18 PDT)
Vijayalaxmi Sahoo
Re: [AMBER] Problem in creating .mol2 and .frcmod files
(Wed Oct 09 2013 - 06:38:28 PDT)
Re: [AMBER] problem in creating .mol2 and .frcmod files
(Mon Oct 07 2013 - 08:33:16 PDT)
[AMBER] problem in creating .mol2 and .frcmod files
(Mon Oct 07 2013 - 06:48:50 PDT)
[AMBER] Error in antechamber Installation
(Sat Oct 05 2013 - 22:27:27 PDT)
Vlad Cojocaru
Re: [AMBER] huge values for the vibrational entropy from ptraj
(Thu Oct 31 2013 - 06:03:40 PDT)
Re: [AMBER] huge values for the vibrational entropy from ptraj
(Thu Oct 31 2013 - 02:21:15 PDT)
Re: [AMBER] huge values for the vibrational entropy from ptraj
(Tue Oct 29 2013 - 08:53:11 PDT)
Re: [AMBER] huge values for the vibrational entropy from ptraj
(Tue Oct 29 2013 - 06:50:53 PDT)
Re: [AMBER] huge values for the vibrational entropy from ptraj
(Tue Oct 29 2013 - 05:37:52 PDT)
[AMBER] huge values for the vibrational entropy from ptraj
(Tue Oct 29 2013 - 01:56:31 PDT)
Re: [AMBER] mmpbsa_py_energy and PBSA options
(Fri Oct 25 2013 - 11:18:02 PDT)
Re: [AMBER] mmpbsa_py_energy and PBSA options
(Fri Oct 25 2013 - 10:08:52 PDT)
[AMBER] mmpbsa_py_energy and PBSA options
(Fri Oct 25 2013 - 09:02:39 PDT)
Re: [AMBER] ionic strength conversion between MMPBSA.py and PBSA
(Fri Oct 25 2013 - 08:44:53 PDT)
[AMBER] ionic strength conversion between MMPBSA.py and PBSA
(Fri Oct 25 2013 - 07:21:12 PDT)
Re: [AMBER] parmed.py bug when using the "parmout" command ?
(Thu Oct 24 2013 - 12:46:11 PDT)
Re: [AMBER] parmed.py bug when using the "parmout" command ?
(Thu Oct 24 2013 - 10:36:33 PDT)
Re: [AMBER] parmed.py bug when using the "parmout" command ?
(Thu Oct 24 2013 - 10:20:35 PDT)
Re: [AMBER] parmed.py bug when using the "parmout" command ?
(Thu Oct 24 2013 - 10:15:31 PDT)
Re: [AMBER] parmed.py bug when using the "parmout" command ?
(Thu Oct 24 2013 - 09:31:41 PDT)
Re: [AMBER] parmed.py bug when using the "parmout" command ?
(Thu Oct 24 2013 - 09:16:04 PDT)
Re: [AMBER] parmed.py bug when using the "parmout" command ?
(Thu Oct 24 2013 - 08:14:02 PDT)
[AMBER] parmed.py bug when using the "parmout" command ?
(Thu Oct 24 2013 - 07:55:12 PDT)
Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB
(Thu Oct 24 2013 - 07:35:17 PDT)
[AMBER] MMGBSA, Generalized Born, protein-nucleic acid complex
(Thu Oct 24 2013 - 05:53:45 PDT)
Ying-Chieh Sun
Re: [AMBER] Trajectory determination and directionality in TI with softcore potentials
(Wed Oct 30 2013 - 01:43:06 PDT)
Re: [AMBER] Soft-core questions for TI method
(Wed Oct 30 2013 - 01:31:57 PDT)
Yongxiu Li
Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much!
(Tue Oct 29 2013 - 01:03:39 PDT)
Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much!
(Tue Oct 15 2013 - 06:09:33 PDT)
[AMBER] about rms atomic fluctuation for protein crystal .thank you very much!
(Mon Oct 14 2013 - 04:36:06 PDT)
yuandandan
Re: [AMBER] [Amber]Question about softcore
(Fri Oct 11 2013 - 06:48:50 PDT)
[AMBER] Questions about softcore part
(Thu Oct 10 2013 - 02:22:14 PDT)
Re: [AMBER] Soft-core questions for TI method
(Mon Oct 07 2013 - 19:58:35 PDT)
[AMBER] Soft-core questions for TI method
(Mon Oct 07 2013 - 00:43:29 PDT)
[AMBER] Soft-core questions for TI method
(Mon Oct 07 2013 - 00:26:16 PDT)
Zhiye Tang
Re: [AMBER] SHAKE flucatuation
(Thu Oct 10 2013 - 13:33:21 PDT)
[AMBER] SHAKE flucatuation
(Thu Oct 10 2013 - 11:54:30 PDT)
冉挺
Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"
(Thu Oct 03 2013 - 06:07:40 PDT)
Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"
(Wed Oct 02 2013 - 03:52:36 PDT)
Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"
(Tue Oct 01 2013 - 05:35:32 PDT)
Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"
(Tue Oct 01 2013 - 02:17:00 PDT)
石坪江梨花
[AMBER] mdcrd to dcd
(Thu Oct 31 2013 - 04:36:18 PDT)
袁丹丹
[AMBER] Questions about VDW process of thermodynamic integration method
(Thu Oct 03 2013 - 06:06:54 PDT)
[AMBER] Questions about VDW process of thermodynamic integration method
(Thu Oct 03 2013 - 05:57:43 PDT)
陈发生
[AMBER] Phenyl-boronic acid derivatives lacking of parameter in Mol2 file
(Sun Oct 06 2013 - 20:48:07 PDT)
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Thu Oct 31 2013 - 15:00:03 PDT
Archived on
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