Amber Archive Apr 2011 by author
723 messages
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Starting
Fri Apr 01 2011 - 00:30:02 PDT,
Ending
Sat Apr 30 2011 - 17:30:02 PDT
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Adrian Roitberg
Re: [AMBER] Post-Processing MD trajectory
(Fri Apr 29 2011 - 04:39:10 PDT)
Re: [AMBER] How to find Acetyl-coa parameters in R.E.D.DB?
(Thu Apr 14 2011 - 09:51:49 PDT)
Re: [AMBER] Implicit solvent and box
(Wed Apr 13 2011 - 10:55:57 PDT)
Re: [AMBER] Implicit solvent and box
(Wed Apr 13 2011 - 10:49:16 PDT)
Re: [AMBER] problem with ptraj trajout in ambertools
(Mon Apr 11 2011 - 11:03:43 PDT)
Agostino Bruno
[AMBER] Spatial Distribution Functions
(Fri Apr 08 2011 - 07:10:10 PDT)
Alan Wilter Sousa da Silva
[AMBER] ambertools 1.5, python and Mac
(Tue Apr 19 2011 - 03:19:49 PDT)
Aldo Segura
Re: [AMBER] Does AMBER 9 has parameters for ions F- Br- I- etc
(Wed Apr 13 2011 - 20:22:52 PDT)
[AMBER] About of MMPBSA.py results
(Fri Apr 08 2011 - 06:46:00 PDT)
[AMBER] MMPBSA.py Tests
(Thu Apr 07 2011 - 13:23:11 PDT)
Alex Spasic
Re: [AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file
(Tue Apr 05 2011 - 13:44:05 PDT)
Re: [AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file
(Tue Apr 05 2011 - 12:03:02 PDT)
Ali M. Naserian-Nik
Re: [AMBER] Steered MD at constant force
(Thu Apr 28 2011 - 07:26:33 PDT)
[AMBER] Steered MD at constant force
(Thu Apr 28 2011 - 05:55:23 PDT)
Re: [AMBER] Calculation of forces using steered MD
(Wed Apr 13 2011 - 01:04:26 PDT)
Re: [AMBER] Calculation of forces using steered MD
(Tue Apr 12 2011 - 23:20:48 PDT)
[AMBER] Calculation of forces using steered MD
(Tue Apr 12 2011 - 10:17:05 PDT)
Almudena Pino
Re: [AMBER] Modified REMD
(Wed Apr 06 2011 - 23:46:12 PDT)
[AMBER] Modified REMD
(Tue Apr 05 2011 - 04:10:36 PDT)
Andreas Goetz
Re: [AMBER] QMMM
(Tue Apr 12 2011 - 11:26:32 PDT)
Andrew Voronkov
[AMBER] mmpbsa, mdfil: Error unknown flag: not
(Sun Apr 24 2011 - 07:07:01 PDT)
Ankita Kumari
Re: [AMBER] Beggining with AMBER
(Tue Apr 12 2011 - 23:01:42 PDT)
Antje Wolf
[AMBER] Compare simulations done with AMBER9 to ones done with AMBER11 Cuda?
(Fri Apr 08 2011 - 02:45:34 PDT)
anyiphysics.gmail.com
Re: [AMBER] mmpbsa nmode problem
(Sat Apr 30 2011 - 15:36:18 PDT)
Re: [AMBER] mmpbsa nmode problem
(Sat Apr 30 2011 - 15:17:36 PDT)
Re: [AMBER] softcore potential and temperature
(Tue Apr 26 2011 - 14:39:02 PDT)
[AMBER] softcore potential and temperature
(Tue Apr 26 2011 - 11:19:40 PDT)
Re: [AMBER] 'shake problem' and soft core potential
(Fri Apr 22 2011 - 13:36:08 PDT)
Re: [AMBER] MMPBSA default input
(Tue Apr 19 2011 - 09:22:44 PDT)
[AMBER] MMPBSA default input
(Tue Apr 19 2011 - 08:02:29 PDT)
[AMBER] 'shake problem' and soft core potential
(Mon Apr 18 2011 - 12:05:55 PDT)
Re: [AMBER] python and perl versions of mmpbsa
(Tue Apr 12 2011 - 11:05:57 PDT)
[AMBER] python and perl versions of mmpbsa
(Tue Apr 12 2011 - 09:22:15 PDT)
Aust, Susanne
[AMBER] new AmberTools
(Thu Apr 07 2011 - 23:28:13 PDT)
Bala subramanian
Re: [AMBER] strange background job crash
(Mon Apr 18 2011 - 09:24:41 PDT)
[AMBER] strange background job crash
(Mon Apr 18 2011 - 08:44:02 PDT)
Re: [AMBER] leap solvateoct question
(Mon Apr 18 2011 - 03:46:36 PDT)
[AMBER] leap solvateoct question
(Mon Apr 18 2011 - 03:23:59 PDT)
Baldoni Hector Armando
Re: [AMBER] Add charges to a prmtop files before simulations
(Mon Apr 11 2011 - 07:38:11 PDT)
Baptiste Legrand
Re: [AMBER] Add charges to a prmtop files before simulations
(Thu Apr 14 2011 - 10:48:37 PDT)
[AMBER] Add charges to a prmtop files before simulations
(Mon Apr 11 2011 - 07:29:45 PDT)
Barbault Florent
Re: [AMBER] Calculation of forces using steered MD
(Wed Apr 13 2011 - 01:55:10 PDT)
Re: [AMBER] QMMM
(Tue Apr 12 2011 - 05:33:02 PDT)
Re: [AMBER] How to apply restraint based on a reference structure?
(Thu Apr 07 2011 - 10:17:08 PDT)
Ben Roberts
Re: [AMBER] Regarding Gaussian Calculations for MTK++ example- sidechain model
(Thu Apr 28 2011 - 09:28:12 PDT)
Re: [AMBER] MTK++ : genMetalFF.sh is not generating gaussian input files
(Tue Apr 26 2011 - 15:45:58 PDT)
Re: [AMBER] MCPB help
(Tue Apr 26 2011 - 11:30:24 PDT)
Re: [AMBER] End of protonate method with amber11?
(Tue Apr 26 2011 - 07:21:44 PDT)
Re: [AMBER] gaussian
(Thu Apr 21 2011 - 07:04:05 PDT)
Re: [AMBER] Regarding understanding MTK++ Document
(Tue Apr 19 2011 - 10:40:49 PDT)
Re: [AMBER] Regarding understanding MTK++ Document
(Tue Apr 19 2011 - 10:31:59 PDT)
Re: [AMBER] FW: Leap error with Zinc ions
(Mon Apr 18 2011 - 09:42:50 PDT)
[AMBER] MCPB instructions (was: Re: MCPB program - how to download)
(Mon Apr 18 2011 - 08:45:00 PDT)
Re: [AMBER] amber parameters for Ni
(Mon Apr 18 2011 - 08:34:18 PDT)
Bernhard Poll
[AMBER] MD with preset start/end structures
(Tue Apr 12 2011 - 04:43:17 PDT)
Re: [AMBER] bad atom type
(Thu Apr 07 2011 - 01:30:12 PDT)
[AMBER] bad atom type
(Tue Apr 05 2011 - 07:56:34 PDT)
Bill Miller III
Re: [AMBER] mmpbsa nmode problem
(Sat Apr 30 2011 - 15:31:02 PDT)
Re: [AMBER] mmpbsa nmode problem
(Fri Apr 29 2011 - 19:54:30 PDT)
Re: [AMBER] ptraj trajectory file size limits?
(Thu Apr 28 2011 - 20:20:15 PDT)
Re: [AMBER] Usage of ambermask within MMPBSA.py
(Thu Apr 28 2011 - 06:07:10 PDT)
Re: [AMBER] igb=8 available for MMPBSA.py ?
(Wed Apr 27 2011 - 09:11:14 PDT)
Re: [AMBER] MMPBSA.py won't understand my trajectories
(Wed Apr 27 2011 - 05:00:52 PDT)
Re: [AMBER] Alanine scanning
(Tue Apr 26 2011 - 06:32:21 PDT)
Re: [AMBER] Alanine scanning
(Tue Apr 26 2011 - 05:59:04 PDT)
Re: [AMBER] mmpbsa, mdfil: Error unknown flag: not
(Sun Apr 24 2011 - 07:54:10 PDT)
Re: [AMBER] MMPBSA.py error
(Tue Apr 19 2011 - 19:44:25 PDT)
Re: [AMBER] No data for 0+0 MM BOND 0
(Sun Apr 17 2011 - 06:16:38 PDT)
Re: [AMBER] MMPBSA.py.MPI error
(Thu Apr 14 2011 - 05:25:12 PDT)
Re: [AMBER] python and perl versions of mmpbsa
(Tue Apr 12 2011 - 09:27:18 PDT)
Re: [AMBER] Error in running MMPBSA.py.MPI with sander.APBS
(Sun Apr 10 2011 - 17:25:53 PDT)
Re: [AMBER] QUESTION ON MMPBSA
(Fri Apr 08 2011 - 11:01:02 PDT)
Re: [AMBER] QUESTION ON MMPBSA
(Fri Apr 08 2011 - 10:15:25 PDT)
Re: [AMBER] problem of installation of MMPBSA.py
(Fri Apr 08 2011 - 04:17:34 PDT)
Re: [AMBER] problems when using mm_pbsa.pl in Amber10
(Fri Apr 08 2011 - 04:03:13 PDT)
Re: [AMBER] MMPBSA error
(Thu Apr 07 2011 - 04:03:09 PDT)
Re: [AMBER] The following error i got at the end of MM_PBSA.pl
(Wed Apr 06 2011 - 04:26:51 PDT)
Re: [AMBER] Error im mm_pbsa.pl
(Tue Apr 05 2011 - 13:56:18 PDT)
Re: [AMBER] PBSA calculations for wild type and a mutant
(Sat Apr 02 2011 - 07:48:53 PDT)
Bill Ross
Re: [AMBER] Xleap problem
(Mon Apr 25 2011 - 22:46:50 PDT)
Re: [AMBER] bond command in tlaep
(Wed Apr 20 2011 - 10:16:29 PDT)
Re: [AMBER] momentum from trajectory
(Thu Apr 14 2011 - 17:29:19 PDT)
Re: [AMBER] solvate with crystal water
(Thu Apr 14 2011 - 10:30:14 PDT)
Re: [AMBER] solvate with crystal water
(Thu Apr 14 2011 - 10:17:27 PDT)
Re: [AMBER] Missing Parameters
(Mon Apr 04 2011 - 20:41:16 PDT)
Bongkeun Kim
[AMBER] Error on compiling cuda_parallel; MPI_Win is undefined
(Thu Apr 14 2011 - 13:02:32 PDT)
Re: [AMBER] segmentation fault on antechamber when using carbon nano tube
(Mon Apr 11 2011 - 14:06:00 PDT)
[AMBER] segmentation fault on antechamber when using carbon nano tube
(Mon Apr 11 2011 - 13:01:48 PDT)
Brendan Duggan
[AMBER] comparing order parameters from MD and NMR
(Wed Apr 13 2011 - 07:11:44 PDT)
Carlos Simmerling
Re: [AMBER] Post-Processing MD trajectory
(Fri Apr 29 2011 - 05:56:01 PDT)
Re: [AMBER] igb=8 available for MMPBSA.py ?
(Wed Apr 27 2011 - 10:48:06 PDT)
Re: [AMBER] Restraining distance between a protein atom and a water of crystalization
(Fri Apr 22 2011 - 05:27:47 PDT)
Re: [AMBER] Restraining distance between a protein atom and a water of crystalization
(Fri Apr 22 2011 - 04:20:39 PDT)
Re: [AMBER] NEB calculations in enzyme?
(Mon Apr 18 2011 - 08:53:52 PDT)
Re: [AMBER] Restraining distance between a protein atom and a water of crystalization
(Mon Apr 18 2011 - 06:33:37 PDT)
Re: [AMBER] Restraining distance between a protein atom and a water of crystalization
(Mon Apr 18 2011 - 04:12:17 PDT)
Re: [AMBER] Restraining non-bonded atoms
(Fri Apr 15 2011 - 06:05:29 PDT)
Re: [AMBER] MD with preset start/end structures
(Thu Apr 14 2011 - 11:41:34 PDT)
Re: [AMBER] Implicit solvent and box
(Wed Apr 13 2011 - 11:38:16 PDT)
Re: [AMBER] Implicit solvent and box
(Wed Apr 13 2011 - 11:01:16 PDT)
Re: [AMBER] Implicit solvent and box
(Wed Apr 13 2011 - 10:53:23 PDT)
Re: [AMBER] Implicit solvent and box
(Wed Apr 13 2011 - 10:46:12 PDT)
Re: [AMBER] MD with preset start/end structures
(Tue Apr 12 2011 - 04:53:03 PDT)
Re: [AMBER] steered MD versus umbrella sampling?
(Mon Apr 11 2011 - 14:16:23 PDT)
Re: [AMBER] distance criteria of TIP3P added to protein-DNA complex
(Sat Apr 09 2011 - 09:48:20 PDT)
Re: [AMBER] Restraint potential in Targeted MD
(Fri Apr 08 2011 - 13:42:31 PDT)
Re: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network"
(Fri Apr 08 2011 - 12:01:23 PDT)
Re: [AMBER] Restraint potential in Targeted MD
(Fri Apr 08 2011 - 11:37:37 PDT)
Re: [AMBER] Restraint potential in Targeted MD
(Fri Apr 08 2011 - 11:06:32 PDT)
Re: [AMBER] How to apply restraint based on a reference structure?
(Thu Apr 07 2011 - 10:16:06 PDT)
Re: [AMBER] potential energy from remd
(Thu Apr 07 2011 - 09:55:20 PDT)
Re: [AMBER] Protein-Drug dissociation PMF: Is large conformational change in protein real or artifacts?
(Thu Apr 07 2011 - 09:21:15 PDT)
Re: [AMBER] Umbrella sampling
(Tue Apr 05 2011 - 11:28:22 PDT)
Re: [AMBER] Umbrella sampling
(Tue Apr 05 2011 - 11:07:18 PDT)
Re: [AMBER] PMEMD and NEB?
(Mon Apr 04 2011 - 12:09:35 PDT)
Re: [AMBER] ptraj rmsd
(Mon Apr 04 2011 - 07:04:20 PDT)
case
Re: [AMBER] puzzle ahout constructing .prepin
(Sat Apr 16 2011 - 06:04:36 PDT)
Re: [AMBER] problem of using leap
(Tue Apr 12 2011 - 20:16:38 PDT)
Re: [AMBER] Editing Protein - Change Bond
(Sun Apr 10 2011 - 08:55:48 PDT)
Catein Catherine
Re: [AMBER] bond command in tlaep
(Wed Apr 20 2011 - 23:11:04 PDT)
[AMBER] Why Gyr and rmsd read mdcrd differently?
(Wed Apr 20 2011 - 07:54:13 PDT)
[AMBER] Can AMBER10 be installed on 64-bit linux computer?
(Wed Apr 20 2011 - 07:29:54 PDT)
Re: [AMBER] How to apply restraint based on a reference structure?
(Thu Apr 07 2011 - 10:33:35 PDT)
Re: [AMBER] How to apply restraint based on a reference structure?
(Thu Apr 07 2011 - 10:30:39 PDT)
[AMBER] How to apply restraint on the root-mean-square deviation along the z-axis of two proteins
(Thu Apr 07 2011 - 10:18:51 PDT)
[AMBER] How to apply restraint based on a reference structure?
(Thu Apr 07 2011 - 10:12:13 PDT)
[AMBER] Protein-Drug dissociation PMF: Is large conformational change in protein real or artifacts?
(Thu Apr 07 2011 - 09:10:29 PDT)
[AMBER] Can I use PMF to study protein-protein complex formation?
(Mon Apr 04 2011 - 08:51:30 PDT)
Chinh Su Tran To
[AMBER] error while editing charge table in Tutorial A1 by Dr. Walker
(Wed Apr 27 2011 - 02:17:45 PDT)
Chirag Vora
[AMBER] Free Energy Perturbation in AMBER 10
(Thu Apr 28 2011 - 21:41:57 PDT)
Christoph Malisi
Re: [AMBER] MMPBSA.py pairwise decomp
(Mon Apr 04 2011 - 07:35:36 PDT)
[AMBER] MMPBSA.py pairwise decomp
(Mon Apr 04 2011 - 07:11:29 PDT)
[AMBER] restart from stopped MMPBSA.py.MPI job
(Fri Apr 01 2011 - 07:06:04 PDT)
cieplak.cgl.ucsf.edu
Re: [AMBER] Atom types in LYN side chain
(Wed Apr 27 2011 - 18:52:07 PDT)
cwt
[AMBER] problems when using mm_pbsa.pl in Amber10
(Thu Apr 07 2011 - 22:58:40 PDT)
dacase.rci.rutgers.edu
Re: [AMBER] compile errors with AmberTools1.5 + Amber11
(Fri Apr 29 2011 - 13:05:49 PDT)
Re: [AMBER] help with antechamber
(Fri Apr 29 2011 - 12:52:29 PDT)
Re: [AMBER] AmberTools 1.4 PGI failed antechamber/sustiva test
(Fri Apr 29 2011 - 12:35:21 PDT)
Dachuan Guo
Re: [AMBER] SQM
(Mon Apr 18 2011 - 22:37:00 PDT)
[AMBER] SQM
(Mon Apr 18 2011 - 06:57:16 PDT)
[AMBER] recalculating atom charges
(Thu Apr 07 2011 - 23:51:42 PDT)
Daniel Roe
Re: [AMBER] Steered MD at constant force
(Thu Apr 28 2011 - 06:41:56 PDT)
Re: [AMBER] a problem about tutorial A12
(Thu Apr 14 2011 - 15:53:34 PDT)
Re: [AMBER] Error while installing amber11
(Thu Apr 14 2011 - 04:41:19 PDT)
Re: [AMBER] velocity units
(Wed Apr 13 2011 - 08:31:53 PDT)
Re: [AMBER] Error while installing amber11
(Wed Apr 13 2011 - 07:48:10 PDT)
Re: [AMBER] solvate with crystal water
(Tue Apr 12 2011 - 06:20:48 PDT)
Re: [AMBER] tleap problem
(Fri Apr 08 2011 - 14:19:27 PDT)
Re: [AMBER] Problem with trajin
(Fri Apr 08 2011 - 08:59:57 PDT)
Re: [AMBER] Problem compiling sander.PUPIL: No rule to build target 'mdread.PUPIL.o'
(Fri Apr 08 2011 - 08:30:40 PDT)
Daniel Sindhikara
Re: [AMBER] momentum from trajectory
(Thu Apr 14 2011 - 20:03:28 PDT)
David A Case
Re: [AMBER] End of protonate method with amber11?
(Tue Apr 26 2011 - 06:44:29 PDT)
Re: [AMBER] Restraining distance between a protein atom and a water of crystalization
(Tue Apr 26 2011 - 06:34:14 PDT)
Re: [AMBER] changing restart file format from 6f12.7 to 6f12.6
(Tue Apr 26 2011 - 05:35:11 PDT)
Re: [AMBER] Xleap problem
(Tue Apr 26 2011 - 05:07:06 PDT)
Re: [AMBER] Xleap problem
(Mon Apr 25 2011 - 07:03:46 PDT)
Re: [AMBER] Restraining distance between a protein atom and a water of crystalization
(Fri Apr 22 2011 - 05:46:52 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs!
(Thu Apr 21 2011 - 05:27:17 PDT)
Re: [AMBER] bond command in tlaep
(Wed Apr 20 2011 - 10:07:06 PDT)
Re: [AMBER] dealing with xleap
(Tue Apr 19 2011 - 04:42:34 PDT)
Re: [AMBER] How can i save this .pdb file to .top and .crd?? using AMBER 9
(Tue Apr 19 2011 - 04:40:15 PDT)
Re: [AMBER] SQM
(Tue Apr 19 2011 - 04:36:50 PDT)
Re: [AMBER] Regarding antechamber
(Tue Apr 19 2011 - 04:25:36 PDT)
Re: [AMBER] Can i addIons F- Br- I- using AMBER 9
(Mon Apr 18 2011 - 05:04:04 PDT)
Re: [AMBER] Error installing amber9 for mpi(sander.MPI)
(Mon Apr 18 2011 - 04:57:43 PDT)
Re: [AMBER] QMMM
(Mon Apr 18 2011 - 04:53:32 PDT)
Re: [AMBER] fe4s4 cubane force field parameters
(Fri Apr 15 2011 - 08:39:04 PDT)
Re: [AMBER] comparing order parameters from MD and NMR
(Fri Apr 15 2011 - 08:32:35 PDT)
[AMBER] Release of AmberTools 1.5
(Fri Apr 15 2011 - 05:48:14 PDT)
Re: [AMBER] Add charges to a prmtop files before simulations
(Thu Apr 14 2011 - 11:03:05 PDT)
[AMBER] weird hydrogen names?
(Thu Apr 14 2011 - 10:39:30 PDT)
Re: [AMBER] How to find Acetyl-coa parameters in R.E.D.DB?
(Thu Apr 14 2011 - 09:35:01 PDT)
Re: [AMBER] solvate with crystal water
(Thu Apr 14 2011 - 09:30:59 PDT)
Re: [AMBER] Does AMBER 9 has parameters for ions F- Br- I- etc
(Thu Apr 14 2011 - 05:11:50 PDT)
Re: [AMBER] nucleosides
(Thu Apr 14 2011 - 04:58:00 PDT)
Re: [AMBER] Error while installing amber11
(Wed Apr 13 2011 - 09:50:59 PDT)
Re: [AMBER] Implicit solvent and box
(Wed Apr 13 2011 - 09:47:50 PDT)
Re: [AMBER] problem of using leap
(Wed Apr 13 2011 - 04:53:42 PDT)
Re: [AMBER] another AmberTools problem
(Tue Apr 12 2011 - 13:06:11 PDT)
Re: [AMBER] ambertools 1.5
(Tue Apr 12 2011 - 08:16:15 PDT)
Re: [AMBER] Maximum number of atoms
(Fri Apr 08 2011 - 13:32:09 PDT)
Re: [AMBER] Maximum number of atoms
(Fri Apr 08 2011 - 05:46:11 PDT)
Re: [AMBER] Default values
(Fri Apr 08 2011 - 05:43:16 PDT)
Re: [AMBER] new AmberTools
(Fri Apr 08 2011 - 05:40:59 PDT)
Re: [AMBER] how to obtain 4x4x1.1nm water
(Thu Apr 07 2011 - 06:20:54 PDT)
Re: [AMBER] is GBSA applicable to organic solvent?
(Wed Apr 06 2011 - 05:38:40 PDT)
Re: [AMBER] opls-aa; ions
(Mon Apr 04 2011 - 05:20:39 PDT)
David A. Case
Re: [AMBER] Free Energy Perturbation in AMBER 10
(Fri Apr 29 2011 - 15:06:06 PDT)
Re: [AMBER] Diffusion coefficient in implicit water
(Wed Apr 27 2011 - 05:01:04 PDT)
David Case
Re: [AMBER] 'shake problem' and soft core potential
(Mon Apr 18 2011 - 14:48:42 PDT)
Re: [AMBER] AmberTools install
(Tue Apr 12 2011 - 05:25:31 PDT)
david condon
Re: [AMBER] what do rdparm dihedral numbers mean?
(Tue Apr 19 2011 - 11:31:29 PDT)
[AMBER] what do rdparm dihedral numbers mean?
(Tue Apr 19 2011 - 09:57:50 PDT)
Re: [AMBER] Implicit solvent and box
(Wed Apr 13 2011 - 08:59:15 PDT)
Dean Cuebas
Re: [AMBER] Installing Ambertools1.5 on Snow Leopard
(Mon Apr 25 2011 - 18:44:01 PDT)
[AMBER] Installing Ambertools1.5 on Snow Leopard
(Sun Apr 24 2011 - 21:13:30 PDT)
Dmitry Mukha
Re: [AMBER] velocity units
(Wed Apr 13 2011 - 08:38:23 PDT)
[AMBER] velocity units
(Wed Apr 13 2011 - 07:04:49 PDT)
Re: [AMBER] Processors, cores and threads
(Wed Apr 13 2011 - 01:29:25 PDT)
[AMBER] SDSC
(Tue Apr 05 2011 - 02:00:53 PDT)
Dmitry Nilov
Re: [AMBER] Beggining with AMBER
(Wed Apr 13 2011 - 22:36:49 PDT)
Re: [AMBER] Calculation of forces using steered MD
(Wed Apr 13 2011 - 01:59:52 PDT)
Re: [AMBER] Beggining with AMBER
(Wed Apr 13 2011 - 01:31:46 PDT)
Re: [AMBER] Calculation of forces using steered MD
(Wed Apr 13 2011 - 00:42:25 PDT)
Re: [AMBER] Calculation of forces using steered MD
(Tue Apr 12 2011 - 21:31:59 PDT)
Re: [AMBER] Problem on SMD
(Wed Apr 06 2011 - 07:28:52 PDT)
Dmitry Osolodkin
Re: [AMBER] AMBER 11 pbsa errors
(Tue Apr 19 2011 - 08:26:13 PDT)
Re: [AMBER] AMBER 11 pbsa errors
(Tue Apr 19 2011 - 08:12:14 PDT)
[AMBER] AMBER 11 pbsa errors
(Tue Apr 19 2011 - 05:42:05 PDT)
Domenica Dibenedetto
[AMBER] parameters sodium phosfate
(Fri Apr 29 2011 - 07:10:09 PDT)
Dwight McGee
Re: [AMBER] MMPBSA.py (AmberTools 1.5) bug in Alanine Scanning (alamdcrd.py)
(Tue Apr 26 2011 - 06:02:55 PDT)
Re: [AMBER] QUESTION ON MMPBSA
(Mon Apr 11 2011 - 06:26:50 PDT)
Re: [AMBER] Error im mm_pbsa.pl
(Tue Apr 05 2011 - 08:37:49 PDT)
Eliac Brown
[AMBER] Electrostatic term
(Tue Apr 19 2011 - 02:30:13 PDT)
Elisa Frezza
Re: [AMBER] PMF
(Thu Apr 21 2011 - 06:23:16 PDT)
[AMBER] PMF
(Tue Apr 19 2011 - 08:40:29 PDT)
Re: [AMBER] Implicit solvent and box
(Wed Apr 13 2011 - 09:02:26 PDT)
[AMBER] Implicit solvent and box
(Wed Apr 13 2011 - 08:49:50 PDT)
Emmanuel Baribefe Naziga
Re: [AMBER] Umbrella sampling procedure
(Mon Apr 04 2011 - 09:07:02 PDT)
fancy2012
Re: [AMBER] problem of using leap
(Mon Apr 18 2011 - 22:59:51 PDT)
Re: [AMBER] problem of using leap
(Tue Apr 12 2011 - 22:24:11 PDT)
[AMBER] problem of using leap
(Tue Apr 12 2011 - 19:46:47 PDT)
Re: [AMBER] problem of installation of MMPBSA.py
(Sun Apr 10 2011 - 03:24:24 PDT)
[AMBER] problem of installation of MMPBSA.py
(Fri Apr 08 2011 - 01:38:52 PDT)
Fernando Blanco
Re: [AMBER] Beggining with AMBER
(Thu Apr 14 2011 - 06:50:08 PDT)
Re: [AMBER] Beggining with AMBER
(Thu Apr 14 2011 - 05:29:10 PDT)
Re: [AMBER] Beggining with AMBER
(Wed Apr 13 2011 - 12:32:19 PDT)
[AMBER] Beggining with AMBER
(Tue Apr 12 2011 - 10:00:21 PDT)
filip fratev
Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? GTX580 tests?
(Mon Apr 11 2011 - 22:07:07 PDT)
Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ?
(Sat Apr 09 2011 - 09:21:32 PDT)
Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? -Test results
(Fri Apr 08 2011 - 02:04:22 PDT)
Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ?
(Thu Apr 07 2011 - 16:52:35 PDT)
Francesco Oteri
[AMBER] Ambertools SDK
(Tue Apr 19 2011 - 09:54:13 PDT)
Re: [AMBER] How to modify .pdb file for Amber input
(Tue Apr 12 2011 - 01:03:00 PDT)
Re: [AMBER] Solute concentration in MD
(Mon Apr 11 2011 - 15:50:56 PDT)
[AMBER] ambertools 1.5
(Mon Apr 11 2011 - 10:34:51 PDT)
FyD
Re: [AMBER] How to find Acetyl-coa parameters in R.E.D.DB?
(Thu Apr 14 2011 - 22:05:34 PDT)
Re: [AMBER] How to find Acetyl-coa parameters in R.E.D.DB?
(Thu Apr 14 2011 - 12:02:20 PDT)
Gabriel Urquiza
Re: [AMBER] MMPBSA.py won't understand my trajectories
(Wed Apr 27 2011 - 06:19:39 PDT)
[AMBER] MMPBSA.py won't understand my trajectories
(Wed Apr 27 2011 - 04:52:51 PDT)
[AMBER] MMPBSA.py error
(Tue Apr 19 2011 - 19:34:37 PDT)
George Tzotzos
Re: [AMBER] Alanine scanning
(Tue Apr 26 2011 - 06:26:34 PDT)
[AMBER] Alanine scanning
(Tue Apr 26 2011 - 05:50:00 PDT)
Re: [AMBER] Equilibration: Using restraintmask
(Mon Apr 25 2011 - 09:05:37 PDT)
[AMBER] Equilibration: Using restraintmask
(Mon Apr 25 2011 - 04:53:53 PDT)
Re: [AMBER] tleap problem
(Sat Apr 09 2011 - 11:30:57 PDT)
Re: [AMBER] tleap problem
(Sat Apr 09 2011 - 01:32:54 PDT)
[AMBER] tleap problem
(Fri Apr 08 2011 - 14:11:43 PDT)
[AMBER] tleap problem
(Fri Apr 08 2011 - 14:07:49 PDT)
gromacs
[AMBER] opls-aa; ions
(Mon Apr 04 2011 - 03:05:29 PDT)
Guenegou, Guillaume [ORDFR]
Re: [AMBER] End of protonate method with amber11?
(Tue Apr 26 2011 - 07:33:22 PDT)
Re: [AMBER] End of protonate method with amber11?
(Tue Apr 26 2011 - 07:12:08 PDT)
[AMBER] End of protonate method with amber11?
(Tue Apr 26 2011 - 04:54:38 PDT)
Gustavo Seabra
Re: [AMBER] masking in the QMMM input
(Fri Apr 15 2011 - 05:45:26 PDT)
Re: [AMBER] QMMM
(Tue Apr 12 2011 - 11:05:55 PDT)
Re: [AMBER] QMMM
(Tue Apr 12 2011 - 06:45:28 PDT)
Re: [AMBER] Multiple links QM-MM
(Mon Apr 11 2011 - 04:21:58 PDT)
hanlu0366
[AMBER] How to add a new force field to Amber 11
(Fri Apr 29 2011 - 20:12:49 PDT)
[AMBER] puzzle ahout constructing .prepin
(Fri Apr 15 2011 - 18:54:40 PDT)
Hashem Taha
Re: [AMBER] MCPB help
(Mon Apr 25 2011 - 10:49:45 PDT)
[AMBER] MCPB help
(Thu Apr 21 2011 - 15:58:22 PDT)
Re: [AMBER] solvate with crystal water
(Thu Apr 14 2011 - 12:12:13 PDT)
Re: [AMBER] solvate with crystal water
(Thu Apr 14 2011 - 09:04:44 PDT)
Re: [AMBER] solvate with crystal water
(Thu Apr 14 2011 - 08:39:02 PDT)
Re: [AMBER] solvate with crystal water
(Thu Apr 14 2011 - 08:37:42 PDT)
Re: [AMBER] solvate with crystal water
(Thu Apr 14 2011 - 08:11:18 PDT)
Re: [AMBER] solvate with crystal water
(Tue Apr 12 2011 - 17:56:39 PDT)
[AMBER] solvate with crystal water
(Mon Apr 11 2011 - 13:09:58 PDT)
Hector A. Baldoni
[AMBER] positive TdS
(Fri Apr 01 2011 - 09:26:01 PDT)
Hopkins, Robert
Re: [AMBER] Processors, cores and threads
(Tue Apr 12 2011 - 10:36:19 PDT)
[AMBER] Processors, cores and threads
(Tue Apr 12 2011 - 09:14:32 PDT)
Hugh Cheng
[AMBER] fe4s4 cubane force field parameters
(Tue Apr 12 2011 - 11:54:10 PDT)
iccy liu
[AMBER] umbrella sampling on a difference of distances RC.
(Fri Apr 29 2011 - 11:06:17 PDT)
Ilyas Yildirim
Re: [AMBER] How to apply restraint based on a reference structure?
(Thu Apr 07 2011 - 10:40:29 PDT)
Re: [AMBER] Missing Parameters
(Mon Apr 04 2011 - 22:42:10 PDT)
Re: [AMBER] Missing Parameters
(Mon Apr 04 2011 - 07:23:58 PDT)
Indrek Morell
[AMBER] Heme .lib file for heme - problem
(Fri Apr 08 2011 - 09:48:55 PDT)
[AMBER] No mdcrd file with PMEMD
(Mon Apr 04 2011 - 10:22:14 PDT)
ivanquirino1928.gmail.com
Re: [AMBER] Problem compiling sander.PUPIL: No rule to build target 'mdread.PUPIL.o'
(Fri Apr 08 2011 - 11:41:46 PDT)
[AMBER] Problem compiling sander.PUPIL: No rule to build target 'mdread.PUPIL.o'
(Fri Apr 08 2011 - 07:17:08 PDT)
J.F.Jiang
[AMBER] peptide-protein complex construction
(Mon Apr 11 2011 - 04:29:53 PDT)
Jacopo Sgrignani
Re: [AMBER] Query about charge on magnesium
(Fri Apr 15 2011 - 08:07:56 PDT)
Re: [AMBER] Heme .lib file for heme - problem
(Fri Apr 08 2011 - 10:51:18 PDT)
Jagur Lambix
Re: [AMBER] parameter for CNTs
(Tue Apr 05 2011 - 15:21:25 PDT)
jani vinod
Re: [AMBER] PMF
(Tue Apr 19 2011 - 21:31:45 PDT)
Jason Swails
Re: [AMBER] Post-Processing MD trajectory
(Sat Apr 30 2011 - 01:51:56 PDT)
Re: [AMBER] umbrella sampling on a difference of distances RC.
(Fri Apr 29 2011 - 13:03:50 PDT)
Re: [AMBER] SURFTEN / SURFOFF values are not consistent across *.all.out files
(Fri Apr 29 2011 - 12:56:44 PDT)
Re: [AMBER] compile errors with AmberTools1.5 + Amber11
(Fri Apr 29 2011 - 12:52:55 PDT)
Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py
(Fri Apr 29 2011 - 07:51:18 PDT)
Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py
(Fri Apr 29 2011 - 07:39:26 PDT)
Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py
(Fri Apr 29 2011 - 07:11:44 PDT)
Re: [AMBER] Post-Processing MD trajectory
(Fri Apr 29 2011 - 05:44:10 PDT)
Re: [AMBER] Post-Processing MD trajectory
(Fri Apr 29 2011 - 05:26:53 PDT)
Re: [AMBER] ptraj trajectory file size limits?
(Fri Apr 29 2011 - 05:10:59 PDT)
Re: [AMBER] compile errors with AmberTools1.5 + Amber11
(Thu Apr 28 2011 - 17:35:17 PDT)
Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py
(Thu Apr 28 2011 - 17:32:29 PDT)
Re: [AMBER] building amber - meaning of file comparison problems?
(Thu Apr 28 2011 - 09:09:15 PDT)
Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py
(Thu Apr 28 2011 - 08:59:40 PDT)
Re: [AMBER] Usage of ambermask within MMPBSA.py
(Thu Apr 28 2011 - 08:36:51 PDT)
Re: [AMBER] MCPB install problem
(Thu Apr 28 2011 - 05:36:17 PDT)
Re: [AMBER] MMPBSA.py error - VDW ****
(Thu Apr 28 2011 - 00:47:31 PDT)
Re: [AMBER] igb=8 available for MMPBSA.py ?
(Wed Apr 27 2011 - 09:57:24 PDT)
Re: [AMBER] MMPBSA.py error
(Tue Apr 26 2011 - 19:46:48 PDT)
Re: [AMBER] Installing Ambertools1.5 on Snow Leopard
(Mon Apr 25 2011 - 22:23:51 PDT)
Re: [AMBER] MMPBSA error
(Mon Apr 25 2011 - 11:56:18 PDT)
Re: [AMBER] Problems with constant pH calc Amber 11
(Mon Apr 25 2011 - 11:55:29 PDT)
Re: [AMBER] MMPBSA error
(Mon Apr 25 2011 - 10:53:40 PDT)
Re: [AMBER] Equilibration: Using restraintmask
(Mon Apr 25 2011 - 09:02:35 PDT)
Re: [AMBER] MMPBSA error
(Mon Apr 25 2011 - 08:56:08 PDT)
Re: [AMBER] Installing Ambertools1.5 on Snow Leopard
(Sun Apr 24 2011 - 23:39:47 PDT)
Re: [AMBER] Question about ptraj artifacts
(Sun Apr 24 2011 - 10:11:10 PDT)
Re: [AMBER] Problems with constant pH calc Amber 11
(Sat Apr 23 2011 - 18:51:59 PDT)
Re: [AMBER] Problems with constant pH calc Amber 11
(Sat Apr 23 2011 - 17:14:19 PDT)
Re: [AMBER] Problems with constant pH calc Amber 11
(Sat Apr 23 2011 - 16:12:24 PDT)
Re: [AMBER] RED conformation weights
(Sat Apr 23 2011 - 09:50:54 PDT)
Re: [AMBER] output velocities with ptraj
(Fri Apr 22 2011 - 07:17:47 PDT)
Re: [AMBER] setting gbsa=0 does not switch off GB calculation
(Thu Apr 21 2011 - 10:03:30 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs!
(Thu Apr 21 2011 - 08:17:24 PDT)
Re: [AMBER] Defining ligand and receptor within MMPBSA.py
(Thu Apr 21 2011 - 08:13:32 PDT)
Re: [AMBER] bond command in tlaep
(Thu Apr 21 2011 - 00:11:49 PDT)
Re: [AMBER] failures in tests of amber tools 1.5
(Thu Apr 21 2011 - 00:00:57 PDT)
Re: [AMBER] Installation Amber Tools 1.5
(Wed Apr 20 2011 - 10:44:33 PDT)
Re: [AMBER] MMPBSA.py error
(Wed Apr 20 2011 - 10:37:07 PDT)
Re: [AMBER] QUESTION ON MMPBSA
(Tue Apr 19 2011 - 20:18:51 PDT)
Re: [AMBER] MMPBSA.py error
(Tue Apr 19 2011 - 20:09:48 PDT)
Re: [AMBER] Ambertools SDK
(Tue Apr 19 2011 - 10:43:54 PDT)
Re: [AMBER] what do rdparm dihedral numbers mean?
(Tue Apr 19 2011 - 10:36:12 PDT)
Re: [AMBER] AMBER 11 pbsa errors
(Tue Apr 19 2011 - 08:18:35 PDT)
Re: [AMBER] AMBER 11 pbsa errors
(Tue Apr 19 2011 - 08:12:53 PDT)
Re: [AMBER] MMPBSA default input
(Tue Apr 19 2011 - 08:09:19 PDT)
Re: [AMBER] ambertools 1.5, python and Mac
(Tue Apr 19 2011 - 08:03:45 PDT)
[AMBER] Fwd: QUESTION ON MMPBSA
(Mon Apr 18 2011 - 12:28:11 PDT)
Re: [AMBER] Number of MMPBSA_Nmode run
(Mon Apr 18 2011 - 10:49:49 PDT)
Re: [AMBER] Number of MMPBSA_Nmode run
(Mon Apr 18 2011 - 08:38:17 PDT)
Re: [AMBER] coordinate updates
(Fri Apr 15 2011 - 23:12:10 PDT)
Re: [AMBER] masking in the QMMM input
(Thu Apr 14 2011 - 23:41:43 PDT)
Re: [AMBER] momentum from trajectory
(Thu Apr 14 2011 - 21:36:44 PDT)
Re: [AMBER] masking in the QMMM input
(Thu Apr 14 2011 - 21:32:32 PDT)
Re: [AMBER] MMPBSA.py.MPI error
(Thu Apr 14 2011 - 19:37:17 PDT)
Re: [AMBER] Error in Installing MTK++ software
(Thu Apr 14 2011 - 14:18:47 PDT)
Re: [AMBER] weird hydrogen names?
(Thu Apr 14 2011 - 11:23:32 PDT)
Re: [AMBER] solvate with crystal water
(Thu Apr 14 2011 - 10:04:54 PDT)
Re: [AMBER] solvate with crystal water
(Thu Apr 14 2011 - 09:18:54 PDT)
Re: [AMBER] MMPBSA.py.MPI error
(Thu Apr 14 2011 - 09:10:29 PDT)
Re: [AMBER] solvate with crystal water
(Thu Apr 14 2011 - 08:20:40 PDT)
Re: [AMBER] MMPBSA.py.MPI error
(Thu Apr 14 2011 - 07:34:52 PDT)
Re: [AMBER] packmol and amber11: the solvent box issue
(Wed Apr 13 2011 - 16:53:25 PDT)
Re: [AMBER] packmol and amber11: the solvent box issue
(Wed Apr 13 2011 - 15:59:32 PDT)
Re: [AMBER] Implicit solvent and box
(Wed Apr 13 2011 - 12:20:08 PDT)
Re: [AMBER] Implicit solvent and box
(Wed Apr 13 2011 - 12:19:08 PDT)
Re: [AMBER] Implicit solvent and box
(Wed Apr 13 2011 - 11:19:16 PDT)
Re: [AMBER] Problem with VMD
(Wed Apr 13 2011 - 09:22:42 PDT)
Re: [AMBER] Error on running parameter 'sander'
(Wed Apr 13 2011 - 09:21:41 PDT)
Re: [AMBER] mmpbsa - nmode calculation
(Wed Apr 13 2011 - 01:09:18 PDT)
Re: [AMBER] errors compiling amber11 for cuda
(Tue Apr 12 2011 - 17:31:13 PDT)
Re: [AMBER] how did the SALTCON parameter work in MMPBSA?
(Tue Apr 12 2011 - 12:22:51 PDT)
Re: [AMBER] QMMM
(Tue Apr 12 2011 - 11:17:47 PDT)
Re: [AMBER] python and perl versions of mmpbsa
(Tue Apr 12 2011 - 11:13:42 PDT)
Re: [AMBER] Processors, cores and threads
(Tue Apr 12 2011 - 10:00:13 PDT)
Re: [AMBER] QMMM
(Tue Apr 12 2011 - 08:00:19 PDT)
Re: [AMBER] AmberTools install
(Mon Apr 11 2011 - 22:25:07 PDT)
Re: [AMBER] segmentation fault on antechamber when using carbon nano tube
(Mon Apr 11 2011 - 14:32:56 PDT)
Re: [AMBER] segmentation fault on antechamber when using carbon nano tube
(Mon Apr 11 2011 - 13:13:01 PDT)
Re: [AMBER] problem with ptraj trajout in ambertools
(Mon Apr 11 2011 - 10:24:35 PDT)
Re: [AMBER] problem with ptraj trajout in ambertools
(Mon Apr 11 2011 - 09:34:39 PDT)
Re: [AMBER] Add charges to a prmtop files before simulations
(Mon Apr 11 2011 - 09:32:24 PDT)
Re: [AMBER] AMBER
(Sun Apr 10 2011 - 22:11:28 PDT)
Re: [AMBER] Error in running MMPBSA.py.MPI with sander.APBS
(Sun Apr 10 2011 - 21:01:54 PDT)
Re: [AMBER] Error in installing Amber Tools
(Sun Apr 10 2011 - 14:43:06 PDT)
Re: [AMBER] Error in installing Amber Tools
(Sun Apr 10 2011 - 13:59:35 PDT)
Re: [AMBER] Error in installing Amber Tools
(Sun Apr 10 2011 - 13:49:23 PDT)
Re: [AMBER] Error in installing Amber Tools
(Sun Apr 10 2011 - 12:55:53 PDT)
Re: [AMBER] Uninstalling Amber Tools
(Sun Apr 10 2011 - 11:35:26 PDT)
Re: [AMBER] QUESTION ON MMPBSA
(Sun Apr 10 2011 - 11:28:12 PDT)
Re: [AMBER] QUESTION ON MMPBSA
(Sun Apr 10 2011 - 10:53:02 PDT)
Re: [AMBER] problem about addions
(Sat Apr 09 2011 - 22:56:07 PDT)
Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ?
(Sat Apr 09 2011 - 10:31:16 PDT)
Re: [AMBER] MMPBSA error
(Sat Apr 09 2011 - 10:07:47 PDT)
Re: [AMBER] tleap problem
(Sat Apr 09 2011 - 10:05:05 PDT)
Re: [AMBER] Maximum number of atoms
(Fri Apr 08 2011 - 12:24:05 PDT)
Re: [AMBER] Compare simulations done with AMBER9 to ones done with AMBER11 Cuda?
(Fri Apr 08 2011 - 11:37:36 PDT)
Re: [AMBER] rfree: Error decoding variable 1 3 from: pmemd.MPI and pmemd error
(Fri Apr 08 2011 - 11:33:56 PDT)
Re: [AMBER] new AmberTools
(Fri Apr 08 2011 - 08:35:12 PDT)
Re: [AMBER] MMPBSA error
(Thu Apr 07 2011 - 12:04:10 PDT)
Re: [AMBER] bad atom type
(Thu Apr 07 2011 - 08:09:01 PDT)
Re: [AMBER] how to obtain 4x4x1.1nm water
(Wed Apr 06 2011 - 23:30:14 PDT)
Re: [AMBER] Modified REMD
(Wed Apr 06 2011 - 14:43:13 PDT)
Re: [AMBER] bad atom type
(Wed Apr 06 2011 - 14:31:19 PDT)
Re: [AMBER] Query regarding considering water molecules
(Wed Apr 06 2011 - 10:22:59 PDT)
Re: [AMBER] Query regarding considering water molecules
(Wed Apr 06 2011 - 10:21:53 PDT)
Re: [AMBER] Error im mm_pbsa.pl
(Tue Apr 05 2011 - 11:29:23 PDT)
Re: [AMBER] MMPBSA.py ala-scanning output results
(Tue Apr 05 2011 - 08:40:51 PDT)
Re: [AMBER] Sugar ring conformation (QM/MM Vs MM)
(Mon Apr 04 2011 - 21:24:23 PDT)
Re: [AMBER] No mdcrd file with PMEMD reply
(Mon Apr 04 2011 - 12:24:56 PDT)
Re: [AMBER] PMEMD and NEB?
(Mon Apr 04 2011 - 12:10:38 PDT)
Re: [AMBER] No mdcrd file with PMEMD
(Mon Apr 04 2011 - 11:27:16 PDT)
Re: [AMBER] sleap with ff02pol.r1
(Mon Apr 04 2011 - 10:15:36 PDT)
Re: [AMBER] Question about Amber output file format
(Mon Apr 04 2011 - 09:12:53 PDT)
Re: [AMBER] MMPBSA.py ala-scanning output results
(Mon Apr 04 2011 - 09:04:31 PDT)
Re: [AMBER] MMPBSA.py pairwise decomp
(Mon Apr 04 2011 - 09:00:21 PDT)
Re: [AMBER] MMPBSA.py pairwise decomp
(Mon Apr 04 2011 - 07:24:51 PDT)
Re: [AMBER] mm_pbsa.pl error
(Sat Apr 02 2011 - 16:02:44 PDT)
Re: [AMBER] mm_pbsa.pl error
(Sat Apr 02 2011 - 16:01:19 PDT)
Re: [AMBER] mm_pbsa.pl error
(Sat Apr 02 2011 - 12:01:12 PDT)
Re: [AMBER] making lib file
(Fri Apr 01 2011 - 11:08:55 PDT)
Re: [AMBER] restart from stopped MMPBSA.py.MPI job
(Fri Apr 01 2011 - 08:35:05 PDT)
Re: [AMBER] bond command in tlaep
(Fri Apr 01 2011 - 08:23:14 PDT)
Re: [AMBER] Ptraj Mask option
(Fri Apr 01 2011 - 00:44:56 PDT)
Jesper Sørensen
Re: [AMBER] MMPBSA.py error - VDW ****
(Fri Apr 29 2011 - 01:38:05 PDT)
[AMBER] MMPBSA.py error - VDW ****
(Thu Apr 28 2011 - 00:29:08 PDT)
[AMBER] mmpbsa.py input - radii to use
(Wed Apr 13 2011 - 08:54:50 PDT)
Re: [AMBER] MMPBSA.py ala-scanning output results
(Tue Apr 05 2011 - 10:06:58 PDT)
Re: [AMBER] MMPBSA.py ala-scanning output results
(Tue Apr 05 2011 - 00:25:47 PDT)
[AMBER] MMPBSA.py ala-scanning output results
(Mon Apr 04 2011 - 07:13:17 PDT)
Jianyin Shao
Re: [AMBER] Problem with cluster?
(Tue Apr 26 2011 - 09:58:58 PDT)
John Khan
Re: [AMBER] Problems with constant pH calc Amber 11
(Mon Apr 25 2011 - 12:23:39 PDT)
Re: [AMBER] Problems with constant pH calc Amber 11
(Mon Apr 25 2011 - 11:10:24 PDT)
Re: [AMBER] Problems with constant pH calc Amber 11
(Sat Apr 23 2011 - 17:37:30 PDT)
Re: [AMBER] Problems with constant pH calc Amber 11
(Sat Apr 23 2011 - 16:55:54 PDT)
[AMBER] Problems with constant pH calc Amber 11
(Sat Apr 23 2011 - 15:22:21 PDT)
John S
[AMBER] output file for contacts
(Wed Apr 06 2011 - 22:20:44 PDT)
[AMBER] Vector analysis
(Wed Apr 06 2011 - 09:01:02 PDT)
Jon Mikel Azpiroz
[AMBER] Se atom type in GAFF
(Wed Apr 06 2011 - 02:33:57 PDT)
Jorgen Simonsen
[AMBER] potential energy from remd
(Thu Apr 07 2011 - 09:50:47 PDT)
Jose Borreguero
[AMBER] steered MD versus umbrella sampling?
(Mon Apr 11 2011 - 14:12:02 PDT)
[AMBER] how to estimate the free energy of folding for the C-terminal of a protein?
(Tue Apr 05 2011 - 17:46:05 PDT)
Joseph André
[AMBER] MMPBSA.py (AmberTools 1.5) bug in Alanine Scanning (alamdcrd.py)
(Tue Apr 26 2011 - 02:48:27 PDT)
juan zeng
[AMBER] parameter about pbsa for sander
(Thu Apr 07 2011 - 07:45:14 PDT)
[AMBER] parameter about pbsa for sander
(Thu Apr 07 2011 - 02:07:49 PDT)
Junjian Miao
Re: [AMBER] RED conformation weights
(Sun Apr 24 2011 - 02:53:42 PDT)
[AMBER] RED conformation weights
(Sat Apr 23 2011 - 05:51:17 PDT)
[AMBER] output velocities with ptraj
(Thu Apr 21 2011 - 23:49:36 PDT)
[AMBER] how to get initial inpcrd files in smd directory of tutorial A12?
(Thu Apr 21 2011 - 21:01:07 PDT)
Re: [AMBER] a problem about tutorial A12
(Thu Apr 14 2011 - 20:40:16 PDT)
[AMBER] a problem about tutorial A12
(Thu Apr 14 2011 - 07:09:03 PDT)
[AMBER] questions about packmol
(Thu Apr 07 2011 - 07:19:26 PDT)
[AMBER] is GBSA applicable to organic solvent?
(Tue Apr 05 2011 - 20:47:53 PDT)
Jurica Novak
Re: [AMBER] QMMM
(Mon Apr 18 2011 - 05:19:17 PDT)
Re: [AMBER] QMMM
(Mon Apr 18 2011 - 02:38:54 PDT)
Re: [AMBER] QMMM
(Tue Apr 12 2011 - 07:13:22 PDT)
Re: [AMBER] QMMM
(Tue Apr 12 2011 - 06:22:21 PDT)
[AMBER] QMMM
(Tue Apr 12 2011 - 05:13:14 PDT)
juzer stationwala
Re: [AMBER] ptraj trajectory file size limits?
(Thu Apr 28 2011 - 21:21:59 PDT)
Re: [AMBER] bond command in tlaep
(Wed Apr 20 2011 - 23:17:36 PDT)
[AMBER] failures in tests of amber tools 1.5
(Wed Apr 20 2011 - 22:31:26 PDT)
Re: [AMBER] Installation Amber Tools 1.5
(Wed Apr 20 2011 - 21:39:06 PDT)
[AMBER] Installation Amber Tools 1.5
(Wed Apr 20 2011 - 10:31:51 PDT)
Re: [AMBER] missing coordinates from pdb
(Wed Apr 13 2011 - 23:33:07 PDT)
[AMBER] Problem with VMD
(Wed Apr 13 2011 - 07:34:34 PDT)
juzer.niper.gmail.com
Re: [AMBER] Problem with VMD
(Wed Apr 13 2011 - 10:03:12 PDT)
Jérôme Golebiowski
Re: [AMBER] Protein-Drug dissociation PMF: Is large conformational change in protein real or artifacts?
(Thu Apr 07 2011 - 09:48:33 PDT)
Kamali Sripathi
Re: [AMBER] Question about ptraj artifacts
(Wed Apr 27 2011 - 08:52:26 PDT)
[AMBER] Question about ptraj artifacts
(Sun Apr 24 2011 - 06:58:53 PDT)
[AMBER] Question about ptraj artifacts
(Wed Apr 20 2011 - 13:06:30 PDT)
Katharina Lang
[AMBER] forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read
(Fri Apr 29 2011 - 07:33:02 PDT)
Kshatresh Dutta Dubey
Re: [AMBER] leap solvateoct question
(Mon Apr 18 2011 - 03:49:12 PDT)
Re: [AMBER] leap solvateoct question
(Mon Apr 18 2011 - 03:34:41 PDT)
Re: [AMBER] MMPBSA error
(Sat Apr 09 2011 - 03:37:51 PDT)
Re: [AMBER] MMPBSA error
(Thu Apr 07 2011 - 04:53:47 PDT)
[AMBER] MMPBSA error
(Thu Apr 07 2011 - 00:52:41 PDT)
kurisaki
[AMBER] Usage of diffuse command
(Wed Apr 13 2011 - 23:46:46 PDT)
Lachele Foley (Lists)
Re: [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap)
(Tue Apr 05 2011 - 10:32:45 PDT)
Re: [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap)
(Tue Apr 05 2011 - 09:46:06 PDT)
Lekpa Duukori
[AMBER] Non bonded interactions
(Wed Apr 13 2011 - 09:31:51 PDT)
Re: [AMBER] Solute concentration in MD
(Mon Apr 11 2011 - 16:03:14 PDT)
[AMBER] Solute concentration in MD
(Tue Apr 05 2011 - 08:26:09 PDT)
Lui
Re: [AMBER] Problem with trajin
(Fri Apr 08 2011 - 09:32:53 PDT)
[AMBER] Problem with trajin
(Fri Apr 08 2011 - 08:48:50 PDT)
M. L. Dodson
Re: [AMBER] packmol and amber11: the solvent box issue
(Wed Apr 13 2011 - 18:30:07 PDT)
Re: [AMBER] packmol and amber11: the solvent box issue
(Wed Apr 13 2011 - 16:39:25 PDT)
M. Shahid
Re: [AMBER] Processors, cores and threads
(Wed Apr 13 2011 - 02:04:32 PDT)
Mahmoud Soliman
Re: [AMBER] parallel QM/MM/MD lasts forever
(Tue Apr 19 2011 - 00:50:37 PDT)
[AMBER] parallel QM/MM/MD lasts forever
(Tue Apr 19 2011 - 00:17:37 PDT)
Re: [AMBER] NEB calculations in enzyme?
(Mon Apr 18 2011 - 09:18:18 PDT)
Re: [AMBER] NEB calculations in enzyme?
(Mon Apr 18 2011 - 09:16:14 PDT)
[AMBER] NEB calculations in enzyme?
(Sun Apr 17 2011 - 08:49:58 PDT)
[AMBER] PMF calculations
(Fri Apr 15 2011 - 11:06:11 PDT)
Re: [AMBER] Sugar ring conformation (QM/MM Vs MM)
(Tue Apr 05 2011 - 08:09:40 PDT)
[AMBER] Sugar ring conformation (QM/MM Vs MM)
(Mon Apr 04 2011 - 21:05:17 PDT)
Re: [AMBER] mm_pbsa.pl error
(Sat Apr 02 2011 - 15:44:39 PDT)
Re: [AMBER] mm_pbsa.pl error
(Sat Apr 02 2011 - 12:52:46 PDT)
[AMBER] mm_pbsa.pl error
(Sat Apr 02 2011 - 12:08:18 PDT)
Re: [AMBER] PBSA calculations for wild type and a mutant
(Sat Apr 02 2011 - 10:03:48 PDT)
[AMBER] PBSA calculations for wild type and a mutant
(Fri Apr 01 2011 - 13:15:09 PDT)
majid hasan
[AMBER] creating ssdna from dsdna
(Sun Apr 10 2011 - 17:23:31 PDT)
Re: [AMBER] Error in installing Amber Tools
(Sun Apr 10 2011 - 15:20:14 PDT)
Re: [AMBER] Error in installing Amber Tools
(Sun Apr 10 2011 - 14:18:15 PDT)
Re: [AMBER] Error in installing Amber Tools
(Sun Apr 10 2011 - 13:50:19 PDT)
Re: [AMBER] Error in installing Amber Tools
(Sun Apr 10 2011 - 13:41:53 PDT)
[AMBER] Error in installing Amber Tools
(Sun Apr 10 2011 - 12:40:40 PDT)
Re: [AMBER] Uninstalling Amber Tools
(Sun Apr 10 2011 - 12:22:53 PDT)
[AMBER] Uninstalling Amber Tools
(Sun Apr 10 2011 - 11:30:05 PDT)
Manish Datt
[AMBER] FW: Leap error with Zinc ions
(Mon Apr 18 2011 - 07:42:32 PDT)
[AMBER] Leap error with Zinc ions
(Thu Apr 14 2011 - 07:22:29 PDT)
Marc van der Kamp
Re: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network"
(Fri Apr 15 2011 - 02:43:46 PDT)
Re: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network"
(Sat Apr 09 2011 - 02:41:21 PDT)
[AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network"
(Fri Apr 08 2011 - 08:06:45 PDT)
Re: [AMBER] CHAMBER conversion: problem with IFBOX == 0
(Thu Apr 07 2011 - 01:38:02 PDT)
[AMBER] CHAMBER conversion: problem with IFBOX == 0
(Thu Apr 07 2011 - 00:53:18 PDT)
Marek Maly
Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ?
(Thu Apr 07 2011 - 17:53:04 PDT)
Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ?
(Fri Apr 01 2011 - 03:32:12 PDT)
Mark M Huntress
Re: [AMBER] making lib file
(Sat Apr 02 2011 - 07:39:06 PDT)
[AMBER] making lib file
(Fri Apr 01 2011 - 10:57:46 PDT)
Markus Kaukonen
Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py
(Thu Apr 28 2011 - 06:38:43 PDT)
Martin Peters
Re: [AMBER] MCPB install problem
(Wed Apr 27 2011 - 00:13:47 PDT)
Re: [AMBER] Regarding MTK++ MCPB tutorials on Small and Large Models of ZN Metalloprotein
(Wed Apr 20 2011 - 14:40:28 PDT)
Re: [AMBER] Side Chain Model building by MCPB
(Wed Apr 20 2011 - 14:24:04 PDT)
Matthias Negri
Re: [AMBER] MD with preset start/end structures and addless "problem in line read"
(Thu Apr 21 2011 - 06:53:40 PDT)
Re: [AMBER] MD with preset start/end structures
(Tue Apr 12 2011 - 06:31:31 PDT)
MD
[AMBER] add polarized ions to pol3 water? Are there polarized ions models in Amber?
(Tue Apr 19 2011 - 22:26:46 PDT)
[AMBER] How can i save this .pdb file to .top and .crd?? using AMBER 9
(Tue Apr 19 2011 - 00:25:30 PDT)
[AMBER] Can i addIons F- Br- I- using AMBER 9
(Sun Apr 17 2011 - 18:35:18 PDT)
Re: [AMBER] Does AMBER 9 has parameters for ions F- Br- I- etc
(Wed Apr 13 2011 - 20:43:42 PDT)
[AMBER] Does AMBER 9 has parameters for ions F- Br- I- etc
(Wed Apr 13 2011 - 20:00:55 PDT)
[AMBER] How to modify .pdb file for Amber input
(Tue Apr 12 2011 - 00:09:05 PDT)
Re: [AMBER] how to obtain 4x4x1.1nm water
(Thu Apr 07 2011 - 00:08:03 PDT)
[AMBER] how to obtain 4x4x1.1nm water
(Wed Apr 06 2011 - 21:16:20 PDT)
Melanie
[AMBER] Editing Protein - Change Bond
(Sun Apr 10 2011 - 02:37:28 PDT)
Re: [AMBER] Missing Parameters
(Mon Apr 04 2011 - 19:41:47 PDT)
Re: [AMBER] Missing Parameters
(Sun Apr 03 2011 - 16:24:32 PDT)
Mengjuei Hsieh
Re: [AMBER] Installing Ambertools1.5 on Snow Leopard
(Sun Apr 24 2011 - 23:55:33 PDT)
Michael Forrester
[AMBER] another AmberTools problem
(Tue Apr 12 2011 - 12:36:31 PDT)
[AMBER] AmberTools install
(Mon Apr 11 2011 - 21:50:35 PDT)
mirage .
Re: [AMBER] No data for 0+0 MM BOND 0
(Sun Apr 17 2011 - 05:34:25 PDT)
[AMBER] No data for 0+0 MM BOND 0
(Thu Apr 14 2011 - 00:30:46 PDT)
miriam sgobba
[AMBER] rfree: Error decoding variable 1 3 from: pmemd.MPI and pmemd error
(Fri Apr 08 2011 - 11:03:21 PDT)
mish
Re: [AMBER] bond command in tlaep
(Wed Apr 20 2011 - 09:31:25 PDT)
Re: [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap)
(Tue Apr 05 2011 - 10:05:12 PDT)
Re: [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap)
(Tue Apr 05 2011 - 09:20:38 PDT)
Re: [AMBER] bond command in tlaep
(Fri Apr 01 2011 - 11:07:36 PDT)
[AMBER] bond command in tlaep
(Fri Apr 01 2011 - 06:20:11 PDT)
mmpbsa amber
Re: [AMBER] MMPBSA.py.MPI error!
(Thu Apr 14 2011 - 01:27:35 PDT)
moitrayee.mbu.iisc.ernet.in
Re: [AMBER] problem with ptraj trajout in ambertools
(Mon Apr 11 2011 - 11:13:43 PDT)
Re: [AMBER] problem with ptraj trajout in ambertools
(Mon Apr 11 2011 - 11:01:24 PDT)
Re: [AMBER] problem with ptraj trajout in ambertools
(Mon Apr 11 2011 - 10:03:02 PDT)
[AMBER] problem with ptraj trajout in ambertools
(Mon Apr 11 2011 - 09:20:17 PDT)
Naveen Samala
[AMBER] Regarding Gaussian Calculations for MTK++ example- sidechain model
(Thu Apr 28 2011 - 09:23:07 PDT)
[AMBER] MTK++ : genMetalFF.sh is not generating gaussian input files
(Tue Apr 26 2011 - 15:22:45 PDT)
[AMBER] Regarding MTK++ MCPB tutorials on Small and Large Models of ZN Metalloprotein
(Wed Apr 20 2011 - 12:55:46 PDT)
Re: [AMBER] Regarding understanding MTK++ Document
(Tue Apr 19 2011 - 11:28:24 PDT)
[AMBER] Regarding understanding MTK++ Document
(Tue Apr 19 2011 - 09:41:49 PDT)
[AMBER] Regarding antechamber
(Mon Apr 18 2011 - 13:09:30 PDT)
[AMBER] Error in Installing MTK++ software
(Thu Apr 14 2011 - 12:58:29 PDT)
nicholus bhattacharjee
Re: [AMBER] Restraining distance between a protein atom and a water of crystalization
(Tue Apr 26 2011 - 06:01:39 PDT)
Re: [AMBER] Restraining distance between a protein atom and a water of crystalization
(Fri Apr 22 2011 - 05:46:48 PDT)
Re: [AMBER] Restraining distance between a protein atom and a water of crystalization
(Fri Apr 22 2011 - 05:24:51 PDT)
Re: [AMBER] Restraining distance between a protein atom and a water of crystalization
(Thu Apr 21 2011 - 22:13:20 PDT)
Re: [AMBER] Restraining distance between a protein atom and a water of crystalization
(Mon Apr 18 2011 - 06:29:46 PDT)
[AMBER] Restraining distance between a protein atom and a water of crystalization
(Mon Apr 18 2011 - 02:46:17 PDT)
[AMBER] coordinate updates
(Fri Apr 15 2011 - 22:01:37 PDT)
[AMBER] Restraining non-bonded atoms
(Fri Apr 15 2011 - 06:01:54 PDT)
[AMBER] Default values
(Fri Apr 08 2011 - 01:33:12 PDT)
Nicole A. Horenstein
[AMBER] ptraj trajectory file size limits?
(Thu Apr 28 2011 - 20:14:27 PDT)
Niel Henriksen
Re: [AMBER] 'shake problem' and soft core potential
(Mon Apr 18 2011 - 14:19:43 PDT)
Oliver Kuhn
Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py
(Fri Apr 29 2011 - 07:48:18 PDT)
Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py
(Thu Apr 28 2011 - 09:10:29 PDT)
[AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py
(Thu Apr 28 2011 - 06:18:12 PDT)
[AMBER] Usage of ambermask within MMPBSA.py
(Thu Apr 28 2011 - 06:04:33 PDT)
[AMBER] igb=8 available for MMPBSA.py ?
(Wed Apr 27 2011 - 07:48:20 PDT)
[AMBER] setting gbsa=0 does not switch off GB calculation
(Thu Apr 21 2011 - 09:26:30 PDT)
[AMBER] Defining ligand and receptor within MMPBSA.py
(Thu Apr 21 2011 - 07:24:34 PDT)
Oxana Plis
[AMBER] GPU Technology Conference, Singapore
(Tue Apr 19 2011 - 03:30:25 PDT)
patrick wintrode
[AMBER] PMEMD and NEB?
(Mon Apr 04 2011 - 11:53:10 PDT)
Paul S. Nerenberg
[AMBER] Atom types in LYN side chain
(Wed Apr 27 2011 - 18:08:19 PDT)
peker milas
Re: [AMBER] momentum from trajectory
(Fri Apr 15 2011 - 06:34:11 PDT)
Re: [AMBER] momentum from trajectory
(Thu Apr 14 2011 - 17:33:14 PDT)
[AMBER] momentum from trajectory
(Thu Apr 14 2011 - 17:24:49 PDT)
py
[AMBER] usage of secstruct and atomicfluct
(Tue Apr 26 2011 - 06:24:26 PDT)
r smith
Re: [AMBER] sleap with ff02pol.r1
(Mon Apr 04 2011 - 11:35:38 PDT)
Re: [AMBER] sleap with ff02pol.r1
(Mon Apr 04 2011 - 11:34:59 PDT)
[AMBER] sleap with ff02pol.r1
(Mon Apr 04 2011 - 07:54:19 PDT)
Rahul Banerjee
Re: [AMBER] Restraint potential in Targeted MD
(Fri Apr 08 2011 - 11:31:38 PDT)
[AMBER] Restraint potential in Targeted MD
(Fri Apr 08 2011 - 10:56:52 PDT)
Rajesh Raju
[AMBER] Thermodynamic Integration--Input doubt
(Wed Apr 06 2011 - 14:32:19 PDT)
Rajeswari A.
Re: [AMBER] Ptraj Mask option
(Fri Apr 01 2011 - 03:00:55 PDT)
[AMBER] Ptraj Mask option
(Fri Apr 01 2011 - 00:03:42 PDT)
Rilei Yu
[AMBER] Problem on SMD
(Wed Apr 06 2011 - 07:15:02 PDT)
[AMBER] amber8-package
(Wed Apr 06 2011 - 01:54:23 PDT)
Robert Wohlhueter
Re: [AMBER] compile errors with AmberTools1.5 + Amber11
(Sat Apr 30 2011 - 17:04:04 PDT)
Re: [AMBER] compile errors with AmberTools1.5 + Amber11
(Fri Apr 29 2011 - 07:06:41 PDT)
[AMBER] compile errors with AmberTools1.5 + Amber11
(Thu Apr 28 2011 - 12:52:22 PDT)
Re: [AMBER] errors compiling amber11 for cuda
(Tue Apr 12 2011 - 20:07:12 PDT)
Re: [AMBER] errors compiling amber11 for cuda
(Tue Apr 12 2011 - 16:45:10 PDT)
[AMBER] errors compiling amber11 for cuda
(Tue Apr 12 2011 - 09:19:04 PDT)
Roman Osman
Re: [AMBER] Problem with cluster?
(Tue Apr 26 2011 - 10:06:04 PDT)
[AMBER] Problem with cluster?
(Tue Apr 26 2011 - 08:39:36 PDT)
Ross Walker
Re: [AMBER] parallel QM/MM/MD lasts forever
(Tue Apr 19 2011 - 00:34:24 PDT)
Re: [AMBER] strange background job crash
(Mon Apr 18 2011 - 09:35:20 PDT)
Re: [AMBER] strange background job crash
(Mon Apr 18 2011 - 09:11:50 PDT)
Re: [AMBER] FW: Leap error with Zinc ions
(Mon Apr 18 2011 - 09:10:06 PDT)
Re: [AMBER] SQM
(Mon Apr 18 2011 - 08:55:28 PDT)
Re: [AMBER] NEB calculations in enzyme?
(Mon Apr 18 2011 - 08:51:29 PDT)
Re: [AMBER] QMMM
(Mon Apr 18 2011 - 07:58:44 PDT)
Re: [AMBER] masking in the QMMM input
(Mon Apr 18 2011 - 07:51:40 PDT)
Re: [AMBER] pmemd.cuda: max pairlist problem with a large system
(Fri Apr 15 2011 - 14:12:00 PDT)
Re: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network"
(Fri Apr 15 2011 - 09:20:14 PDT)
Re: [AMBER] Coupled torsions from Amber
(Tue Apr 12 2011 - 22:41:26 PDT)
Re: [AMBER] errors compiling amber11 for cuda
(Tue Apr 12 2011 - 19:25:32 PDT)
Re: [AMBER] Error on running parameter 'sander'
(Tue Apr 12 2011 - 15:31:19 PDT)
Re: [AMBER] errors compiling amber11 for cuda
(Tue Apr 12 2011 - 15:27:34 PDT)
Re: [AMBER] problem about addions
(Sat Apr 09 2011 - 22:20:16 PDT)
Re: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network"
(Sat Apr 09 2011 - 21:29:39 PDT)
Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ?
(Sat Apr 09 2011 - 21:29:39 PDT)
Re: [AMBER] Maximum number of atoms
(Fri Apr 08 2011 - 16:37:11 PDT)
Re: [AMBER] Compare simulations done with AMBER9 to ones done with AMBER11 Cuda?
(Fri Apr 08 2011 - 13:11:09 PDT)
Re: [AMBER] Maximum number of atoms
(Fri Apr 08 2011 - 12:01:36 PDT)
Re: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network"
(Fri Apr 08 2011 - 11:59:52 PDT)
Re: [AMBER] Compare simulations done with AMBER9 to ones done with AMBER11 Cuda?
(Fri Apr 08 2011 - 11:56:26 PDT)
Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ?
(Thu Apr 07 2011 - 17:22:12 PDT)
Re: [AMBER] problem about addions
(Wed Apr 06 2011 - 13:42:46 PDT)
Re: [AMBER] SDSC
(Tue Apr 05 2011 - 10:45:00 PDT)
Sajad Ahrari
[AMBER] dealing with xleap
(Tue Apr 19 2011 - 02:22:07 PDT)
Samuel Genheden
Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py
(Fri Apr 29 2011 - 08:05:59 PDT)
Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py
(Fri Apr 29 2011 - 07:47:07 PDT)
Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py
(Fri Apr 29 2011 - 07:34:08 PDT)
Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py
(Fri Apr 29 2011 - 06:45:06 PDT)
[AMBER] New equilibrated solvent box, how to use it?
(Fri Apr 29 2011 - 05:28:15 PDT)
Sangita Kachhap
Re: [AMBER] Number of MMPBSA_Nmode run
(Mon Apr 18 2011 - 10:56:51 PDT)
Re: [AMBER] Number of MMPBSA_Nmode run
(Mon Apr 18 2011 - 10:19:48 PDT)
[AMBER] Number of MMPBSA_Nmode run
(Mon Apr 18 2011 - 01:31:35 PDT)
[AMBER] missing coordinates from pdb
(Wed Apr 13 2011 - 23:28:30 PDT)
Re: [AMBER] mmpbsa - nmode calculation
(Wed Apr 13 2011 - 01:58:01 PDT)
[AMBER] mmpbsa - nmode calculation
(Wed Apr 13 2011 - 00:40:39 PDT)
[AMBER] distance criteria of TIP3P added to protein-DNA complex
(Sat Apr 09 2011 - 09:20:35 PDT)
Re: [AMBER] Umbrella sampling
(Tue Apr 05 2011 - 11:21:17 PDT)
[AMBER] Umbrella sampling
(Tue Apr 05 2011 - 10:55:42 PDT)
[AMBER] water mediated interaction
(Sun Apr 03 2011 - 08:47:59 PDT)
Sanjay kundu
[AMBER] Error installing amber9 for mpi(sander.MPI)
(Mon Apr 18 2011 - 03:01:24 PDT)
Re: [AMBER] Error on running parameter 'sander'
(Wed Apr 13 2011 - 02:23:27 PDT)
[AMBER] Error on running parameter 'sander'
(Mon Apr 11 2011 - 22:52:53 PDT)
Santosh Mogurampelly
Re: [AMBER] changing restart file format from 6f12.7 to 6f12.6
(Tue Apr 26 2011 - 07:45:32 PDT)
[AMBER] changing restart file format from 6f12.7 to 6f12.6
(Mon Apr 25 2011 - 23:30:26 PDT)
Sarah Eliabeth Rowe
[AMBER] ptraj rmsd
(Mon Apr 04 2011 - 07:00:19 PDT)
Sasha Buzko
Re: [AMBER] pmemd.cuda: max pairlist problem with a large system
(Fri Apr 15 2011 - 14:47:23 PDT)
[AMBER] pmemd.cuda: max pairlist problem with a large system
(Fri Apr 15 2011 - 13:52:29 PDT)
Re: [AMBER] packmol and amber11: the solvent box issue
(Wed Apr 13 2011 - 17:07:08 PDT)
Re: [AMBER] packmol and amber11: the solvent box issue
(Wed Apr 13 2011 - 16:33:02 PDT)
[AMBER] packmol and amber11: the solvent box issue
(Wed Apr 13 2011 - 15:47:16 PDT)
Scott Le Grand
Re: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network"
(Fri Apr 08 2011 - 16:09:21 PDT)
setyanto md
Re: [AMBER] MCPB install problem
(Thu Apr 28 2011 - 04:47:56 PDT)
[AMBER] MCPB install problem
(Tue Apr 26 2011 - 23:28:09 PDT)
Re: [AMBER] FW: Leap error with Zinc ions
(Tue Apr 19 2011 - 06:21:17 PDT)
Re: [AMBER] masking in the QMMM input
(Tue Apr 19 2011 - 06:14:57 PDT)
Re: [AMBER] masking in the QMMM input
(Sun Apr 17 2011 - 20:57:27 PDT)
Re: [AMBER] masking in the QMMM input
(Fri Apr 15 2011 - 01:32:03 PDT)
Re: [AMBER] masking in the QMMM input
(Thu Apr 14 2011 - 23:23:01 PDT)
[AMBER] masking in the QMMM input
(Thu Apr 14 2011 - 21:25:43 PDT)
Shan-ho Tsai
Re: [AMBER] AmberTools 1.4 PGI failed antechamber/sustiva test
(Fri Apr 29 2011 - 13:41:25 PDT)
[AMBER] AmberTools 1.4 PGI failed antechamber/sustiva test
(Fri Apr 29 2011 - 09:25:02 PDT)
Shesh Nath
[AMBER] AMBER
(Sun Apr 10 2011 - 21:24:04 PDT)
Shruti Koulgi
[AMBER] Multiple links QM-MM
(Mon Apr 11 2011 - 02:21:37 PDT)
siddesh southekal
[AMBER] Fwd: docked complex file preparation
(Mon Apr 11 2011 - 10:44:17 PDT)
Re: [AMBER] tleap problem
(Fri Apr 08 2011 - 14:18:30 PDT)
[AMBER] Umbrella sampling procedure
(Mon Apr 04 2011 - 08:50:15 PDT)
sonali dhindwal
Re: [AMBER] Error while installing amber11
(Thu Apr 14 2011 - 06:52:19 PDT)
Re: [AMBER] Error while installing amber11
(Wed Apr 13 2011 - 21:26:21 PDT)
Re: [AMBER] Error while installing amber11
(Wed Apr 13 2011 - 08:52:36 PDT)
[AMBER] Error while installing amber11
(Wed Apr 13 2011 - 07:42:15 PDT)
sonam bhatia
[AMBER] Query regarding considering water molecules
(Wed Apr 06 2011 - 08:46:02 PDT)
souvik sur
[AMBER] xleap problem
(Tue Apr 26 2011 - 20:58:55 PDT)
[AMBER] xleap problem
(Tue Apr 26 2011 - 06:21:17 PDT)
Re: [AMBER] Xleap problem
(Tue Apr 26 2011 - 00:46:04 PDT)
Re: [AMBER] Xleap problem
(Mon Apr 25 2011 - 22:40:01 PDT)
[AMBER] Xleap problem
(Mon Apr 25 2011 - 06:55:54 PDT)
steinbrt.rci.rutgers.edu
Re: [AMBER] Free Energy Perturbation in AMBER 10
(Fri Apr 29 2011 - 01:53:31 PDT)
Re: [AMBER] softcore potential and temperature
(Tue Apr 26 2011 - 12:25:44 PDT)
Re: [AMBER] PMF
(Wed Apr 20 2011 - 01:08:04 PDT)
Re: [AMBER] 'shake problem' and soft core potential
(Tue Apr 19 2011 - 02:02:59 PDT)
Steven M. Graham
Re: [AMBER] nucleosides
(Thu Apr 14 2011 - 05:26:12 PDT)
[AMBER] nucleosides
(Wed Apr 13 2011 - 14:33:10 PDT)
sunita gupta
Re: [AMBER] Post-Processing MD trajectory
(Sat Apr 30 2011 - 01:00:46 PDT)
Re: [AMBER] Post-Processing MD trajectory
(Fri Apr 29 2011 - 05:40:25 PDT)
Re: [AMBER] Post-Processing MD trajectory
(Fri Apr 29 2011 - 04:42:37 PDT)
[AMBER] Post-Processing MD trajectory
(Fri Apr 29 2011 - 04:36:27 PDT)
Re: [AMBER] Thermodynamic Integration--Input doubt
(Wed Apr 06 2011 - 22:24:22 PDT)
TAEJIN KIM
[AMBER] Question about Amber output file format
(Mon Apr 04 2011 - 07:45:51 PDT)
Thomas Cheatham III
Re: [AMBER] Question about ptraj artifacts
(Wed Apr 27 2011 - 09:31:32 PDT)
Re: [AMBER] Question about ptraj artifacts
(Wed Apr 27 2011 - 09:14:00 PDT)
Re: [AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file
(Tue Apr 05 2011 - 12:42:56 PDT)
Re: [AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file
(Tue Apr 05 2011 - 09:31:08 PDT)
tommaso.casalini.mail.polimi.it
[AMBER] Diffusion coefficient in implicit water
(Wed Apr 27 2011 - 02:07:53 PDT)
[AMBER] Maximum number of atoms
(Fri Apr 08 2011 - 01:40:32 PDT)
tsurma.umich.edu
[AMBER] help with antechamber
(Fri Apr 29 2011 - 12:42:57 PDT)
[AMBER] help with antechamber
(Fri Apr 29 2011 - 12:12:35 PDT)
Vaibhav Jain
Re: [AMBER] MMPBSA error
(Mon Apr 25 2011 - 11:04:40 PDT)
Re: [AMBER] MMPBSA error
(Mon Apr 25 2011 - 10:35:39 PDT)
[AMBER] MMPBSA error
(Mon Apr 25 2011 - 08:16:46 PDT)
[AMBER] Query about charge on magnesium
(Fri Apr 15 2011 - 07:07:16 PDT)
vani panguluri
Re: [AMBER] QUESTION ON MMPBSA
(Tue Apr 19 2011 - 19:59:43 PDT)
Re: [AMBER] QUESTION ON MMPBSA
(Sun Apr 10 2011 - 18:16:40 PDT)
Re: [AMBER] QUESTION ON MMPBSA
(Sun Apr 10 2011 - 11:01:05 PDT)
Re: [AMBER] QUESTION ON MMPBSA
(Sun Apr 10 2011 - 09:55:13 PDT)
Re: [AMBER] QUESTION ON MMPBSA
(Fri Apr 08 2011 - 10:48:38 PDT)
[AMBER] QUESTION ON MMPBSA
(Fri Apr 08 2011 - 10:01:09 PDT)
[AMBER] The following error i got at the end of MM_PBSA.pl
(Wed Apr 06 2011 - 04:18:21 PDT)
Re: [AMBER] Error im mm_pbsa.pl
(Tue Apr 05 2011 - 15:22:26 PDT)
Re: [AMBER] Error im mm_pbsa.pl
(Tue Apr 05 2011 - 13:44:46 PDT)
Re: [AMBER] Error im mm_pbsa.pl
(Tue Apr 05 2011 - 11:06:58 PDT)
[AMBER] Error im mm_pbsa.pl
(Mon Apr 04 2011 - 16:11:40 PDT)
Vernon Bailey
[AMBER] building amber - meaning of file comparison problems?
(Thu Apr 28 2011 - 09:07:27 PDT)
vhakkim boy
Re: [AMBER] xleap problem
(Tue Apr 26 2011 - 21:14:14 PDT)
[AMBER] PMEMD does not support intermolecular PRFs!
(Thu Apr 21 2011 - 05:14:56 PDT)
Vo Cam Quy
[AMBER] Side Chain Model building by MCPB
(Wed Apr 20 2011 - 09:11:12 PDT)
Wei Huang
Re: [AMBER] Error in running MMPBSA.py.MPI with sander.APBS
(Sun Apr 10 2011 - 21:25:28 PDT)
Re: [AMBER] Error in running MMPBSA.py.MPI with sander.APBS
(Sun Apr 10 2011 - 18:34:44 PDT)
[AMBER] Error in running MMPBSA.py.MPI with sander.APBS
(Sun Apr 10 2011 - 15:52:55 PDT)
Wei Zhang
Re: [AMBER] sleap with ff02pol.r1
(Mon Apr 04 2011 - 11:33:08 PDT)
Yao-Chi Chen
[AMBER] how did the SALTCON parameter work in MMPBSA?
(Tue Apr 12 2011 - 12:12:01 PDT)
Ye MEI
Re: [AMBER] Query about charge on magnesium
(Fri Apr 15 2011 - 08:51:50 PDT)
Yi An
[AMBER] question on scmask
(Fri Apr 29 2011 - 13:36:15 PDT)
[AMBER] mmpbsa nmode problem
(Fri Apr 29 2011 - 13:29:26 PDT)
Yuan Yao
Re: [AMBER] How to find Acetyl-coa parameters in R.E.D.DB?
(Thu Apr 14 2011 - 14:17:22 PDT)
Re: [AMBER] How to find Acetyl-coa parameters in R.E.D.DB?
(Thu Apr 14 2011 - 10:05:12 PDT)
Re: [AMBER] How to find Acetyl-coa parameters in R.E.D.DB?
(Thu Apr 14 2011 - 09:46:29 PDT)
[AMBER] How to find Acetyl-coa parameters in R.E.D.DB?
(Thu Apr 14 2011 - 09:26:39 PDT)
Zachary Davis
[AMBER] Best Force Field for Beta Peptides
(Tue Apr 19 2011 - 11:54:49 PDT)
zhihong ke
[AMBER] SURFTEN / SURFOFF values are not consistent across *.all.out files
(Fri Apr 29 2011 - 09:29:18 PDT)
姜笑楠
Re: [AMBER] Amber
(Mon Apr 25 2011 - 04:57:19 PDT)
陳昭同
Re: [AMBER] MMPBSA.py.MPI error
(Thu Apr 14 2011 - 19:58:38 PDT)
Re: [AMBER] MMPBSA.py.MPI error
(Thu Apr 14 2011 - 19:02:04 PDT)
Re: [AMBER] MMPBSA.py.MPI error
(Thu Apr 14 2011 - 08:53:11 PDT)
[AMBER] MMPBSA.py.MPI error
(Thu Apr 14 2011 - 02:34:04 PDT)
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Sat Apr 30 2011 - 17:30:02 PDT
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