Amber Archive Apr 2011 by subject
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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[AMBER] 'shake problem' and soft core potential
anyiphysics.gmail.com
(Fri Apr 22 2011 - 13:36:08 PDT)
steinbrt.rci.rutgers.edu
(Tue Apr 19 2011 - 02:02:59 PDT)
David Case
(Mon Apr 18 2011 - 14:48:42 PDT)
Niel Henriksen
(Mon Apr 18 2011 - 14:19:43 PDT)
anyiphysics.gmail.com
(Mon Apr 18 2011 - 12:05:55 PDT)
[AMBER] a problem about tutorial A12
Junjian Miao
(Thu Apr 14 2011 - 20:40:16 PDT)
Daniel Roe
(Thu Apr 14 2011 - 15:53:34 PDT)
Junjian Miao
(Thu Apr 14 2011 - 07:09:03 PDT)
[AMBER] About of MMPBSA.py results
Aldo Segura
(Fri Apr 08 2011 - 06:46:00 PDT)
[AMBER] Add charges to a prmtop files before simulations
David A Case
(Thu Apr 14 2011 - 11:03:05 PDT)
Baptiste Legrand
(Thu Apr 14 2011 - 10:48:37 PDT)
Jason Swails
(Mon Apr 11 2011 - 09:32:24 PDT)
Baldoni Hector Armando
(Mon Apr 11 2011 - 07:38:11 PDT)
Baptiste Legrand
(Mon Apr 11 2011 - 07:29:45 PDT)
[AMBER] add polarized ions to pol3 water? Are there polarized ions models in Amber?
MD
(Tue Apr 19 2011 - 22:26:46 PDT)
[AMBER] Alanine scanning
Bill Miller III
(Tue Apr 26 2011 - 06:32:21 PDT)
George Tzotzos
(Tue Apr 26 2011 - 06:26:34 PDT)
Bill Miller III
(Tue Apr 26 2011 - 05:59:04 PDT)
George Tzotzos
(Tue Apr 26 2011 - 05:50:00 PDT)
[AMBER] Amber
姜笑楠
(Mon Apr 25 2011 - 04:57:19 PDT)
Jason Swails
(Sun Apr 10 2011 - 22:11:28 PDT)
Shesh Nath
(Sun Apr 10 2011 - 21:24:04 PDT)
[AMBER] AMBER 11 pbsa errors
Dmitry Osolodkin
(Tue Apr 19 2011 - 08:26:13 PDT)
Jason Swails
(Tue Apr 19 2011 - 08:18:35 PDT)
Dmitry Osolodkin
(Tue Apr 19 2011 - 08:12:14 PDT)
Jason Swails
(Tue Apr 19 2011 - 08:12:53 PDT)
Dmitry Osolodkin
(Tue Apr 19 2011 - 05:42:05 PDT)
[AMBER] Amber CUDA calcualtion on GeForce GTX 590 ?
Ross Walker
(Sat Apr 09 2011 - 21:29:39 PDT)
Jason Swails
(Sat Apr 09 2011 - 10:31:16 PDT)
filip fratev
(Sat Apr 09 2011 - 09:21:32 PDT)
Marek Maly
(Thu Apr 07 2011 - 17:53:04 PDT)
Ross Walker
(Thu Apr 07 2011 - 17:22:12 PDT)
filip fratev
(Thu Apr 07 2011 - 16:52:35 PDT)
Marek Maly
(Fri Apr 01 2011 - 03:32:12 PDT)
[AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? -Test results
filip fratev
(Fri Apr 08 2011 - 02:04:22 PDT)
[AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? GTX580 tests?
filip fratev
(Mon Apr 11 2011 - 22:07:07 PDT)
[AMBER] amber parameters for Ni
Ben Roberts
(Mon Apr 18 2011 - 08:34:18 PDT)
[AMBER] amber8-package
Rilei Yu
(Wed Apr 06 2011 - 01:54:23 PDT)
[AMBER] AmberTools 1.4 PGI failed antechamber/sustiva test
Shan-ho Tsai
(Fri Apr 29 2011 - 13:41:25 PDT)
dacase.rci.rutgers.edu
(Fri Apr 29 2011 - 12:35:21 PDT)
Shan-ho Tsai
(Fri Apr 29 2011 - 09:25:02 PDT)
[AMBER] ambertools 1.5
David A Case
(Tue Apr 12 2011 - 08:16:15 PDT)
Francesco Oteri
(Mon Apr 11 2011 - 10:34:51 PDT)
[AMBER] ambertools 1.5, python and Mac
Jason Swails
(Tue Apr 19 2011 - 08:03:45 PDT)
Alan Wilter Sousa da Silva
(Tue Apr 19 2011 - 03:19:49 PDT)
[AMBER] AmberTools install
David Case
(Tue Apr 12 2011 - 05:25:31 PDT)
Jason Swails
(Mon Apr 11 2011 - 22:25:07 PDT)
Michael Forrester
(Mon Apr 11 2011 - 21:50:35 PDT)
[AMBER] Ambertools SDK
Jason Swails
(Tue Apr 19 2011 - 10:43:54 PDT)
Francesco Oteri
(Tue Apr 19 2011 - 09:54:13 PDT)
[AMBER] another AmberTools problem
David A Case
(Tue Apr 12 2011 - 13:06:11 PDT)
Michael Forrester
(Tue Apr 12 2011 - 12:36:31 PDT)
[AMBER] Atom types in LYN side chain
cieplak.cgl.ucsf.edu
(Wed Apr 27 2011 - 18:52:07 PDT)
Paul S. Nerenberg
(Wed Apr 27 2011 - 18:08:19 PDT)
[AMBER] bad atom type
Jason Swails
(Thu Apr 07 2011 - 08:09:01 PDT)
Bernhard Poll
(Thu Apr 07 2011 - 01:30:12 PDT)
Jason Swails
(Wed Apr 06 2011 - 14:31:19 PDT)
Bernhard Poll
(Tue Apr 05 2011 - 07:56:34 PDT)
[AMBER] Beggining with AMBER
Fernando Blanco
(Thu Apr 14 2011 - 06:50:08 PDT)
Fernando Blanco
(Thu Apr 14 2011 - 05:29:10 PDT)
Dmitry Nilov
(Wed Apr 13 2011 - 22:36:49 PDT)
Fernando Blanco
(Wed Apr 13 2011 - 12:32:19 PDT)
Dmitry Nilov
(Wed Apr 13 2011 - 01:31:46 PDT)
Ankita Kumari
(Tue Apr 12 2011 - 23:01:42 PDT)
Fernando Blanco
(Tue Apr 12 2011 - 10:00:21 PDT)
[AMBER] Best Force Field for Beta Peptides
Zachary Davis
(Tue Apr 19 2011 - 11:54:49 PDT)
[AMBER] bond command in tlaep
Jason Swails
(Thu Apr 21 2011 - 00:11:49 PDT)
juzer stationwala
(Wed Apr 20 2011 - 23:17:36 PDT)
Catein Catherine
(Wed Apr 20 2011 - 23:11:04 PDT)
Bill Ross
(Wed Apr 20 2011 - 10:16:29 PDT)
David A Case
(Wed Apr 20 2011 - 10:07:06 PDT)
mish
(Wed Apr 20 2011 - 09:31:25 PDT)
mish
(Fri Apr 01 2011 - 11:07:36 PDT)
Jason Swails
(Fri Apr 01 2011 - 08:23:14 PDT)
mish
(Fri Apr 01 2011 - 06:20:11 PDT)
[AMBER] building amber - meaning of file comparison problems?
Jason Swails
(Thu Apr 28 2011 - 09:09:15 PDT)
Vernon Bailey
(Thu Apr 28 2011 - 09:07:27 PDT)
[AMBER] Calculation of forces using steered MD
Dmitry Nilov
(Wed Apr 13 2011 - 01:59:52 PDT)
Barbault Florent
(Wed Apr 13 2011 - 01:55:10 PDT)
Ali M. Naserian-Nik
(Wed Apr 13 2011 - 01:04:26 PDT)
Dmitry Nilov
(Wed Apr 13 2011 - 00:42:25 PDT)
Ali M. Naserian-Nik
(Tue Apr 12 2011 - 23:20:48 PDT)
Dmitry Nilov
(Tue Apr 12 2011 - 21:31:59 PDT)
Ali M. Naserian-Nik
(Tue Apr 12 2011 - 10:17:05 PDT)
[AMBER] Can AMBER10 be installed on 64-bit linux computer?
Catein Catherine
(Wed Apr 20 2011 - 07:29:54 PDT)
[AMBER] Can i addIons F- Br- I- using AMBER 9
David A Case
(Mon Apr 18 2011 - 05:04:04 PDT)
MD
(Sun Apr 17 2011 - 18:35:18 PDT)
[AMBER] Can I use PMF to study protein-protein complex formation?
Catein Catherine
(Mon Apr 04 2011 - 08:51:30 PDT)
[AMBER] CHAMBER conversion: problem with IFBOX == 0
Marc van der Kamp
(Thu Apr 07 2011 - 01:38:02 PDT)
Marc van der Kamp
(Thu Apr 07 2011 - 00:53:18 PDT)
[AMBER] changing restart file format from 6f12.7 to 6f12.6
Santosh Mogurampelly
(Tue Apr 26 2011 - 07:45:32 PDT)
David A Case
(Tue Apr 26 2011 - 05:35:11 PDT)
Santosh Mogurampelly
(Mon Apr 25 2011 - 23:30:26 PDT)
[AMBER] Compare simulations done with AMBER9 to ones done with AMBER11 Cuda?
Ross Walker
(Fri Apr 08 2011 - 13:11:09 PDT)
Ross Walker
(Fri Apr 08 2011 - 11:56:26 PDT)
Jason Swails
(Fri Apr 08 2011 - 11:37:36 PDT)
Antje Wolf
(Fri Apr 08 2011 - 02:45:34 PDT)
[AMBER] comparing order parameters from MD and NMR
David A Case
(Fri Apr 15 2011 - 08:32:35 PDT)
Brendan Duggan
(Wed Apr 13 2011 - 07:11:44 PDT)
[AMBER] compile errors with AmberTools1.5 + Amber11
Robert Wohlhueter
(Sat Apr 30 2011 - 17:04:04 PDT)
dacase.rci.rutgers.edu
(Fri Apr 29 2011 - 13:05:49 PDT)
Jason Swails
(Fri Apr 29 2011 - 12:52:55 PDT)
Robert Wohlhueter
(Fri Apr 29 2011 - 07:06:41 PDT)
Jason Swails
(Thu Apr 28 2011 - 17:35:17 PDT)
Robert Wohlhueter
(Thu Apr 28 2011 - 12:52:22 PDT)
[AMBER] coordinate updates
Jason Swails
(Fri Apr 15 2011 - 23:12:10 PDT)
nicholus bhattacharjee
(Fri Apr 15 2011 - 22:01:37 PDT)
[AMBER] Coupled torsions from Amber
Ross Walker
(Tue Apr 12 2011 - 22:41:26 PDT)
[AMBER] creating ssdna from dsdna
majid hasan
(Sun Apr 10 2011 - 17:23:31 PDT)
[AMBER] dealing with xleap
David A Case
(Tue Apr 19 2011 - 04:42:34 PDT)
Sajad Ahrari
(Tue Apr 19 2011 - 02:22:07 PDT)
[AMBER] Default values
David A Case
(Fri Apr 08 2011 - 05:43:16 PDT)
nicholus bhattacharjee
(Fri Apr 08 2011 - 01:33:12 PDT)
[AMBER] Defining ligand and receptor within MMPBSA.py
Jason Swails
(Thu Apr 21 2011 - 08:13:32 PDT)
Oliver Kuhn
(Thu Apr 21 2011 - 07:24:34 PDT)
[AMBER] Diffusion coefficient in implicit water
David A. Case
(Wed Apr 27 2011 - 05:01:04 PDT)
tommaso.casalini.mail.polimi.it
(Wed Apr 27 2011 - 02:07:53 PDT)
[AMBER] distance criteria of TIP3P added to protein-DNA complex
Carlos Simmerling
(Sat Apr 09 2011 - 09:48:20 PDT)
Sangita Kachhap
(Sat Apr 09 2011 - 09:20:35 PDT)
[AMBER] Does AMBER 9 has parameters for ions F- Br- I- etc
David A Case
(Thu Apr 14 2011 - 05:11:50 PDT)
MD
(Wed Apr 13 2011 - 20:43:42 PDT)
Aldo Segura
(Wed Apr 13 2011 - 20:22:52 PDT)
MD
(Wed Apr 13 2011 - 20:00:55 PDT)
[AMBER] Editing Protein - Change Bond
case
(Sun Apr 10 2011 - 08:55:48 PDT)
Melanie
(Sun Apr 10 2011 - 02:37:28 PDT)
[AMBER] Electrostatic term
Eliac Brown
(Tue Apr 19 2011 - 02:30:13 PDT)
[AMBER] End of protonate method with amber11?
Guenegou, Guillaume [ORDFR]
(Tue Apr 26 2011 - 07:33:22 PDT)
Ben Roberts
(Tue Apr 26 2011 - 07:21:44 PDT)
Guenegou, Guillaume [ORDFR]
(Tue Apr 26 2011 - 07:12:08 PDT)
David A Case
(Tue Apr 26 2011 - 06:44:29 PDT)
Guenegou, Guillaume [ORDFR]
(Tue Apr 26 2011 - 04:54:38 PDT)
[AMBER] Equilibration: Using restraintmask
George Tzotzos
(Mon Apr 25 2011 - 09:05:37 PDT)
Jason Swails
(Mon Apr 25 2011 - 09:02:35 PDT)
George Tzotzos
(Mon Apr 25 2011 - 04:53:53 PDT)
[AMBER] Error im mm_pbsa.pl
vani panguluri
(Tue Apr 05 2011 - 15:22:26 PDT)
Bill Miller III
(Tue Apr 05 2011 - 13:56:18 PDT)
vani panguluri
(Tue Apr 05 2011 - 13:44:46 PDT)
Jason Swails
(Tue Apr 05 2011 - 11:29:23 PDT)
vani panguluri
(Tue Apr 05 2011 - 11:06:58 PDT)
Dwight McGee
(Tue Apr 05 2011 - 08:37:49 PDT)
vani panguluri
(Mon Apr 04 2011 - 16:11:40 PDT)
[AMBER] Error in installing Amber Tools
majid hasan
(Sun Apr 10 2011 - 15:20:14 PDT)
Jason Swails
(Sun Apr 10 2011 - 14:43:06 PDT)
majid hasan
(Sun Apr 10 2011 - 14:18:15 PDT)
Jason Swails
(Sun Apr 10 2011 - 13:59:35 PDT)
majid hasan
(Sun Apr 10 2011 - 13:50:19 PDT)
Jason Swails
(Sun Apr 10 2011 - 13:49:23 PDT)
majid hasan
(Sun Apr 10 2011 - 13:41:53 PDT)
Jason Swails
(Sun Apr 10 2011 - 12:55:53 PDT)
majid hasan
(Sun Apr 10 2011 - 12:40:40 PDT)
[AMBER] Error in Installing MTK++ software
Jason Swails
(Thu Apr 14 2011 - 14:18:47 PDT)
Naveen Samala
(Thu Apr 14 2011 - 12:58:29 PDT)
[AMBER] Error in running MMPBSA.py.MPI with sander.APBS
Wei Huang
(Sun Apr 10 2011 - 21:25:28 PDT)
Jason Swails
(Sun Apr 10 2011 - 21:01:54 PDT)
Wei Huang
(Sun Apr 10 2011 - 18:34:44 PDT)
Bill Miller III
(Sun Apr 10 2011 - 17:25:53 PDT)
Wei Huang
(Sun Apr 10 2011 - 15:52:55 PDT)
[AMBER] Error installing amber9 for mpi(sander.MPI)
David A Case
(Mon Apr 18 2011 - 04:57:43 PDT)
Sanjay kundu
(Mon Apr 18 2011 - 03:01:24 PDT)
[AMBER] Error on compiling cuda_parallel; MPI_Win is undefined
Bongkeun Kim
(Thu Apr 14 2011 - 13:02:32 PDT)
[AMBER] Error on running parameter 'sander'
Jason Swails
(Wed Apr 13 2011 - 09:21:41 PDT)
Sanjay kundu
(Wed Apr 13 2011 - 02:23:27 PDT)
Ross Walker
(Tue Apr 12 2011 - 15:31:19 PDT)
Sanjay kundu
(Mon Apr 11 2011 - 22:52:53 PDT)
[AMBER] error while editing charge table in Tutorial A1 by Dr. Walker
Chinh Su Tran To
(Wed Apr 27 2011 - 02:17:45 PDT)
[AMBER] Error while installing amber11
sonali dhindwal
(Thu Apr 14 2011 - 06:52:19 PDT)
Daniel Roe
(Thu Apr 14 2011 - 04:41:19 PDT)
sonali dhindwal
(Wed Apr 13 2011 - 21:26:21 PDT)
David A Case
(Wed Apr 13 2011 - 09:50:59 PDT)
sonali dhindwal
(Wed Apr 13 2011 - 08:52:36 PDT)
Daniel Roe
(Wed Apr 13 2011 - 07:48:10 PDT)
sonali dhindwal
(Wed Apr 13 2011 - 07:42:15 PDT)
[AMBER] errors compiling amber11 for cuda
Robert Wohlhueter
(Tue Apr 12 2011 - 20:07:12 PDT)
Ross Walker
(Tue Apr 12 2011 - 19:25:32 PDT)
Jason Swails
(Tue Apr 12 2011 - 17:31:13 PDT)
Robert Wohlhueter
(Tue Apr 12 2011 - 16:45:10 PDT)
Ross Walker
(Tue Apr 12 2011 - 15:27:34 PDT)
Robert Wohlhueter
(Tue Apr 12 2011 - 09:19:04 PDT)
[AMBER] failures in tests of amber tools 1.5
Jason Swails
(Thu Apr 21 2011 - 00:00:57 PDT)
juzer stationwala
(Wed Apr 20 2011 - 22:31:26 PDT)
[AMBER] fe4s4 cubane force field parameters
David A Case
(Fri Apr 15 2011 - 08:39:04 PDT)
Hugh Cheng
(Tue Apr 12 2011 - 11:54:10 PDT)
[AMBER] forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read
Katharina Lang
(Fri Apr 29 2011 - 07:33:02 PDT)
[AMBER] Free Energy Perturbation in AMBER 10
David A. Case
(Fri Apr 29 2011 - 15:06:06 PDT)
steinbrt.rci.rutgers.edu
(Fri Apr 29 2011 - 01:53:31 PDT)
Chirag Vora
(Thu Apr 28 2011 - 21:41:57 PDT)
[AMBER] Fwd: docked complex file preparation
siddesh southekal
(Mon Apr 11 2011 - 10:44:17 PDT)
[AMBER] Fwd: QUESTION ON MMPBSA
Jason Swails
(Mon Apr 18 2011 - 12:28:11 PDT)
[AMBER] gaussian
Ben Roberts
(Thu Apr 21 2011 - 07:04:05 PDT)
[AMBER] GPU Technology Conference, Singapore
Oxana Plis
(Tue Apr 19 2011 - 03:30:25 PDT)
[AMBER] help with antechamber
dacase.rci.rutgers.edu
(Fri Apr 29 2011 - 12:52:29 PDT)
tsurma.umich.edu
(Fri Apr 29 2011 - 12:42:57 PDT)
tsurma.umich.edu
(Fri Apr 29 2011 - 12:12:35 PDT)
[AMBER] Heme .lib file for heme - problem
Jacopo Sgrignani
(Fri Apr 08 2011 - 10:51:18 PDT)
Indrek Morell
(Fri Apr 08 2011 - 09:48:55 PDT)
[AMBER] How can i save this .pdb file to .top and .crd?? using AMBER 9
David A Case
(Tue Apr 19 2011 - 04:40:15 PDT)
MD
(Tue Apr 19 2011 - 00:25:30 PDT)
[AMBER] how did the SALTCON parameter work in MMPBSA?
Jason Swails
(Tue Apr 12 2011 - 12:22:51 PDT)
Yao-Chi Chen
(Tue Apr 12 2011 - 12:12:01 PDT)
[AMBER] How to add a new force field to Amber 11
hanlu0366
(Fri Apr 29 2011 - 20:12:49 PDT)
[AMBER] How to apply restraint based on a reference structure?
Ilyas Yildirim
(Thu Apr 07 2011 - 10:40:29 PDT)
Catein Catherine
(Thu Apr 07 2011 - 10:33:35 PDT)
Catein Catherine
(Thu Apr 07 2011 - 10:30:39 PDT)
Barbault Florent
(Thu Apr 07 2011 - 10:17:08 PDT)
Carlos Simmerling
(Thu Apr 07 2011 - 10:16:06 PDT)
Catein Catherine
(Thu Apr 07 2011 - 10:12:13 PDT)
[AMBER] How to apply restraint on the root-mean-square deviation along the z-axis of two proteins
Catein Catherine
(Thu Apr 07 2011 - 10:18:51 PDT)
[AMBER] how to estimate the free energy of folding for the C-terminal of a protein?
Jose Borreguero
(Tue Apr 05 2011 - 17:46:05 PDT)
[AMBER] How to find Acetyl-coa parameters in R.E.D.DB?
FyD
(Thu Apr 14 2011 - 22:05:34 PDT)
Yuan Yao
(Thu Apr 14 2011 - 14:17:22 PDT)
FyD
(Thu Apr 14 2011 - 12:02:20 PDT)
Yuan Yao
(Thu Apr 14 2011 - 10:05:12 PDT)
Adrian Roitberg
(Thu Apr 14 2011 - 09:51:49 PDT)
Yuan Yao
(Thu Apr 14 2011 - 09:46:29 PDT)
David A Case
(Thu Apr 14 2011 - 09:35:01 PDT)
Yuan Yao
(Thu Apr 14 2011 - 09:26:39 PDT)
[AMBER] how to get initial inpcrd files in smd directory of tutorial A12?
Junjian Miao
(Thu Apr 21 2011 - 21:01:07 PDT)
[AMBER] How to modify .pdb file for Amber input
Francesco Oteri
(Tue Apr 12 2011 - 01:03:00 PDT)
MD
(Tue Apr 12 2011 - 00:09:05 PDT)
[AMBER] how to obtain 4x4x1.1nm water
David A Case
(Thu Apr 07 2011 - 06:20:54 PDT)
MD
(Thu Apr 07 2011 - 00:08:03 PDT)
Jason Swails
(Wed Apr 06 2011 - 23:30:14 PDT)
MD
(Wed Apr 06 2011 - 21:16:20 PDT)
[AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap)
Lachele Foley (Lists)
(Tue Apr 05 2011 - 10:32:45 PDT)
mish
(Tue Apr 05 2011 - 10:05:12 PDT)
Lachele Foley (Lists)
(Tue Apr 05 2011 - 09:46:06 PDT)
mish
(Tue Apr 05 2011 - 09:20:38 PDT)
[AMBER] igb=8 available for MMPBSA.py ?
Carlos Simmerling
(Wed Apr 27 2011 - 10:48:06 PDT)
Jason Swails
(Wed Apr 27 2011 - 09:57:24 PDT)
Bill Miller III
(Wed Apr 27 2011 - 09:11:14 PDT)
Oliver Kuhn
(Wed Apr 27 2011 - 07:48:20 PDT)
[AMBER] Implicit solvent and box
Jason Swails
(Wed Apr 13 2011 - 12:20:08 PDT)
Jason Swails
(Wed Apr 13 2011 - 12:19:08 PDT)
Carlos Simmerling
(Wed Apr 13 2011 - 11:38:16 PDT)
Jason Swails
(Wed Apr 13 2011 - 11:19:16 PDT)
Carlos Simmerling
(Wed Apr 13 2011 - 11:01:16 PDT)
Adrian Roitberg
(Wed Apr 13 2011 - 10:55:57 PDT)
Carlos Simmerling
(Wed Apr 13 2011 - 10:53:23 PDT)
Adrian Roitberg
(Wed Apr 13 2011 - 10:49:16 PDT)
Carlos Simmerling
(Wed Apr 13 2011 - 10:46:12 PDT)
David A Case
(Wed Apr 13 2011 - 09:47:50 PDT)
Elisa Frezza
(Wed Apr 13 2011 - 09:02:26 PDT)
david condon
(Wed Apr 13 2011 - 08:59:15 PDT)
Elisa Frezza
(Wed Apr 13 2011 - 08:49:50 PDT)
[AMBER] Installation Amber Tools 1.5
juzer stationwala
(Wed Apr 20 2011 - 21:39:06 PDT)
Jason Swails
(Wed Apr 20 2011 - 10:44:33 PDT)
juzer stationwala
(Wed Apr 20 2011 - 10:31:51 PDT)
[AMBER] Installing Ambertools1.5 on Snow Leopard
Jason Swails
(Mon Apr 25 2011 - 22:23:51 PDT)
Dean Cuebas
(Mon Apr 25 2011 - 18:44:01 PDT)
Mengjuei Hsieh
(Sun Apr 24 2011 - 23:55:33 PDT)
Jason Swails
(Sun Apr 24 2011 - 23:39:47 PDT)
Dean Cuebas
(Sun Apr 24 2011 - 21:13:30 PDT)
[AMBER] is GBSA applicable to organic solvent?
David A Case
(Wed Apr 06 2011 - 05:38:40 PDT)
Junjian Miao
(Tue Apr 05 2011 - 20:47:53 PDT)
[AMBER] Leap error with Zinc ions
Manish Datt
(Thu Apr 14 2011 - 07:22:29 PDT)
[AMBER] leap solvateoct question
Kshatresh Dutta Dubey
(Mon Apr 18 2011 - 03:49:12 PDT)
Bala subramanian
(Mon Apr 18 2011 - 03:46:36 PDT)
Kshatresh Dutta Dubey
(Mon Apr 18 2011 - 03:34:41 PDT)
Bala subramanian
(Mon Apr 18 2011 - 03:23:59 PDT)
[AMBER] making lib file
Mark M Huntress
(Sat Apr 02 2011 - 07:39:06 PDT)
Jason Swails
(Fri Apr 01 2011 - 11:08:55 PDT)
Mark M Huntress
(Fri Apr 01 2011 - 10:57:46 PDT)
[AMBER] masking in the QMMM input
setyanto md
(Tue Apr 19 2011 - 06:14:57 PDT)
Ross Walker
(Mon Apr 18 2011 - 07:51:40 PDT)
setyanto md
(Sun Apr 17 2011 - 20:57:27 PDT)
Gustavo Seabra
(Fri Apr 15 2011 - 05:45:26 PDT)
setyanto md
(Fri Apr 15 2011 - 01:32:03 PDT)
Jason Swails
(Thu Apr 14 2011 - 23:41:43 PDT)
setyanto md
(Thu Apr 14 2011 - 23:23:01 PDT)
Jason Swails
(Thu Apr 14 2011 - 21:32:32 PDT)
setyanto md
(Thu Apr 14 2011 - 21:25:43 PDT)
[AMBER] Maximum number of atoms
Ross Walker
(Fri Apr 08 2011 - 16:37:11 PDT)
David A Case
(Fri Apr 08 2011 - 13:32:09 PDT)
Jason Swails
(Fri Apr 08 2011 - 12:24:05 PDT)
Ross Walker
(Fri Apr 08 2011 - 12:01:36 PDT)
David A Case
(Fri Apr 08 2011 - 05:46:11 PDT)
tommaso.casalini.mail.polimi.it
(Fri Apr 08 2011 - 01:40:32 PDT)
[AMBER] MCPB help
Ben Roberts
(Tue Apr 26 2011 - 11:30:24 PDT)
Hashem Taha
(Mon Apr 25 2011 - 10:49:45 PDT)
Hashem Taha
(Thu Apr 21 2011 - 15:58:22 PDT)
[AMBER] MCPB install problem
Jason Swails
(Thu Apr 28 2011 - 05:36:17 PDT)
setyanto md
(Thu Apr 28 2011 - 04:47:56 PDT)
Martin Peters
(Wed Apr 27 2011 - 00:13:47 PDT)
setyanto md
(Tue Apr 26 2011 - 23:28:09 PDT)
[AMBER] MD with preset start/end structures
Carlos Simmerling
(Thu Apr 14 2011 - 11:41:34 PDT)
Matthias Negri
(Tue Apr 12 2011 - 06:31:31 PDT)
Carlos Simmerling
(Tue Apr 12 2011 - 04:53:03 PDT)
Bernhard Poll
(Tue Apr 12 2011 - 04:43:17 PDT)
[AMBER] MD with preset start/end structures and addless "problem in line read"
Matthias Negri
(Thu Apr 21 2011 - 06:53:40 PDT)
[AMBER] missing coordinates from pdb
juzer stationwala
(Wed Apr 13 2011 - 23:33:07 PDT)
Sangita Kachhap
(Wed Apr 13 2011 - 23:28:30 PDT)
[AMBER] Missing Parameters
Ilyas Yildirim
(Mon Apr 04 2011 - 22:42:10 PDT)
Bill Ross
(Mon Apr 04 2011 - 20:41:16 PDT)
Melanie
(Mon Apr 04 2011 - 19:41:47 PDT)
Ilyas Yildirim
(Mon Apr 04 2011 - 07:23:58 PDT)
Melanie
(Sun Apr 03 2011 - 16:24:32 PDT)
[AMBER] mm_pbsa.pl error
Jason Swails
(Sat Apr 02 2011 - 16:02:44 PDT)
Jason Swails
(Sat Apr 02 2011 - 16:01:19 PDT)
Mahmoud Soliman
(Sat Apr 02 2011 - 15:44:39 PDT)
Mahmoud Soliman
(Sat Apr 02 2011 - 12:52:46 PDT)
Jason Swails
(Sat Apr 02 2011 - 12:01:12 PDT)
Mahmoud Soliman
(Sat Apr 02 2011 - 12:08:18 PDT)
[AMBER] mmpbsa - nmode calculation
Sangita Kachhap
(Wed Apr 13 2011 - 01:58:01 PDT)
Jason Swails
(Wed Apr 13 2011 - 01:09:18 PDT)
Sangita Kachhap
(Wed Apr 13 2011 - 00:40:39 PDT)
[AMBER] MMPBSA default input
anyiphysics.gmail.com
(Tue Apr 19 2011 - 09:22:44 PDT)
Jason Swails
(Tue Apr 19 2011 - 08:09:19 PDT)
anyiphysics.gmail.com
(Tue Apr 19 2011 - 08:02:29 PDT)
[AMBER] MMPBSA error
Jason Swails
(Mon Apr 25 2011 - 11:56:18 PDT)
Vaibhav Jain
(Mon Apr 25 2011 - 11:04:40 PDT)
Jason Swails
(Mon Apr 25 2011 - 10:53:40 PDT)
Vaibhav Jain
(Mon Apr 25 2011 - 10:35:39 PDT)
Jason Swails
(Mon Apr 25 2011 - 08:56:08 PDT)
Vaibhav Jain
(Mon Apr 25 2011 - 08:16:46 PDT)
Jason Swails
(Sat Apr 09 2011 - 10:07:47 PDT)
Kshatresh Dutta Dubey
(Sat Apr 09 2011 - 03:37:51 PDT)
Jason Swails
(Thu Apr 07 2011 - 12:04:10 PDT)
Kshatresh Dutta Dubey
(Thu Apr 07 2011 - 04:53:47 PDT)
Bill Miller III
(Thu Apr 07 2011 - 04:03:09 PDT)
Kshatresh Dutta Dubey
(Thu Apr 07 2011 - 00:52:41 PDT)
[AMBER] mmpbsa nmode problem
anyiphysics.gmail.com
(Sat Apr 30 2011 - 15:36:18 PDT)
Bill Miller III
(Sat Apr 30 2011 - 15:31:02 PDT)
anyiphysics.gmail.com
(Sat Apr 30 2011 - 15:17:36 PDT)
Bill Miller III
(Fri Apr 29 2011 - 19:54:30 PDT)
Yi An
(Fri Apr 29 2011 - 13:29:26 PDT)
[AMBER] mmpbsa, mdfil: Error unknown flag: not
Bill Miller III
(Sun Apr 24 2011 - 07:54:10 PDT)
Andrew Voronkov
(Sun Apr 24 2011 - 07:07:01 PDT)
[AMBER] MMPBSA.py (AmberTools 1.5) bug in Alanine Scanning (alamdcrd.py)
Dwight McGee
(Tue Apr 26 2011 - 06:02:55 PDT)
Joseph André
(Tue Apr 26 2011 - 02:48:27 PDT)
[AMBER] MMPBSA.py ala-scanning output results
Jesper Sørensen
(Tue Apr 05 2011 - 10:06:58 PDT)
Jason Swails
(Tue Apr 05 2011 - 08:40:51 PDT)
Jesper Sørensen
(Tue Apr 05 2011 - 00:25:47 PDT)
Jason Swails
(Mon Apr 04 2011 - 09:04:31 PDT)
Jesper Sørensen
(Mon Apr 04 2011 - 07:13:17 PDT)
[AMBER] MMPBSA.py error
Jason Swails
(Tue Apr 26 2011 - 19:46:48 PDT)
Jason Swails
(Wed Apr 20 2011 - 10:37:07 PDT)
Jason Swails
(Tue Apr 19 2011 - 20:09:48 PDT)
Bill Miller III
(Tue Apr 19 2011 - 19:44:25 PDT)
Gabriel Urquiza
(Tue Apr 19 2011 - 19:34:37 PDT)
[AMBER] MMPBSA.py error - VDW ****
Jesper Sørensen
(Fri Apr 29 2011 - 01:38:05 PDT)
Jason Swails
(Thu Apr 28 2011 - 00:47:31 PDT)
Jesper Sørensen
(Thu Apr 28 2011 - 00:29:08 PDT)
[AMBER] mmpbsa.py input - radii to use
Jesper Sørensen
(Wed Apr 13 2011 - 08:54:50 PDT)
[AMBER] MMPBSA.py pairwise decomp
Jason Swails
(Mon Apr 04 2011 - 09:00:21 PDT)
Christoph Malisi
(Mon Apr 04 2011 - 07:35:36 PDT)
Jason Swails
(Mon Apr 04 2011 - 07:24:51 PDT)
Christoph Malisi
(Mon Apr 04 2011 - 07:11:29 PDT)
[AMBER] MMPBSA.py Tests
Aldo Segura
(Thu Apr 07 2011 - 13:23:11 PDT)
[AMBER] MMPBSA.py won't understand my trajectories
Gabriel Urquiza
(Wed Apr 27 2011 - 06:19:39 PDT)
Bill Miller III
(Wed Apr 27 2011 - 05:00:52 PDT)
Gabriel Urquiza
(Wed Apr 27 2011 - 04:52:51 PDT)
[AMBER] MMPBSA.py.MPI error
陳昭同
(Thu Apr 14 2011 - 19:58:38 PDT)
Jason Swails
(Thu Apr 14 2011 - 19:37:17 PDT)
陳昭同
(Thu Apr 14 2011 - 19:02:04 PDT)
Jason Swails
(Thu Apr 14 2011 - 09:10:29 PDT)
陳昭同
(Thu Apr 14 2011 - 08:53:11 PDT)
Jason Swails
(Thu Apr 14 2011 - 07:34:52 PDT)
Bill Miller III
(Thu Apr 14 2011 - 05:25:12 PDT)
陳昭同
(Thu Apr 14 2011 - 02:34:04 PDT)
[AMBER] MMPBSA.py.MPI error!
mmpbsa amber
(Thu Apr 14 2011 - 01:27:35 PDT)
[AMBER] Modified REMD
Almudena Pino
(Wed Apr 06 2011 - 23:46:12 PDT)
Jason Swails
(Wed Apr 06 2011 - 14:43:13 PDT)
Almudena Pino
(Tue Apr 05 2011 - 04:10:36 PDT)
[AMBER] momentum from trajectory
peker milas
(Fri Apr 15 2011 - 06:34:11 PDT)
Jason Swails
(Thu Apr 14 2011 - 21:36:44 PDT)
Daniel Sindhikara
(Thu Apr 14 2011 - 20:03:28 PDT)
peker milas
(Thu Apr 14 2011 - 17:33:14 PDT)
Bill Ross
(Thu Apr 14 2011 - 17:29:19 PDT)
peker milas
(Thu Apr 14 2011 - 17:24:49 PDT)
[AMBER] MTK++ : genMetalFF.sh is not generating gaussian input files
Ben Roberts
(Tue Apr 26 2011 - 15:45:58 PDT)
Naveen Samala
(Tue Apr 26 2011 - 15:22:45 PDT)
[AMBER] Multiple links QM-MM
Gustavo Seabra
(Mon Apr 11 2011 - 04:21:58 PDT)
Shruti Koulgi
(Mon Apr 11 2011 - 02:21:37 PDT)
[AMBER] NEB calculations in enzyme?
Mahmoud Soliman
(Mon Apr 18 2011 - 09:18:18 PDT)
Mahmoud Soliman
(Mon Apr 18 2011 - 09:16:14 PDT)
Carlos Simmerling
(Mon Apr 18 2011 - 08:53:52 PDT)
Ross Walker
(Mon Apr 18 2011 - 08:51:29 PDT)
Mahmoud Soliman
(Sun Apr 17 2011 - 08:49:58 PDT)
[AMBER] new AmberTools
Jason Swails
(Fri Apr 08 2011 - 08:35:12 PDT)
David A Case
(Fri Apr 08 2011 - 05:40:59 PDT)
Aust, Susanne
(Thu Apr 07 2011 - 23:28:13 PDT)
[AMBER] New equilibrated solvent box, how to use it?
Samuel Genheden
(Fri Apr 29 2011 - 05:28:15 PDT)
[AMBER] No data for 0+0 MM BOND 0
Bill Miller III
(Sun Apr 17 2011 - 06:16:38 PDT)
mirage .
(Sun Apr 17 2011 - 05:34:25 PDT)
mirage .
(Thu Apr 14 2011 - 00:30:46 PDT)
[AMBER] No mdcrd file with PMEMD
Jason Swails
(Mon Apr 04 2011 - 11:27:16 PDT)
Indrek Morell
(Mon Apr 04 2011 - 10:22:14 PDT)
[AMBER] No mdcrd file with PMEMD reply
Jason Swails
(Mon Apr 04 2011 - 12:24:56 PDT)
[AMBER] Non bonded interactions
Lekpa Duukori
(Wed Apr 13 2011 - 09:31:51 PDT)
[AMBER] nucleosides
Steven M. Graham
(Thu Apr 14 2011 - 05:26:12 PDT)
David A Case
(Thu Apr 14 2011 - 04:58:00 PDT)
Steven M. Graham
(Wed Apr 13 2011 - 14:33:10 PDT)
[AMBER] Number of MMPBSA_Nmode run
Sangita Kachhap
(Mon Apr 18 2011 - 10:56:51 PDT)
Jason Swails
(Mon Apr 18 2011 - 10:49:49 PDT)
Sangita Kachhap
(Mon Apr 18 2011 - 10:19:48 PDT)
Jason Swails
(Mon Apr 18 2011 - 08:38:17 PDT)
Sangita Kachhap
(Mon Apr 18 2011 - 01:31:35 PDT)
[AMBER] opls-aa; ions
David A Case
(Mon Apr 04 2011 - 05:20:39 PDT)
gromacs
(Mon Apr 04 2011 - 03:05:29 PDT)
[AMBER] output file for contacts
John S
(Wed Apr 06 2011 - 22:20:44 PDT)
[AMBER] output velocities with ptraj
Jason Swails
(Fri Apr 22 2011 - 07:17:47 PDT)
Junjian Miao
(Thu Apr 21 2011 - 23:49:36 PDT)
[AMBER] packmol and amber11: the solvent box issue
M. L. Dodson
(Wed Apr 13 2011 - 18:30:07 PDT)
Sasha Buzko
(Wed Apr 13 2011 - 17:07:08 PDT)
Jason Swails
(Wed Apr 13 2011 - 16:53:25 PDT)
M. L. Dodson
(Wed Apr 13 2011 - 16:39:25 PDT)
Sasha Buzko
(Wed Apr 13 2011 - 16:33:02 PDT)
Jason Swails
(Wed Apr 13 2011 - 15:59:32 PDT)
Sasha Buzko
(Wed Apr 13 2011 - 15:47:16 PDT)
[AMBER] parallel QM/MM/MD lasts forever
Mahmoud Soliman
(Tue Apr 19 2011 - 00:50:37 PDT)
Ross Walker
(Tue Apr 19 2011 - 00:34:24 PDT)
Mahmoud Soliman
(Tue Apr 19 2011 - 00:17:37 PDT)
[AMBER] parameter about pbsa for sander
juan zeng
(Thu Apr 07 2011 - 07:45:14 PDT)
juan zeng
(Thu Apr 07 2011 - 02:07:49 PDT)
[AMBER] parameter for CNTs
Jagur Lambix
(Tue Apr 05 2011 - 15:21:25 PDT)
[AMBER] parameters sodium phosfate
Domenica Dibenedetto
(Fri Apr 29 2011 - 07:10:09 PDT)
[AMBER] PBSA calculations for wild type and a mutant
Mahmoud Soliman
(Sat Apr 02 2011 - 10:03:48 PDT)
Bill Miller III
(Sat Apr 02 2011 - 07:48:53 PDT)
Mahmoud Soliman
(Fri Apr 01 2011 - 13:15:09 PDT)
[AMBER] peptide-protein complex construction
J.F.Jiang
(Mon Apr 11 2011 - 04:29:53 PDT)
[AMBER] PMEMD and NEB?
Jason Swails
(Mon Apr 04 2011 - 12:10:38 PDT)
Carlos Simmerling
(Mon Apr 04 2011 - 12:09:35 PDT)
patrick wintrode
(Mon Apr 04 2011 - 11:53:10 PDT)
[AMBER] PMEMD does not support intermolecular PRFs!
Jason Swails
(Thu Apr 21 2011 - 08:17:24 PDT)
David A Case
(Thu Apr 21 2011 - 05:27:17 PDT)
vhakkim boy
(Thu Apr 21 2011 - 05:14:56 PDT)
[AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network"
Ross Walker
(Fri Apr 15 2011 - 09:20:14 PDT)
Marc van der Kamp
(Fri Apr 15 2011 - 02:43:46 PDT)
Ross Walker
(Sat Apr 09 2011 - 21:29:39 PDT)
Marc van der Kamp
(Sat Apr 09 2011 - 02:41:21 PDT)
Scott Le Grand
(Fri Apr 08 2011 - 16:09:21 PDT)
Carlos Simmerling
(Fri Apr 08 2011 - 12:01:23 PDT)
Ross Walker
(Fri Apr 08 2011 - 11:59:52 PDT)
Marc van der Kamp
(Fri Apr 08 2011 - 08:06:45 PDT)
[AMBER] pmemd.cuda: max pairlist problem with a large system
Sasha Buzko
(Fri Apr 15 2011 - 14:47:23 PDT)
Ross Walker
(Fri Apr 15 2011 - 14:12:00 PDT)
Sasha Buzko
(Fri Apr 15 2011 - 13:52:29 PDT)
[AMBER] PMF
Elisa Frezza
(Thu Apr 21 2011 - 06:23:16 PDT)
steinbrt.rci.rutgers.edu
(Wed Apr 20 2011 - 01:08:04 PDT)
jani vinod
(Tue Apr 19 2011 - 21:31:45 PDT)
Elisa Frezza
(Tue Apr 19 2011 - 08:40:29 PDT)
[AMBER] PMF calculations
Mahmoud Soliman
(Fri Apr 15 2011 - 11:06:11 PDT)
[AMBER] positive TdS
Hector A. Baldoni
(Fri Apr 01 2011 - 09:26:01 PDT)
[AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file
Alex Spasic
(Tue Apr 05 2011 - 13:44:05 PDT)
Thomas Cheatham III
(Tue Apr 05 2011 - 12:42:56 PDT)
Alex Spasic
(Tue Apr 05 2011 - 12:03:02 PDT)
Thomas Cheatham III
(Tue Apr 05 2011 - 09:31:08 PDT)
[AMBER] Post-Processing MD trajectory
Jason Swails
(Sat Apr 30 2011 - 01:51:56 PDT)
sunita gupta
(Sat Apr 30 2011 - 01:00:46 PDT)
Carlos Simmerling
(Fri Apr 29 2011 - 05:56:01 PDT)
Jason Swails
(Fri Apr 29 2011 - 05:44:10 PDT)
sunita gupta
(Fri Apr 29 2011 - 05:40:25 PDT)
Jason Swails
(Fri Apr 29 2011 - 05:26:53 PDT)
sunita gupta
(Fri Apr 29 2011 - 04:42:37 PDT)
Adrian Roitberg
(Fri Apr 29 2011 - 04:39:10 PDT)
sunita gupta
(Fri Apr 29 2011 - 04:36:27 PDT)
[AMBER] potential energy from remd
Carlos Simmerling
(Thu Apr 07 2011 - 09:55:20 PDT)
Jorgen Simonsen
(Thu Apr 07 2011 - 09:50:47 PDT)
[AMBER] problem about addions
Jason Swails
(Sat Apr 09 2011 - 22:56:07 PDT)
Ross Walker
(Sat Apr 09 2011 - 22:20:16 PDT)
Ross Walker
(Wed Apr 06 2011 - 13:42:46 PDT)
[AMBER] Problem compiling sander.PUPIL: No rule to build target 'mdread.PUPIL.o'
ivanquirino1928.gmail.com
(Fri Apr 08 2011 - 11:41:46 PDT)
Daniel Roe
(Fri Apr 08 2011 - 08:30:40 PDT)
ivanquirino1928.gmail.com
(Fri Apr 08 2011 - 07:17:08 PDT)
[AMBER] problem of installation of MMPBSA.py
fancy2012
(Sun Apr 10 2011 - 03:24:24 PDT)
Bill Miller III
(Fri Apr 08 2011 - 04:17:34 PDT)
fancy2012
(Fri Apr 08 2011 - 01:38:52 PDT)
[AMBER] problem of using leap
fancy2012
(Mon Apr 18 2011 - 22:59:51 PDT)
David A Case
(Wed Apr 13 2011 - 04:53:42 PDT)
fancy2012
(Tue Apr 12 2011 - 22:24:11 PDT)
case
(Tue Apr 12 2011 - 20:16:38 PDT)
fancy2012
(Tue Apr 12 2011 - 19:46:47 PDT)
[AMBER] Problem on SMD
Dmitry Nilov
(Wed Apr 06 2011 - 07:28:52 PDT)
Rilei Yu
(Wed Apr 06 2011 - 07:15:02 PDT)
[AMBER] Problem with cluster?
Roman Osman
(Tue Apr 26 2011 - 10:06:04 PDT)
Jianyin Shao
(Tue Apr 26 2011 - 09:58:58 PDT)
Roman Osman
(Tue Apr 26 2011 - 08:39:36 PDT)
[AMBER] problem with ptraj trajout in ambertools
moitrayee.mbu.iisc.ernet.in
(Mon Apr 11 2011 - 11:13:43 PDT)
Adrian Roitberg
(Mon Apr 11 2011 - 11:03:43 PDT)
moitrayee.mbu.iisc.ernet.in
(Mon Apr 11 2011 - 11:01:24 PDT)
Jason Swails
(Mon Apr 11 2011 - 10:24:35 PDT)
moitrayee.mbu.iisc.ernet.in
(Mon Apr 11 2011 - 10:03:02 PDT)
Jason Swails
(Mon Apr 11 2011 - 09:34:39 PDT)
moitrayee.mbu.iisc.ernet.in
(Mon Apr 11 2011 - 09:20:17 PDT)
[AMBER] Problem with trajin
Lui
(Fri Apr 08 2011 - 09:32:53 PDT)
Daniel Roe
(Fri Apr 08 2011 - 08:59:57 PDT)
Lui
(Fri Apr 08 2011 - 08:48:50 PDT)
[AMBER] Problem with VMD
juzer.niper.gmail.com
(Wed Apr 13 2011 - 10:03:12 PDT)
Jason Swails
(Wed Apr 13 2011 - 09:22:42 PDT)
juzer stationwala
(Wed Apr 13 2011 - 07:34:34 PDT)
[AMBER] problems when using mm_pbsa.pl in Amber10
Bill Miller III
(Fri Apr 08 2011 - 04:03:13 PDT)
cwt
(Thu Apr 07 2011 - 22:58:40 PDT)
[AMBER] Problems with constant pH calc Amber 11
John Khan
(Mon Apr 25 2011 - 12:23:39 PDT)
Jason Swails
(Mon Apr 25 2011 - 11:55:29 PDT)
John Khan
(Mon Apr 25 2011 - 11:10:24 PDT)
Jason Swails
(Sat Apr 23 2011 - 18:51:59 PDT)
John Khan
(Sat Apr 23 2011 - 17:37:30 PDT)
Jason Swails
(Sat Apr 23 2011 - 17:14:19 PDT)
John Khan
(Sat Apr 23 2011 - 16:55:54 PDT)
Jason Swails
(Sat Apr 23 2011 - 16:12:24 PDT)
John Khan
(Sat Apr 23 2011 - 15:22:21 PDT)
[AMBER] Processors, cores and threads
M. Shahid
(Wed Apr 13 2011 - 02:04:32 PDT)
Dmitry Mukha
(Wed Apr 13 2011 - 01:29:25 PDT)
Hopkins, Robert
(Tue Apr 12 2011 - 10:36:19 PDT)
Jason Swails
(Tue Apr 12 2011 - 10:00:13 PDT)
Hopkins, Robert
(Tue Apr 12 2011 - 09:14:32 PDT)
[AMBER] Protein-Drug dissociation PMF: Is large conformational change in protein real or artifacts?
Jérôme Golebiowski
(Thu Apr 07 2011 - 09:48:33 PDT)
Carlos Simmerling
(Thu Apr 07 2011 - 09:21:15 PDT)
Catein Catherine
(Thu Apr 07 2011 - 09:10:29 PDT)
[AMBER] Ptraj Mask option
Rajeswari A.
(Fri Apr 01 2011 - 03:00:55 PDT)
Jason Swails
(Fri Apr 01 2011 - 00:44:56 PDT)
Rajeswari A.
(Fri Apr 01 2011 - 00:03:42 PDT)
[AMBER] ptraj rmsd
Carlos Simmerling
(Mon Apr 04 2011 - 07:04:20 PDT)
Sarah Eliabeth Rowe
(Mon Apr 04 2011 - 07:00:19 PDT)
[AMBER] ptraj trajectory file size limits?
Jason Swails
(Fri Apr 29 2011 - 05:10:59 PDT)
juzer stationwala
(Thu Apr 28 2011 - 21:21:59 PDT)
Bill Miller III
(Thu Apr 28 2011 - 20:20:15 PDT)
Nicole A. Horenstein
(Thu Apr 28 2011 - 20:14:27 PDT)
[AMBER] puzzle ahout constructing .prepin
case
(Sat Apr 16 2011 - 06:04:36 PDT)
hanlu0366
(Fri Apr 15 2011 - 18:54:40 PDT)
[AMBER] python and perl versions of mmpbsa
Jason Swails
(Tue Apr 12 2011 - 11:13:42 PDT)
anyiphysics.gmail.com
(Tue Apr 12 2011 - 11:05:57 PDT)
Bill Miller III
(Tue Apr 12 2011 - 09:27:18 PDT)
anyiphysics.gmail.com
(Tue Apr 12 2011 - 09:22:15 PDT)
[AMBER] QMMM
Ross Walker
(Mon Apr 18 2011 - 07:58:44 PDT)
Jurica Novak
(Mon Apr 18 2011 - 05:19:17 PDT)
David A Case
(Mon Apr 18 2011 - 04:53:32 PDT)
Jurica Novak
(Mon Apr 18 2011 - 02:38:54 PDT)
Andreas Goetz
(Tue Apr 12 2011 - 11:26:32 PDT)
Jason Swails
(Tue Apr 12 2011 - 11:17:47 PDT)
Gustavo Seabra
(Tue Apr 12 2011 - 11:05:55 PDT)
Jason Swails
(Tue Apr 12 2011 - 08:00:19 PDT)
Jurica Novak
(Tue Apr 12 2011 - 07:13:22 PDT)
Gustavo Seabra
(Tue Apr 12 2011 - 06:45:28 PDT)
Jurica Novak
(Tue Apr 12 2011 - 06:22:21 PDT)
Barbault Florent
(Tue Apr 12 2011 - 05:33:02 PDT)
Jurica Novak
(Tue Apr 12 2011 - 05:13:14 PDT)
[AMBER] Query about charge on magnesium
Ye MEI
(Fri Apr 15 2011 - 08:51:50 PDT)
Jacopo Sgrignani
(Fri Apr 15 2011 - 08:07:56 PDT)
Vaibhav Jain
(Fri Apr 15 2011 - 07:07:16 PDT)
[AMBER] Query regarding considering water molecules
Jason Swails
(Wed Apr 06 2011 - 10:22:59 PDT)
Jason Swails
(Wed Apr 06 2011 - 10:21:53 PDT)
sonam bhatia
(Wed Apr 06 2011 - 08:46:02 PDT)
[AMBER] Question about Amber output file format
Jason Swails
(Mon Apr 04 2011 - 09:12:53 PDT)
TAEJIN KIM
(Mon Apr 04 2011 - 07:45:51 PDT)
[AMBER] Question about ptraj artifacts
Thomas Cheatham III
(Wed Apr 27 2011 - 09:31:32 PDT)
Thomas Cheatham III
(Wed Apr 27 2011 - 09:14:00 PDT)
Kamali Sripathi
(Wed Apr 27 2011 - 08:52:26 PDT)
Jason Swails
(Sun Apr 24 2011 - 10:11:10 PDT)
Kamali Sripathi
(Sun Apr 24 2011 - 06:58:53 PDT)
Kamali Sripathi
(Wed Apr 20 2011 - 13:06:30 PDT)
[AMBER] QUESTION ON MMPBSA
Jason Swails
(Tue Apr 19 2011 - 20:18:51 PDT)
vani panguluri
(Tue Apr 19 2011 - 19:59:43 PDT)
Dwight McGee
(Mon Apr 11 2011 - 06:26:50 PDT)
vani panguluri
(Sun Apr 10 2011 - 18:16:40 PDT)
Jason Swails
(Sun Apr 10 2011 - 11:28:12 PDT)
vani panguluri
(Sun Apr 10 2011 - 11:01:05 PDT)
Jason Swails
(Sun Apr 10 2011 - 10:53:02 PDT)
vani panguluri
(Sun Apr 10 2011 - 09:55:13 PDT)
Bill Miller III
(Fri Apr 08 2011 - 11:01:02 PDT)
vani panguluri
(Fri Apr 08 2011 - 10:48:38 PDT)
Bill Miller III
(Fri Apr 08 2011 - 10:15:25 PDT)
vani panguluri
(Fri Apr 08 2011 - 10:01:09 PDT)
[AMBER] question on scmask
Yi An
(Fri Apr 29 2011 - 13:36:15 PDT)
[AMBER] questions about packmol
Junjian Miao
(Thu Apr 07 2011 - 07:19:26 PDT)
[AMBER] recalculating atom charges
Dachuan Guo
(Thu Apr 07 2011 - 23:51:42 PDT)
[AMBER] RED conformation weights
Junjian Miao
(Sun Apr 24 2011 - 02:53:42 PDT)
Jason Swails
(Sat Apr 23 2011 - 09:50:54 PDT)
Junjian Miao
(Sat Apr 23 2011 - 05:51:17 PDT)
[AMBER] Regarding antechamber
David A Case
(Tue Apr 19 2011 - 04:25:36 PDT)
Naveen Samala
(Mon Apr 18 2011 - 13:09:30 PDT)
[AMBER] Regarding Gaussian Calculations for MTK++ example- sidechain model
Ben Roberts
(Thu Apr 28 2011 - 09:28:12 PDT)
Naveen Samala
(Thu Apr 28 2011 - 09:23:07 PDT)
[AMBER] Regarding MTK++ MCPB tutorials on Small and Large Models of ZN Metalloprotein
Martin Peters
(Wed Apr 20 2011 - 14:40:28 PDT)
Naveen Samala
(Wed Apr 20 2011 - 12:55:46 PDT)
[AMBER] Regarding understanding MTK++ Document
Naveen Samala
(Tue Apr 19 2011 - 11:28:24 PDT)
Ben Roberts
(Tue Apr 19 2011 - 10:40:49 PDT)
Ben Roberts
(Tue Apr 19 2011 - 10:31:59 PDT)
Naveen Samala
(Tue Apr 19 2011 - 09:41:49 PDT)
[AMBER] Release of AmberTools 1.5
David A Case
(Fri Apr 15 2011 - 05:48:14 PDT)
[AMBER] restart from stopped MMPBSA.py.MPI job
Jason Swails
(Fri Apr 01 2011 - 08:35:05 PDT)
Christoph Malisi
(Fri Apr 01 2011 - 07:06:04 PDT)
[AMBER] Restraining distance between a protein atom and a water of crystalization
David A Case
(Tue Apr 26 2011 - 06:34:14 PDT)
nicholus bhattacharjee
(Tue Apr 26 2011 - 06:01:39 PDT)
David A Case
(Fri Apr 22 2011 - 05:46:52 PDT)
nicholus bhattacharjee
(Fri Apr 22 2011 - 05:46:48 PDT)
Carlos Simmerling
(Fri Apr 22 2011 - 05:27:47 PDT)
nicholus bhattacharjee
(Fri Apr 22 2011 - 05:24:51 PDT)
Carlos Simmerling
(Fri Apr 22 2011 - 04:20:39 PDT)
nicholus bhattacharjee
(Thu Apr 21 2011 - 22:13:20 PDT)
Carlos Simmerling
(Mon Apr 18 2011 - 06:33:37 PDT)
nicholus bhattacharjee
(Mon Apr 18 2011 - 06:29:46 PDT)
Carlos Simmerling
(Mon Apr 18 2011 - 04:12:17 PDT)
nicholus bhattacharjee
(Mon Apr 18 2011 - 02:46:17 PDT)
[AMBER] Restraining non-bonded atoms
Carlos Simmerling
(Fri Apr 15 2011 - 06:05:29 PDT)
nicholus bhattacharjee
(Fri Apr 15 2011 - 06:01:54 PDT)
[AMBER] Restraint potential in Targeted MD
Carlos Simmerling
(Fri Apr 08 2011 - 13:42:31 PDT)
Carlos Simmerling
(Fri Apr 08 2011 - 11:37:37 PDT)
Rahul Banerjee
(Fri Apr 08 2011 - 11:31:38 PDT)
Carlos Simmerling
(Fri Apr 08 2011 - 11:06:32 PDT)
Rahul Banerjee
(Fri Apr 08 2011 - 10:56:52 PDT)
[AMBER] rfree: Error decoding variable 1 3 from: pmemd.MPI and pmemd error
Jason Swails
(Fri Apr 08 2011 - 11:33:56 PDT)
miriam sgobba
(Fri Apr 08 2011 - 11:03:21 PDT)
[AMBER] SDSC
Ross Walker
(Tue Apr 05 2011 - 10:45:00 PDT)
Dmitry Mukha
(Tue Apr 05 2011 - 02:00:53 PDT)
[AMBER] Se atom type in GAFF
Jon Mikel Azpiroz
(Wed Apr 06 2011 - 02:33:57 PDT)
[AMBER] segmentation fault on antechamber when using carbon nano tube
Jason Swails
(Mon Apr 11 2011 - 14:32:56 PDT)
Bongkeun Kim
(Mon Apr 11 2011 - 14:06:00 PDT)
Jason Swails
(Mon Apr 11 2011 - 13:13:01 PDT)
Bongkeun Kim
(Mon Apr 11 2011 - 13:01:48 PDT)
[AMBER] setting gbsa=0 does not switch off GB calculation
Jason Swails
(Thu Apr 21 2011 - 10:03:30 PDT)
Oliver Kuhn
(Thu Apr 21 2011 - 09:26:30 PDT)
[AMBER] Side Chain Model building by MCPB
Martin Peters
(Wed Apr 20 2011 - 14:24:04 PDT)
Vo Cam Quy
(Wed Apr 20 2011 - 09:11:12 PDT)
[AMBER] sleap with ff02pol.r1
r smith
(Mon Apr 04 2011 - 11:35:38 PDT)
r smith
(Mon Apr 04 2011 - 11:34:59 PDT)
Wei Zhang
(Mon Apr 04 2011 - 11:33:08 PDT)
Jason Swails
(Mon Apr 04 2011 - 10:15:36 PDT)
r smith
(Mon Apr 04 2011 - 07:54:19 PDT)
[AMBER] softcore potential and temperature
anyiphysics.gmail.com
(Tue Apr 26 2011 - 14:39:02 PDT)
steinbrt.rci.rutgers.edu
(Tue Apr 26 2011 - 12:25:44 PDT)
anyiphysics.gmail.com
(Tue Apr 26 2011 - 11:19:40 PDT)
[AMBER] Solute concentration in MD
Lekpa Duukori
(Mon Apr 11 2011 - 16:03:14 PDT)
Francesco Oteri
(Mon Apr 11 2011 - 15:50:56 PDT)
Lekpa Duukori
(Tue Apr 05 2011 - 08:26:09 PDT)
[AMBER] solvate with crystal water
Hashem Taha
(Thu Apr 14 2011 - 12:12:13 PDT)
Bill Ross
(Thu Apr 14 2011 - 10:30:14 PDT)
Bill Ross
(Thu Apr 14 2011 - 10:17:27 PDT)
Jason Swails
(Thu Apr 14 2011 - 10:04:54 PDT)
David A Case
(Thu Apr 14 2011 - 09:30:59 PDT)
Jason Swails
(Thu Apr 14 2011 - 09:18:54 PDT)
Hashem Taha
(Thu Apr 14 2011 - 09:04:44 PDT)
Hashem Taha
(Thu Apr 14 2011 - 08:39:02 PDT)
Hashem Taha
(Thu Apr 14 2011 - 08:37:42 PDT)
Jason Swails
(Thu Apr 14 2011 - 08:20:40 PDT)
Hashem Taha
(Thu Apr 14 2011 - 08:11:18 PDT)
Hashem Taha
(Tue Apr 12 2011 - 17:56:39 PDT)
Daniel Roe
(Tue Apr 12 2011 - 06:20:48 PDT)
Hashem Taha
(Mon Apr 11 2011 - 13:09:58 PDT)
[AMBER] Spatial Distribution Functions
Agostino Bruno
(Fri Apr 08 2011 - 07:10:10 PDT)
[AMBER] SQM
David A Case
(Tue Apr 19 2011 - 04:36:50 PDT)
Dachuan Guo
(Mon Apr 18 2011 - 22:37:00 PDT)
Ross Walker
(Mon Apr 18 2011 - 08:55:28 PDT)
Dachuan Guo
(Mon Apr 18 2011 - 06:57:16 PDT)
[AMBER] Steered MD at constant force
Ali M. Naserian-Nik
(Thu Apr 28 2011 - 07:26:33 PDT)
Daniel Roe
(Thu Apr 28 2011 - 06:41:56 PDT)
Ali M. Naserian-Nik
(Thu Apr 28 2011 - 05:55:23 PDT)
[AMBER] steered MD versus umbrella sampling?
Carlos Simmerling
(Mon Apr 11 2011 - 14:16:23 PDT)
Jose Borreguero
(Mon Apr 11 2011 - 14:12:02 PDT)
[AMBER] strange background job crash
Ross Walker
(Mon Apr 18 2011 - 09:35:20 PDT)
Bala subramanian
(Mon Apr 18 2011 - 09:24:41 PDT)
Ross Walker
(Mon Apr 18 2011 - 09:11:50 PDT)
Bala subramanian
(Mon Apr 18 2011 - 08:44:02 PDT)
[AMBER] Sugar ring conformation (QM/MM Vs MM)
Mahmoud Soliman
(Tue Apr 05 2011 - 08:09:40 PDT)
Jason Swails
(Mon Apr 04 2011 - 21:24:23 PDT)
Mahmoud Soliman
(Mon Apr 04 2011 - 21:05:17 PDT)
[AMBER] SURFTEN / SURFOFF values are not consistent across *.all.out files
Jason Swails
(Fri Apr 29 2011 - 12:56:44 PDT)
zhihong ke
(Fri Apr 29 2011 - 09:29:18 PDT)
[AMBER] The following error i got at the end of MM_PBSA.pl
Bill Miller III
(Wed Apr 06 2011 - 04:26:51 PDT)
vani panguluri
(Wed Apr 06 2011 - 04:18:21 PDT)
[AMBER] Thermodynamic Integration--Input doubt
sunita gupta
(Wed Apr 06 2011 - 22:24:22 PDT)
Rajesh Raju
(Wed Apr 06 2011 - 14:32:19 PDT)
[AMBER] tleap problem
George Tzotzos
(Sat Apr 09 2011 - 11:30:57 PDT)
Jason Swails
(Sat Apr 09 2011 - 10:05:05 PDT)
George Tzotzos
(Sat Apr 09 2011 - 01:32:54 PDT)
Daniel Roe
(Fri Apr 08 2011 - 14:19:27 PDT)
siddesh southekal
(Fri Apr 08 2011 - 14:18:30 PDT)
George Tzotzos
(Fri Apr 08 2011 - 14:11:43 PDT)
George Tzotzos
(Fri Apr 08 2011 - 14:07:49 PDT)
[AMBER] Umbrella sampling
Carlos Simmerling
(Tue Apr 05 2011 - 11:28:22 PDT)
Sangita Kachhap
(Tue Apr 05 2011 - 11:21:17 PDT)
Carlos Simmerling
(Tue Apr 05 2011 - 11:07:18 PDT)
Sangita Kachhap
(Tue Apr 05 2011 - 10:55:42 PDT)
[AMBER] umbrella sampling on a difference of distances RC.
Jason Swails
(Fri Apr 29 2011 - 13:03:50 PDT)
iccy liu
(Fri Apr 29 2011 - 11:06:17 PDT)
[AMBER] Umbrella sampling procedure
Emmanuel Baribefe Naziga
(Mon Apr 04 2011 - 09:07:02 PDT)
siddesh southekal
(Mon Apr 04 2011 - 08:50:15 PDT)
[AMBER] Uninstalling Amber Tools
majid hasan
(Sun Apr 10 2011 - 12:22:53 PDT)
Jason Swails
(Sun Apr 10 2011 - 11:35:26 PDT)
majid hasan
(Sun Apr 10 2011 - 11:30:05 PDT)
[AMBER] Usage of ambermask within MMPBSA.py
Jason Swails
(Thu Apr 28 2011 - 08:36:51 PDT)
Bill Miller III
(Thu Apr 28 2011 - 06:07:10 PDT)
Oliver Kuhn
(Thu Apr 28 2011 - 06:04:33 PDT)
[AMBER] Usage of diffuse command
kurisaki
(Wed Apr 13 2011 - 23:46:46 PDT)
[AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py
Samuel Genheden
(Fri Apr 29 2011 - 08:05:59 PDT)
Jason Swails
(Fri Apr 29 2011 - 07:51:18 PDT)
Oliver Kuhn
(Fri Apr 29 2011 - 07:48:18 PDT)
Samuel Genheden
(Fri Apr 29 2011 - 07:47:07 PDT)
Jason Swails
(Fri Apr 29 2011 - 07:39:26 PDT)
Samuel Genheden
(Fri Apr 29 2011 - 07:34:08 PDT)
Jason Swails
(Fri Apr 29 2011 - 07:11:44 PDT)
Samuel Genheden
(Fri Apr 29 2011 - 06:45:06 PDT)
Jason Swails
(Thu Apr 28 2011 - 17:32:29 PDT)
Oliver Kuhn
(Thu Apr 28 2011 - 09:10:29 PDT)
Jason Swails
(Thu Apr 28 2011 - 08:59:40 PDT)
Markus Kaukonen
(Thu Apr 28 2011 - 06:38:43 PDT)
Oliver Kuhn
(Thu Apr 28 2011 - 06:18:12 PDT)
[AMBER] usage of secstruct and atomicfluct
py
(Tue Apr 26 2011 - 06:24:26 PDT)
[AMBER] Vector analysis
John S
(Wed Apr 06 2011 - 09:01:02 PDT)
[AMBER] velocity units
Dmitry Mukha
(Wed Apr 13 2011 - 08:38:23 PDT)
Daniel Roe
(Wed Apr 13 2011 - 08:31:53 PDT)
Dmitry Mukha
(Wed Apr 13 2011 - 07:04:49 PDT)
[AMBER] water mediated interaction
Sangita Kachhap
(Sun Apr 03 2011 - 08:47:59 PDT)
[AMBER] weird hydrogen names?
Jason Swails
(Thu Apr 14 2011 - 11:23:32 PDT)
David A Case
(Thu Apr 14 2011 - 10:39:30 PDT)
[AMBER] what do rdparm dihedral numbers mean?
david condon
(Tue Apr 19 2011 - 11:31:29 PDT)
Jason Swails
(Tue Apr 19 2011 - 10:36:12 PDT)
david condon
(Tue Apr 19 2011 - 09:57:50 PDT)
[AMBER] Why Gyr and rmsd read mdcrd differently?
Catein Catherine
(Wed Apr 20 2011 - 07:54:13 PDT)
[AMBER] xleap problem
vhakkim boy
(Tue Apr 26 2011 - 21:14:14 PDT)
souvik sur
(Tue Apr 26 2011 - 20:58:55 PDT)
souvik sur
(Tue Apr 26 2011 - 06:21:17 PDT)
David A Case
(Tue Apr 26 2011 - 05:07:06 PDT)
souvik sur
(Tue Apr 26 2011 - 00:46:04 PDT)
Bill Ross
(Mon Apr 25 2011 - 22:46:50 PDT)
souvik sur
(Mon Apr 25 2011 - 22:40:01 PDT)
David A Case
(Mon Apr 25 2011 - 07:03:46 PDT)
souvik sur
(Mon Apr 25 2011 - 06:55:54 PDT)
Leap error with Zinc ions
setyanto md
(Tue Apr 19 2011 - 06:21:17 PDT)
Ben Roberts
(Mon Apr 18 2011 - 09:42:50 PDT)
Ross Walker
(Mon Apr 18 2011 - 09:10:06 PDT)
Manish Datt
(Mon Apr 18 2011 - 07:42:32 PDT)
MCPB program - how to download)
Ben Roberts
(Mon Apr 18 2011 - 08:45:00 PDT)
Last message date
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Sat Apr 30 2011 - 17:30:02 PDT
Archived on
: Wed Oct 09 2024 - 05:54:20 PDT
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