Amber Archive Apr 2011: by subject

[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)

Amber Archive Apr 2011 by subject