Amber Archive Jun 2007: by subject

AMBER:
- David A. Case (Tue Jun 12 2007 - 12:29:06 PDT)
- Steve Seibold (Tue Jun 12 2007 - 09:21:15 PDT)
- Steve Seibold (Mon Jun 11 2007 - 10:31:47 PDT)
- Carlos Simmerling (Fri Jun 08 2007 - 11:47:43 PDT)
- Taryn Hartley (Fri Jun 08 2007 - 11:39:15 PDT)
AMBER: "distance" command in ptraj
- Barbault Florent (Sat Jun 02 2007 - 08:28:44 PDT)
- Carlos Simmerling (Sat Jun 02 2007 - 04:56:15 PDT)
- Roberto Veiga (Sat Jun 02 2007 - 04:19:42 PDT)
AMBER: "FATAL: Atom xxx does not have a type."
- David A. Case (Tue Jun 26 2007 - 15:20:21 PDT)
- Fred Baba (Tue Jun 26 2007 - 10:59:51 PDT)
AMBER: $AMBERHOME on PATH
- David A. Case (Fri Jun 29 2007 - 09:05:09 PDT)
- M. L. Dodson (Fri Jun 29 2007 - 06:34:08 PDT)
- Francesco Pietra (Thu Jun 28 2007 - 22:58:19 PDT)
- Francesco Pietra (Thu Jun 28 2007 - 13:55:53 PDT)
- Francesco Pietra (Thu Jun 28 2007 - 13:01:11 PDT)
- David A. Case (Thu Jun 28 2007 - 11:37:58 PDT)
- Ross Walker (Thu Jun 28 2007 - 10:58:09 PDT)
- Francesco Pietra (Thu Jun 28 2007 - 10:12:43 PDT)
- David A. Case (Thu Jun 28 2007 - 09:00:55 PDT)
- Alexandar T Tzanov (Thu Jun 28 2007 - 08:39:57 PDT)
- Ross Walker (Thu Jun 28 2007 - 08:33:20 PDT)
- Francesco Pietra (Thu Jun 28 2007 - 07:40:09 PDT)
- Ross Walker (Wed Jun 27 2007 - 09:11:34 PDT)
- Francesco Pietra (Wed Jun 27 2007 - 07:59:02 PDT)
- Francesco Pietra (Wed Jun 27 2007 - 07:30:09 PDT)
- Francesco Pietra (Tue Jun 26 2007 - 13:15:11 PDT)
- David A. Case (Tue Jun 26 2007 - 11:01:02 PDT)
- Francesco Pietra (Tue Jun 26 2007 - 10:38:35 PDT)
AMBER: $AMBERHOME on PATH & compilations
- David A. Case (Wed Jun 27 2007 - 10:06:38 PDT)
- Francesco Pietra (Wed Jun 27 2007 - 09:10:38 PDT)
AMBER: $AMBERHOME on PATH)
- Alexandar T Tzanov (Fri Jun 29 2007 - 07:48:13 PDT)
- Ross Walker (Thu Jun 28 2007 - 09:53:44 PDT)
AMBER: (no subject)
- Franck Vendeix (Thu Jun 14 2007 - 06:32:54 PDT)
- Catein Catherine (Wed Jun 13 2007 - 22:54:28 PDT)
AMBER: .lib files
- Ilyas Yildirim (Fri Jun 15 2007 - 12:50:34 PDT)
- Taryn Hartley (Fri Jun 15 2007 - 12:42:16 PDT)
AMBER: 5 Ligands and 1 Protein
- David A. Case (Fri Jun 22 2007 - 08:05:28 PDT)
- Colby C (Thu Jun 21 2007 - 14:45:46 PDT)
- David A. Case (Wed Jun 20 2007 - 22:02:20 PDT)
- Colby C (Wed Jun 20 2007 - 19:01:40 PDT)
- David A. Case (Wed Jun 20 2007 - 17:16:27 PDT)
- Scott Brozell (Wed Jun 20 2007 - 17:25:05 PDT)
- Colby C (Wed Jun 20 2007 - 17:10:22 PDT)
- David A. Case (Wed Jun 20 2007 - 16:46:23 PDT)
- Colby C (Wed Jun 20 2007 - 11:07:33 PDT)
AMBER: [Fwd: Tr: H bonds]
- Guillaume Renvez (Wed Jun 13 2007 - 05:37:20 PDT)
AMBER: Algorithm for integration of equations of motion
- Ross Walker (Wed Jun 20 2007 - 12:38:36 PDT)
- Roberto Veiga (Wed Jun 20 2007 - 11:55:45 PDT)
AMBER: Amber 9 on IRIX 6.5
- Colby C (Mon Jun 11 2007 - 18:55:25 PDT)
AMBER: Amber Installation Error
- Joe Nolan (Mon Jun 18 2007 - 12:08:48 PDT)
- Mark Williamson (Mon Jun 18 2007 - 11:19:27 PDT)
- Joe Nolan (Mon Jun 18 2007 - 08:52:16 PDT)
- David A. Case (Mon Jun 18 2007 - 10:52:05 PDT)
- Mark Williamson (Mon Jun 18 2007 - 08:35:18 PDT)
- Joe Nolan (Mon Jun 18 2007 - 07:34:12 PDT)
- Ross Walker (Fri Jun 15 2007 - 12:25:28 PDT)
- David A. Case (Fri Jun 15 2007 - 11:56:29 PDT)
AMBER: amber7 and xleap
- David A. Case (Sat Jun 30 2007 - 17:57:13 PDT)
- Saiful Islam (Sat Jun 30 2007 - 06:14:21 PDT)
AMBER: amber9 compile problem
- Robert Duke (Wed Jun 13 2007 - 11:07:37 PDT)
- Henk Meij (Tue Jun 12 2007 - 11:30:54 PDT)
- Ross Walker (Tue Jun 12 2007 - 10:04:54 PDT)
- Henk Meij (Tue Jun 12 2007 - 07:13:01 PDT)
- Ross Walker (Mon Jun 11 2007 - 15:06:30 PDT)
- Henk Meij (Mon Jun 11 2007 - 12:04:05 PDT)
- Ross Walker (Mon Jun 11 2007 - 09:16:58 PDT)
- Henk Meij (Mon Jun 11 2007 - 06:51:12 PDT)
- Mark Williamson (Mon Jun 11 2007 - 06:28:30 PDT)
- Henk Meij (Mon Jun 11 2007 - 06:20:17 PDT)
- Ross Walker (Sun Jun 10 2007 - 10:15:18 PDT)
- Mark Williamson (Sun Jun 10 2007 - 09:03:28 PDT)
- hmeij.wesleyan.edu (Sun Jun 10 2007 - 06:58:54 PDT)
AMBER: Amber9's sander.MPI on x86_64
- Ross Walker (Wed Jun 06 2007 - 09:18:33 PDT)
- Steve Young (Tue Jun 05 2007 - 10:23:43 PDT)
- Ross Walker (Mon Jun 04 2007 - 11:20:43 PDT)
- Thomas Steinbrecher (Mon Jun 04 2007 - 10:26:55 PDT)
- kkirschn.hamilton.edu (Mon Jun 04 2007 - 10:13:51 PDT)
AMBER: amber94 parameters for cholesterol
- paula lario (Thu Jun 07 2007 - 15:57:38 PDT)
AMBER: Amber: Number density profile, pucker..reg
- Praveena Gopal (Mon Jun 11 2007 - 23:17:37 PDT)
AMBER: Antechamber--Boron Parameters
- David A. Case (Mon Jun 25 2007 - 18:08:48 PDT)
- brmeher.iitg.ernet.in (Mon Jun 25 2007 - 03:04:30 PDT)
AMBER: antechamber/charges/conformation
- Francesco Pietra (Mon Jun 11 2007 - 02:44:21 PDT)
- FyD (Mon Jun 11 2007 - 01:40:11 PDT)
- Francesco Pietra (Sun Jun 10 2007 - 00:02:15 PDT)
AMBER: Atom types
- Melinda Layten (Tue Jun 12 2007 - 11:16:34 PDT)
- Taryn Hartley (Tue Jun 12 2007 - 10:25:30 PDT)
AMBER: box size bomb in QMMM calculation
- M. L. Dodson (Wed Jun 13 2007 - 02:43:52 PDT)
- Ross Walker (Tue Jun 12 2007 - 20:39:35 PDT)
- M. L. Dodson (Tue Jun 12 2007 - 16:23:50 PDT)
- Ross Walker (Tue Jun 12 2007 - 15:29:26 PDT)
- M. L. Dodson (Tue Jun 12 2007 - 12:46:00 PDT)
AMBER: BUG? Does TLEAP understand SPC/E water?
- David A. Case (Fri Jun 01 2007 - 11:39:42 PDT)
- David A. Case (Fri Jun 01 2007 - 11:37:10 PDT)
- Thomas Steinbrecher (Fri Jun 01 2007 - 11:30:54 PDT)
- Ross Walker (Fri Jun 01 2007 - 11:23:35 PDT)
- David Cerutti (Fri Jun 01 2007 - 10:35:02 PDT)
AMBER: bugfix.all
- Francesco Pietra (Wed Jun 27 2007 - 23:14:33 PDT)
- Ross Walker (Wed Jun 27 2007 - 14:19:32 PDT)
- David A. Case (Wed Jun 27 2007 - 13:55:52 PDT)
- Carlos Simmerling (Wed Jun 27 2007 - 13:52:15 PDT)
- M. L. Dodson (Wed Jun 27 2007 - 13:52:07 PDT)
- Francesco Pietra (Wed Jun 27 2007 - 13:26:15 PDT)
AMBER: building water box with desired number of molecules
- gurpreet singh (Tue Jun 12 2007 - 02:09:10 PDT)
- Vijay Manickam Achari (Tue Jun 12 2007 - 00:33:21 PDT)
AMBER: Charge not integral. Head-to-tail cyclic peptides
- Laurent Chiche (Mon Jun 18 2007 - 07:37:53 PDT)
- Melinda Layten (Mon Jun 18 2007 - 07:28:57 PDT)
- Giacomo Bastianelli (Mon Jun 18 2007 - 06:55:46 PDT)
AMBER: Compile openmpi
- Francesco Pietra (Thu Jun 14 2007 - 10:11:02 PDT)
AMBER: Compiling openmpi/icc/icpc
- Francesco Pietra (Fri Jun 08 2007 - 23:04:45 PDT)
- Ross Walker (Fri Jun 08 2007 - 14:30:02 PDT)
- Francesco Pietra (Fri Jun 08 2007 - 10:27:20 PDT)
AMBER: configure question
- Steve Young (Fri Jun 29 2007 - 07:31:19 PDT)
- Robert Duke (Thu Jun 28 2007 - 15:18:53 PDT)
- Ross Walker (Thu Jun 28 2007 - 10:06:40 PDT)
- Andreas Svrcek-Seiler (Thu Jun 28 2007 - 09:49:38 PDT)
- David A. Case (Thu Jun 28 2007 - 09:26:34 PDT)
- Steve Young (Thu Jun 28 2007 - 08:52:48 PDT)
AMBER: conversion of Macromodel substructure format to .frcmod file
- brmeher.iitg.ernet.in (Thu Jun 28 2007 - 03:24:24 PDT)
AMBER: Dihedral driver
- Ilyas Yildirim (Thu Jun 07 2007 - 13:16:15 PDT)
- Beale, John (Thu Jun 07 2007 - 13:08:35 PDT)
AMBER: dihedral parameters
- Jardas sucuriba (Tue Jun 12 2007 - 19:18:12 PDT)
- David A. Case (Tue Jun 12 2007 - 12:35:57 PDT)
- Jardas sucuriba (Mon Jun 11 2007 - 15:13:36 PDT)
AMBER: dihedral simulation
- David A. Case (Sun Jun 03 2007 - 20:06:26 PDT)
- lishan yao (Sun Jun 03 2007 - 08:49:33 PDT)
AMBER: distance scan
- David A. Case (Sat Jun 16 2007 - 08:21:05 PDT)
- Miguel Ferreira (Sat Jun 16 2007 - 03:25:59 PDT)
- Miguel Ferreira (Sat Jun 16 2007 - 03:16:15 PDT)
AMBER: Does Chimera support AMBER file formats?
- Mingfeng Yang (Tue Jun 26 2007 - 17:12:53 PDT)
- Ilyas Yildirim (Tue Jun 26 2007 - 16:58:56 PDT)
AMBER: Energy outputs in TI Approach
- David A. Case (Sat Jun 16 2007 - 08:19:23 PDT)
- Ilyas Yildirim (Fri Jun 15 2007 - 22:03:26 PDT)
AMBER: environment variables
- Ross Walker (Mon Jun 25 2007 - 12:43:39 PDT)
- Francesco Pietra (Mon Jun 25 2007 - 08:51:05 PDT)
AMBER: equilibrium constants via MMPBSA
- David Mobley (Mon Jun 04 2007 - 06:11:25 PDT)
- Julien Michel (Fri Jun 01 2007 - 09:48:55 PDT)
- Sean Rathlef (Fri Jun 01 2007 - 09:57:46 PDT)
AMBER: error due to exceeding left-hand side digital numbers in restart output
- David A. Case (Mon Jun 18 2007 - 11:06:16 PDT)
- Cenk Andac (Mon Jun 18 2007 - 01:09:36 PDT)
AMBER: explanation to edit and use the script
- Syed Tarique Moin (Wed Jun 20 2007 - 02:33:15 PDT)
- Syed Tarique Moin (Sun Jun 17 2007 - 21:26:38 PDT)
AMBER: extracting starting structures from equilibration trajectory
- Nikola Trbovic (Thu Jun 07 2007 - 13:07:48 PDT)
- Ilyas Yildirim (Thu Jun 07 2007 - 12:58:19 PDT)
- Nikola Trbovic (Thu Jun 07 2007 - 12:54:35 PDT)
- Ilyas Yildirim (Thu Jun 07 2007 - 12:54:06 PDT)
- Carlos Simmerling (Thu Jun 07 2007 - 12:41:36 PDT)
- Nikola Trbovic (Thu Jun 07 2007 - 12:33:35 PDT)
- Ilyas Yildirim (Thu Jun 07 2007 - 11:14:18 PDT)
- Nikola Trbovic (Thu Jun 07 2007 - 11:06:15 PDT)
AMBER: ff99 vs ff99SB for RNA
- Thomas Cheatham III (Thu Jun 14 2007 - 09:17:46 PDT)
- Carlos Simmerling (Thu Jun 14 2007 - 09:03:03 PDT)
- j j (Thu Jun 14 2007 - 08:30:21 PDT)
- Carlos Simmerling (Thu Jun 14 2007 - 07:57:02 PDT)
- Brent Krueger (Thu Jun 14 2007 - 07:05:12 PDT)
AMBER: frcmod
- Brooke Elizabeth Adams (Mon Jun 18 2007 - 13:02:13 PDT)
- David A. Case (Mon Jun 18 2007 - 12:37:52 PDT)
- Brooke Elizabeth Adams (Mon Jun 18 2007 - 12:06:34 PDT)
- David A. Case (Fri Jun 15 2007 - 14:43:48 PDT)
- Brooke Elizabeth Adams (Fri Jun 15 2007 - 12:11:00 PDT)
- David A. Case (Tue Jun 12 2007 - 14:34:35 PDT)
- Brooke Elizabeth Adams (Tue Jun 12 2007 - 13:38:50 PDT)
AMBER: Fwd: Serial "make" failure with xleap
- Francesco Pietra (Fri Jun 29 2007 - 10:26:54 PDT)
AMBER: g(r)
- khn _ (Wed Jun 13 2007 - 09:43:25 PDT)
AMBER: g(r) in mixtures?
- BJÖRN KARLSSON (Wed Jun 06 2007 - 00:56:05 PDT)
AMBER: GB vs. Invacuo Energies
- Seth Lilavivat (Wed Jun 06 2007 - 07:38:32 PDT)
AMBER: H bond
- Carlos Simmerling (Tue Jun 19 2007 - 04:24:27 PDT)
- Guillaume Renvez (Tue Jun 19 2007 - 01:18:45 PDT)
AMBER: Hardware recommendations please
- David LeBard (Thu Jun 07 2007 - 11:31:21 PDT)
- Jeremy Weedon (Thu Jun 07 2007 - 08:24:54 PDT)
- Jeremy Weedon (Wed Jun 06 2007 - 09:15:16 PDT)
AMBER: Hbonds
- David A. Case (Fri Jun 15 2007 - 11:06:26 PDT)
- mbrut.laas.fr (Thu Jun 14 2007 - 00:45:25 PDT)
- David A. Case (Wed Jun 13 2007 - 13:50:11 PDT)
- mbrut.laas.fr (Wed Jun 13 2007 - 05:54:52 PDT)
AMBER: How to add semi-experience parameter in divcon?
- clarkzhy (Thu Jun 21 2007 - 18:19:23 PDT)
- Seth Hayik (Tue Jun 19 2007 - 09:15:03 PDT)
- Ross Walker (Tue Jun 19 2007 - 08:44:59 PDT)
- clarkzhy (Tue Jun 19 2007 - 07:23:04 PDT)
AMBER: how to calculate energy of the peptide
- priya priya (Mon Jun 25 2007 - 06:56:54 PDT)
AMBER: How to fix two angle but do umberlla sampling for distance?
- Jerome.GOLEBIOWSKI.unice.fr (Thu Jun 07 2007 - 08:38:26 PDT)
- Catein Catherine (Thu Jun 07 2007 - 08:14:30 PDT)
AMBER: how to stop ptraj atom renumbering
- Russell Green (Wed Jun 27 2007 - 13:25:53 PDT)
AMBER: hydrogen bond
- Guillaume Renvez (Wed Jun 13 2007 - 01:49:22 PDT)
AMBER: implementation of GB model in AMBER
- Carlos Simmerling (Sun Jun 17 2007 - 05:58:11 PDT)
- john chen (Sun Jun 17 2007 - 05:49:24 PDT)
AMBER: Improving pmemd parallel scaling
- Robert Duke (Thu Jun 28 2007 - 15:27:24 PDT)
- Mark Williamson (Thu Jun 28 2007 - 09:19:06 PDT)
- Alessandro Nascimento (Thu Jun 28 2007 - 09:07:15 PDT)
AMBER: Input files for the Potential of mean force.
- Catein Catherine (Sun Jun 10 2007 - 19:43:12 PDT)
AMBER: Installation Question
- Jianmin Feng (Mon Jun 04 2007 - 07:33:20 PDT)
- Carlos Simmerling (Mon Jun 04 2007 - 07:16:30 PDT)
- Chrystal Bruce (Mon Jun 04 2007 - 07:53:46 PDT)
AMBER: Installing amber9 in IBM P5?
- Ross Walker (Wed Jun 13 2007 - 16:39:11 PDT)
- Du, Shiyu (Wed Jun 13 2007 - 14:20:37 PDT)
- Du, Shiyu (Wed Jun 13 2007 - 10:52:11 PDT)
- Ross Walker (Wed Jun 13 2007 - 08:17:45 PDT)
- Jed W Pitera (Wed Jun 13 2007 - 08:04:31 PDT)
- Du, Shiyu (Tue Jun 12 2007 - 22:01:56 PDT)
- Ross Walker (Tue Jun 12 2007 - 20:34:33 PDT)
- Du, Shiyu (Tue Jun 12 2007 - 19:09:34 PDT)
AMBER: Installing on windows
- Bill Ross (Mon Jun 11 2007 - 12:14:04 PDT)
- Bill Ross (Mon Jun 11 2007 - 12:01:06 PDT)
- Gustavo Seabra (Mon Jun 11 2007 - 11:56:48 PDT)
- Colby C (Mon Jun 11 2007 - 10:14:33 PDT)
- Gustavo Seabra (Mon Jun 11 2007 - 08:41:05 PDT)
- Colby C (Mon Jun 11 2007 - 08:17:07 PDT)
- Colby C (Mon Jun 11 2007 - 07:42:40 PDT)
- Gustavo Seabra (Mon Jun 11 2007 - 06:59:29 PDT)
- Colby C (Mon Jun 11 2007 - 05:56:39 PDT)
- David A. Case (Sun Jun 10 2007 - 21:25:28 PDT)
- Colby C (Sun Jun 10 2007 - 20:34:58 PDT)
- Gustavo Seabra (Sun Jun 10 2007 - 19:20:05 PDT)
- Colby C (Sun Jun 10 2007 - 18:48:30 PDT)
- Gustavo Seabra (Sun Jun 10 2007 - 17:28:01 PDT)
- Carlos Simmerling (Sun Jun 10 2007 - 16:54:04 PDT)
- Colby C (Sun Jun 10 2007 - 16:42:25 PDT)
AMBER: Internal dielectric and MMPBSA
- Ileana Stoica (Tue Jun 12 2007 - 04:32:17 PDT)
AMBER: isolated NTP
- David A. Case (Mon Jun 18 2007 - 08:39:06 PDT)
- Steve Seibold (Mon Jun 18 2007 - 05:20:21 PDT)
- David A. Case (Sun Jun 17 2007 - 22:40:29 PDT)
- Steve Seibold (Fri Jun 15 2007 - 07:07:16 PDT)
AMBER: LES problem
- Vlad Cojocaru (Tue Jun 05 2007 - 05:41:19 PDT)
- Carlos Simmerling (Tue Jun 05 2007 - 05:14:15 PDT)
- Urszula Uciechowska (Mon Jun 04 2007 - 06:34:42 PDT)
AMBER: Limitation in number of atoms/residues
- Sascha Rehm (Fri Jun 22 2007 - 06:46:05 PDT)
- Robert Duke (Fri Jun 22 2007 - 05:37:30 PDT)
- Sascha Rehm (Fri Jun 22 2007 - 03:47:35 PDT)
AMBER: make serial failure for xleap
- Francesco Pietra (Sat Jun 30 2007 - 06:00:31 PDT)
- Francesco Pietra (Sat Jun 30 2007 - 01:39:32 PDT)
- David A. Case (Fri Jun 29 2007 - 16:28:36 PDT)
- M. L. Dodson (Fri Jun 29 2007 - 15:33:37 PDT)
- Francesco Pietra (Fri Jun 29 2007 - 14:05:52 PDT)
AMBER: make test serial
- Ross Walker (Sat Jun 30 2007 - 10:00:13 PDT)
- M. L. Dodson (Sat Jun 30 2007 - 09:30:05 PDT)
- Francesco Pietra (Sat Jun 30 2007 - 09:18:38 PDT)
- David A. Case (Sat Jun 30 2007 - 08:28:01 PDT)
- Francesco Pietra (Sat Jun 30 2007 - 06:42:56 PDT)
AMBER: Math libraries
- Francesco Pietra (Thu Jun 28 2007 - 13:12:28 PDT)
- Andreas Svrcek-Seiler (Thu Jun 28 2007 - 09:27:28 PDT)
- Robert Duke (Thu Jun 28 2007 - 05:15:07 PDT)
- Francesco Pietra (Thu Jun 28 2007 - 02:56:45 PDT)
AMBER: metal ions
- Wei Chen (Tue Jun 12 2007 - 14:20:26 PDT)
AMBER: Metal ions in GBSA
- Wei Chen (Tue Jun 12 2007 - 06:13:36 PDT)
AMBER: MM-GBSA: pairwise decompose energy calculation can't read snapshot_com.all.out
- jitrayut jitonnom (Sun Jun 03 2007 - 09:08:16 PDT)
AMBER: MM-PBSA calcuation for drug dna complex in 2:1 ratio
- saurabh agrawal (Tue Jun 12 2007 - 06:25:09 PDT)
AMBER: MM-PBSA POPC/TIP3P/GPCR/LIGAND
- Jojart Balazs (Sat Jun 30 2007 - 11:25:49 PDT)
AMBER: mmpbsa decomposition error
- cristian (Fri Jun 08 2007 - 08:34:21 PDT)
AMBER: MMPBSA-nmode .top question
- David A. Case (Sun Jun 17 2007 - 22:35:39 PDT)
- Matthew Danielson (Fri Jun 15 2007 - 14:11:52 PDT)
AMBER: NMR vs. X-ray structures
- Sally Pias (Wed Jun 13 2007 - 21:33:06 PDT)
- Carlos Simmerling (Tue Jun 12 2007 - 03:57:12 PDT)
- Marc Baaden (Mon Jun 11 2007 - 22:51:21 PDT)
- Sally Pias (Mon Jun 11 2007 - 22:22:19 PDT)
AMBER: Nucleic acid analyse : base pair parameters, backbone torsions...
- Stéphane Téletchéa (Tue Jun 05 2007 - 01:01:10 PDT)
- Thomas Cheatham (Mon Jun 04 2007 - 22:04:34 PDT)
- Cenk Andac (Mon Jun 04 2007 - 15:00:25 PDT)
- Sophie Barbe (Mon Jun 04 2007 - 14:16:48 PDT)
AMBER: Offending restraints????
- saccenti.cerm.unifi.it (Wed Jun 27 2007 - 02:33:16 PDT)
- David A. Case (Tue Jun 26 2007 - 09:37:21 PDT)
- saccenti.cerm.unifi.it (Tue Jun 26 2007 - 08:36:44 PDT)
- saccenti.cerm.unifi.it (Tue Jun 26 2007 - 08:34:37 PDT)
- Carlos Simmerling (Tue Jun 26 2007 - 08:33:47 PDT)
- David A. Case (Tue Jun 26 2007 - 08:27:18 PDT)
- saccenti.cerm.unifi.it (Tue Jun 26 2007 - 07:34:05 PDT)
- saccenti.cerm.unifi.it (Tue Jun 26 2007 - 07:23:45 PDT)
- Gustavo Seabra (Tue Jun 26 2007 - 07:09:18 PDT)
- Carlos Simmerling (Tue Jun 26 2007 - 06:59:24 PDT)
- saccenti.cerm.unifi.it (Tue Jun 26 2007 - 06:48:21 PDT)
AMBER: Once again, "distance" command in ptraj
- Roberto Veiga (Tue Jun 05 2007 - 02:20:27 PDT)
- Thomas Cheatham (Mon Jun 04 2007 - 21:22:45 PDT)
- Roberto Veiga (Mon Jun 04 2007 - 09:47:01 PDT)
- Roberto Veiga (Mon Jun 04 2007 - 07:20:34 PDT)
- Carlos Simmerling (Mon Jun 04 2007 - 07:15:22 PDT)
- Roberto Veiga (Mon Jun 04 2007 - 07:06:19 PDT)
AMBER: pair distribution function
- khn _ (Sun Jun 17 2007 - 01:25:56 PDT)
- Thomas Cheatham III (Thu Jun 14 2007 - 16:41:51 PDT)
- khn _ (Thu Jun 14 2007 - 16:20:47 PDT)
AMBER: PBSA Error
- Pankaj R. Daga (Tue Jun 26 2007 - 07:03:41 PDT)
AMBER: pdb flie format
- j j (Mon Jun 04 2007 - 14:10:32 PDT)
- David A. Case (Sun Jun 03 2007 - 20:04:58 PDT)
- Fenghui Fan (Sun Jun 03 2007 - 10:57:02 PDT)
- Mr Defang Ouyang (Sun Jun 03 2007 - 05:53:08 PDT)
AMBER: PDB problems
- Ilyas Yildirim (Fri Jun 15 2007 - 15:30:45 PDT)
- David A. Case (Fri Jun 15 2007 - 13:24:44 PDT)
- Taryn Hartley (Fri Jun 15 2007 - 13:17:13 PDT)
AMBER: performance with implicit solvent
- David A. Case (Fri Jun 15 2007 - 13:18:31 PDT)
- Carlos Simmerling (Fri Jun 15 2007 - 13:17:28 PDT)
- Kijeong Kwac (Fri Jun 15 2007 - 13:02:49 PDT)
AMBER: PMF calculation
- David A. Case (Mon Jun 25 2007 - 17:47:25 PDT)
- Jena M (Mon Jun 25 2007 - 12:59:02 PDT)
AMBER: Potential of mean force.
- Carlos Simmerling (Fri Jun 08 2007 - 05:08:06 PDT)
- Catein Catherine (Fri Jun 08 2007 - 05:01:42 PDT)
AMBER: prepin for metal centre
- David A. Case (Mon Jun 25 2007 - 17:43:26 PDT)
- Mattias Blomberg (Mon Jun 25 2007 - 11:17:02 PDT)
AMBER: Problem about prepare the model when running antechamber
- Liang, Lei (Mon Jun 04 2007 - 14:03:45 PDT)
- Liang, Lei (Mon Jun 04 2007 - 14:02:04 PDT)
- Carlos Simmerling (Mon Jun 04 2007 - 13:52:23 PDT)
- Ross Walker (Mon Jun 04 2007 - 13:47:24 PDT)
- Liang, Lei (Mon Jun 04 2007 - 13:04:36 PDT)
AMBER: problem in installing amber9
- Henk Meij (Wed Jun 13 2007 - 13:32:18 PDT)
- Robert Duke (Wed Jun 13 2007 - 12:11:40 PDT)
- Ross Walker (Wed Jun 13 2007 - 11:29:04 PDT)
- Henk Meij (Wed Jun 13 2007 - 10:30:59 PDT)
- Ross Walker (Wed Jun 13 2007 - 08:25:19 PDT)
- Henk Meij (Wed Jun 13 2007 - 06:41:27 PDT)
- Ross Walker (Tue Jun 12 2007 - 20:44:16 PDT)
- David A. Case (Tue Jun 12 2007 - 14:29:14 PDT)
- Syed Tarique Moin (Tue Jun 12 2007 - 01:04:57 PDT)
- David A. Case (Fri Jun 01 2007 - 18:12:56 PDT)
- Syed Tarique Moin (Fri Jun 01 2007 - 00:10:44 PDT)
AMBER: problem in installing amber9 SOLVED!
- Henk Meij (Wed Jun 13 2007 - 13:43:06 PDT)
AMBER: problem installing amber7
- David A. Case (Sun Jun 10 2007 - 19:59:17 PDT)
- Carlos Simmerling (Sun Jun 10 2007 - 08:23:10 PDT)
- Saiful Islam (Sun Jun 10 2007 - 07:55:19 PDT)
AMBER: problem running parallel jobs
- Nikola Trbovic (Thu Jun 07 2007 - 07:58:47 PDT)
- Andy Purkiss-Trew (Thu Jun 07 2007 - 02:53:34 PDT)
- Robert Duke (Wed Jun 06 2007 - 12:08:08 PDT)
- Nikola Trbovic (Wed Jun 06 2007 - 11:43:14 PDT)
- Robert Duke (Wed Jun 06 2007 - 11:03:19 PDT)
- Nikola Trbovic (Wed Jun 06 2007 - 10:31:16 PDT)
- Robert Konecny (Tue Jun 05 2007 - 14:34:44 PDT)
- Nikola Trbovic (Tue Jun 05 2007 - 13:43:02 PDT)
AMBER: Problem with leaprc
- Francesco Pietra (Sat Jun 30 2007 - 09:23:59 PDT)
- David A. Case (Sat Jun 30 2007 - 08:32:03 PDT)
- yen li (Sat Jun 30 2007 - 07:11:47 PDT)
- David A. Case (Fri Jun 29 2007 - 08:47:51 PDT)
- yen li (Thu Jun 28 2007 - 20:27:52 PDT)
AMBER: problem with running rem on amber9
- David A. Case (Mon Jun 18 2007 - 11:22:01 PDT)
- priya priya (Mon Jun 18 2007 - 08:25:37 PDT)
- Carlos Simmerling (Mon Jun 18 2007 - 08:10:37 PDT)
- priya priya (Mon Jun 18 2007 - 08:02:55 PDT)
- priya priya (Mon Jun 18 2007 - 05:59:38 PDT)
- Carlos Simmerling (Mon Jun 18 2007 - 05:46:29 PDT)
- priya priya (Mon Jun 18 2007 - 05:41:02 PDT)
AMBER: problem with running rem on amber9 (NOT A REMD PROBLEM)
- Carlos Simmerling (Mon Jun 18 2007 - 08:31:19 PDT)
AMBER: problem with starting REM on amber9
- priya priya (Wed Jun 06 2007 - 00:07:14 PDT)
- Ross Walker (Tue Jun 05 2007 - 08:36:07 PDT)
- priya priya (Tue Jun 05 2007 - 07:21:12 PDT)
- Carlos Simmerling (Tue Jun 05 2007 - 06:42:29 PDT)
- priya priya (Tue Jun 05 2007 - 06:32:50 PDT)
AMBER: problems in adding ACE and NME group
- David A. Case (Thu Jun 28 2007 - 09:04:52 PDT)
- backy (Wed Jun 27 2007 - 23:13:02 PDT)
- David A. Case (Wed Jun 27 2007 - 09:19:51 PDT)
- Ross Walker (Wed Jun 27 2007 - 09:02:10 PDT)
- Melinda Layten (Wed Jun 27 2007 - 09:01:00 PDT)
- backy (Tue Jun 26 2007 - 23:55:47 PDT)
- Melinda Layten (Tue Jun 26 2007 - 13:02:12 PDT)
- priya priya (Mon Jun 25 2007 - 07:01:52 PDT)
- backy (Mon Jun 25 2007 - 06:21:47 PDT)
- backy (Wed Jun 20 2007 - 22:45:56 PDT)
- David A. Case (Wed Jun 20 2007 - 22:10:43 PDT)
- backy (Wed Jun 20 2007 - 22:00:12 PDT)
- Carlos Simmerling (Wed Jun 20 2007 - 21:28:30 PDT)
- backy (Wed Jun 20 2007 - 21:00:39 PDT)
- backy (Wed Jun 20 2007 - 20:54:47 PDT)
- David A. Case (Wed Jun 20 2007 - 08:41:43 PDT)
- Carlos Simmerling (Wed Jun 20 2007 - 08:37:45 PDT)
- Gustavo Seabra (Wed Jun 20 2007 - 07:14:26 PDT)
- backy (Wed Jun 20 2007 - 06:15:25 PDT)
- Carlos Simmerling (Wed Jun 20 2007 - 04:28:46 PDT)
- backy (Wed Jun 20 2007 - 02:09:26 PDT)
AMBER: problems using TIP4PBOX
- Andy Purkiss-Trew (Wed Jun 13 2007 - 05:36:14 PDT)
- David A. Case (Wed Jun 13 2007 - 05:26:11 PDT)
- john chen (Wed Jun 13 2007 - 03:53:30 PDT)
AMBER: Ptraj hbond analysis
- Achuth Prabhu (Tue Jun 05 2007 - 07:51:54 PDT)
AMBER: Ptraj: reading PDB files
- Austin B. Yongye (Thu Jun 07 2007 - 07:16:10 PDT)
- Austin B. Yongye (Wed Jun 06 2007 - 14:37:31 PDT)
AMBER: ptray segfault: vector out
- Nicolas Lux Fawzi (Thu Jun 21 2007 - 12:19:49 PDT)
AMBER: Question about MPI-IO
- David LeBard (Mon Jun 11 2007 - 18:59:33 PDT)
- Ross Walker (Mon Jun 11 2007 - 16:16:02 PDT)
- Robert Duke (Mon Jun 11 2007 - 14:51:56 PDT)
- Thomas Cheatham III (Mon Jun 11 2007 - 14:40:08 PDT)
- David LeBard (Mon Jun 11 2007 - 13:58:54 PDT)
AMBER: Question about separating bonded force
- David A. Case (Fri Jun 01 2007 - 08:42:29 PDT)
- Shawn yy (Fri Jun 01 2007 - 08:31:04 PDT)
AMBER: Questions about how ptraj calculates solvent shells
- Roberto Veiga (Mon Jun 18 2007 - 11:46:59 PDT)
AMBER: radial distribution function in ptraj
- khn _ (Fri Jun 22 2007 - 18:25:05 PDT)
AMBER: radius of gyration
- priya priya (Fri Jun 29 2007 - 06:14:49 PDT)
- Carlos Simmerling (Fri Jun 29 2007 - 04:54:28 PDT)
- priya priya (Fri Jun 29 2007 - 02:16:24 PDT)
- priya priya (Mon Jun 25 2007 - 05:57:39 PDT)
- priya priya (Mon Jun 25 2007 - 05:59:39 PDT)
- Thomas Cheatham III (Fri Jun 22 2007 - 09:30:01 PDT)
- Carlos Simmerling (Fri Jun 22 2007 - 08:40:27 PDT)
- priya priya (Fri Jun 22 2007 - 08:23:03 PDT)
- Carlos Simmerling (Fri Jun 22 2007 - 08:14:19 PDT)
- priya priya (Fri Jun 22 2007 - 08:10:36 PDT)
AMBER: RDF of pure chloroform
- BJÖRN KARLSSON (Mon Jun 25 2007 - 08:56:19 PDT)
AMBER: Rdf question
- BJÖRN KARLSSON (Sun Jun 10 2007 - 12:51:16 PDT)
AMBER: Reg COM restraint to DNA
- D.Usharani (Wed Jun 06 2007 - 02:56:00 PDT)
AMBER: Reg restraint value obtained during umbrella sampling
- D.Usharani (Thu Jun 07 2007 - 23:01:46 PDT)
- David A. Case (Sat Jun 02 2007 - 13:07:47 PDT)
- D.Usharani (Sat Jun 02 2007 - 04:07:43 PDT)
- David A. Case (Fri Jun 01 2007 - 18:19:35 PDT)
- D.Usharani (Fri Jun 01 2007 - 10:12:23 PDT)
AMBER: Regarding conversion of CHARMM force field parameters to AMBER parameters.
- nag raj (Wed Jun 13 2007 - 20:58:22 PDT)
AMBER: REMD and mpiexec
- Steve Young (Thu Jun 07 2007 - 10:47:37 PDT)
- Ross Walker (Wed Jun 06 2007 - 09:06:06 PDT)
- Steve Young (Tue Jun 05 2007 - 17:53:14 PDT)
AMBER: remd/rdc's
- David A. Case (Thu Jun 28 2007 - 08:37:44 PDT)
- McElheny, Dan (Mon Jun 25 2007 - 09:12:20 PDT)
- David A. Case (Sat Jun 23 2007 - 10:44:17 PDT)
- Carlos Simmerling (Sat Jun 23 2007 - 05:43:21 PDT)
- McElheny, Dan (Fri Jun 22 2007 - 11:04:59 PDT)
AMBER: Reply regarding PCA with ptraj and IED
- Hannes Loeffler (Tue Jun 19 2007 - 19:43:21 PDT)
- Steve Spronk (Tue Jun 19 2007 - 14:00:37 PDT)
AMBER: Restraining valence angles
- David A. Case (Wed Jun 06 2007 - 07:49:08 PDT)
- Abi Ghanem josephine (Wed Jun 06 2007 - 01:35:12 PDT)
AMBER: RESTRAINTMASK
- Roberto Veiga (Mon Jun 04 2007 - 13:09:23 PDT)
- Sandeep Kaushik (Sun Jun 03 2007 - 22:38:21 PDT)
AMBER: rms in nmode
- David A. Case (Fri Jun 01 2007 - 08:50:27 PDT)
- cristian (Fri Jun 01 2007 - 00:59:18 PDT)
- Marie Brut (Fri Jun 01 2007 - 00:22:22 PDT)
AMBER: rst overflow for implicit REMD
- Carlos Simmerling (Tue Jun 26 2007 - 08:35:47 PDT)
- David A. Case (Tue Jun 26 2007 - 08:28:28 PDT)
- In Hee Park (Tue Jun 26 2007 - 07:37:45 PDT)
AMBER: S-nitrocysteine
- FyD (Wed Jun 13 2007 - 14:44:59 PDT)
- Anthony Cruz Balberdi (Wed Jun 13 2007 - 06:12:00 PDT)
AMBER: sander core dumped during minimization
- David A. Case (Wed Jun 20 2007 - 22:16:11 PDT)
- zgleo (Wed Jun 20 2007 - 18:51:04 PDT)
AMBER: Sander Error
- Ross Walker (Fri Jun 29 2007 - 20:42:50 PDT)
- Carlos Simmerling (Fri Jun 29 2007 - 19:04:29 PDT)
- Colby C (Fri Jun 29 2007 - 14:25:35 PDT)
- Ross Walker (Fri Jun 29 2007 - 09:28:44 PDT)
- Phineus Markwick (Fri Jun 29 2007 - 08:48:04 PDT)
- Phineus Markwick (Fri Jun 29 2007 - 08:45:18 PDT)
- Ross Walker (Fri Jun 29 2007 - 08:40:08 PDT)
- Colby C (Fri Jun 29 2007 - 07:47:05 PDT)
AMBER: SANDER error: 'angles are not correct'
- Fred Baba (Wed Jun 13 2007 - 14:47:14 PDT)
AMBER: sander MPI fails included tests
- Ross Walker (Thu Jun 28 2007 - 21:17:50 PDT)
- Sergio Wong (Thu Jun 28 2007 - 17:05:08 PDT)
- Ross Walker (Thu Jun 28 2007 - 14:06:19 PDT)
- Sergio Wong (Thu Jun 28 2007 - 12:14:02 PDT)
- Ross Walker (Tue Jun 26 2007 - 15:06:30 PDT)
- Sergio Wong (Tue Jun 26 2007 - 13:58:04 PDT)
- Ross Walker (Mon Jun 25 2007 - 19:08:22 PDT)
- Sergio Wong (Mon Jun 25 2007 - 12:06:21 PDT)
- Ross Walker (Mon Jun 25 2007 - 11:17:34 PDT)
- Sergio Wong (Mon Jun 25 2007 - 10:20:55 PDT)
AMBER: Saving a structuring from trajectory
- Bill Ross (Fri Jun 15 2007 - 13:43:23 PDT)
- Ilyas Yildirim (Fri Jun 15 2007 - 11:59:50 PDT)
- Seth Lilavivat (Fri Jun 15 2007 - 11:42:12 PDT)
AMBER: Serial "make" failure
- Francesco Pietra (Fri Jun 29 2007 - 13:59:42 PDT)
AMBER: Serial "make" failure with xleap
- Francesco Pietra (Fri Jun 29 2007 - 13:53:52 PDT)
- David A. Case (Fri Jun 29 2007 - 11:16:54 PDT)
- Francesco Pietra (Fri Jun 29 2007 - 10:17:39 PDT)
AMBER: set up system solution with 3 different components, each with multiple copies
- M. L. Dodson (Tue Jun 26 2007 - 08:27:41 PDT)
- Nicolas Lux Fawzi (Tue Jun 26 2007 - 08:16:54 PDT)
- David A. Case (Tue Jun 26 2007 - 08:08:50 PDT)
- Nicolas Lux Fawzi (Thu Jun 21 2007 - 08:56:57 PDT)
AMBER: shell model MD
- Stern, Julie (Mon Jun 18 2007 - 09:48:54 PDT)
- Carlos Simmerling (Mon Jun 18 2007 - 09:53:56 PDT)
AMBER: Should we just vary one parameter at a time only for PMF calculations?
- David A. Case (Fri Jun 08 2007 - 08:55:12 PDT)
- Catein Catherine (Thu Jun 07 2007 - 08:18:51 PDT)
AMBER: Simulated Annealing
- Carlos Simmerling (Tue Jun 26 2007 - 04:16:25 PDT)
- Hayden Eastwood (Tue Jun 26 2007 - 02:14:57 PDT)
- David A. Case (Mon Jun 25 2007 - 17:34:38 PDT)
- Joseph Maxwell (Mon Jun 25 2007 - 16:28:14 PDT)
AMBER: Solvent models
- FyD (Fri Jun 01 2007 - 01:14:20 PDT)
- Francesco Pietra (Fri Jun 01 2007 - 00:00:36 PDT)
AMBER: SPCFW water: angle problems in leap
- Ross Walker (Sat Jun 23 2007 - 09:47:25 PDT)
- Thomas Hofer (Sat Jun 23 2007 - 09:02:32 PDT)
AMBER: spring constant for restraint
- Catein Catherine (Thu Jun 14 2007 - 02:29:17 PDT)
AMBER: testing protein stability
- Sally Pias (Fri Jun 22 2007 - 14:57:27 PDT)
- Carlos Simmerling (Fri Jun 22 2007 - 04:06:16 PDT)
- Sally Pias (Thu Jun 21 2007 - 22:24:58 PDT)
AMBER: Trouble on wiki about GAFF
- David A. Case (Fri Jun 08 2007 - 09:11:17 PDT)
- j j (Fri Jun 08 2007 - 00:14:13 PDT)
- David A. Case (Thu Jun 07 2007 - 20:31:12 PDT)
- j j (Thu Jun 07 2007 - 16:29:37 PDT)
AMBER: umbrella sampling dihedral restraint question
- David A. Case (Sun Jun 17 2007 - 22:46:16 PDT)
- Cen Gao (Thu Jun 14 2007 - 13:33:51 PDT)
AMBER: Unexpected Failure in XLeap
- David A. Case (Tue Jun 26 2007 - 13:47:30 PDT)
- Jason Brown (Tue Jun 26 2007 - 11:45:14 PDT)
AMBER: unres
- Piotr Cieplak (Mon Jun 18 2007 - 17:00:47 PDT)
- Carra, Claudio (JSC-SK)[USRA] (Mon Jun 18 2007 - 13:55:20 PDT)
AMBER: Using position restraints during constant pressure equilibration
- priya priya (Tue Jun 12 2007 - 06:17:44 PDT)
AMBER: xleap on cygwin
- Colby C (Tue Jun 12 2007 - 17:42:52 PDT)
- Steven Winfield (Tue Jun 12 2007 - 09:45:09 PDT)
- Colby C (Tue Jun 12 2007 - 09:34:21 PDT)
- Wei Chen (Tue Jun 12 2007 - 06:06:45 PDT)
- Colby C (Mon Jun 11 2007 - 18:59:17 PDT)
ff02 and ff03 parameters
- Carlos Simmerling (Mon Jun 25 2007 - 16:28:02 PDT)
- Pavan G (Mon Jun 25 2007 - 12:34:30 PDT)
Fwd: joshua
- j j (Wed Jun 20 2007 - 06:01:00 PDT)
- j j (Wed Jun 20 2007 - 04:27:43 PDT)
Need your gudiance
- Ross Walker (Fri Jun 08 2007 - 14:24:47 PDT)
- Ross Walker (Fri Jun 08 2007 - 14:18:23 PDT)
process_mdout.perl
- Ross Walker (Fri Jun 01 2007 - 12:47:04 PDT)
SANDER error: 'angles are not correct'
- Fred Baba (Thu Jun 14 2007 - 10:08:47 PDT)
Strange shape in my MD simulations
- Ross Walker (Wed Jun 20 2007 - 08:27:37 PDT)
- gurpreet singh (Wed Jun 20 2007 - 00:58:03 PDT)
- Pavan G (Tue Jun 19 2007 - 11:37:18 PDT)
- Ross Walker (Tue Jun 19 2007 - 08:42:08 PDT)
- Pavan G (Tue Jun 19 2007 - 07:34:45 PDT)
- Adrian Roitberg (Tue Jun 19 2007 - 07:16:17 PDT)
- Pavan G (Tue Jun 19 2007 - 07:09:48 PDT)
- Adrian Roitberg (Tue Jun 19 2007 - 05:57:07 PDT)
- Pavan G (Tue Jun 19 2007 - 05:47:58 PDT)

Amber Archive Jun 2007 by subject