Amber Archive Aug 2008: by subject

AMBER: addles
- Carlos Simmerling (Tue Aug 05 2008 - 04:02:47 PDT)
- Urszula Uciechowska (Tue Aug 05 2008 - 01:30:20 PDT)
AMBER: aggregation or cluster detection
- Lachele Foley (Lists) (Thu Aug 07 2008 - 08:44:07 PDT)
- Carlos Simmerling (Thu Aug 07 2008 - 08:38:52 PDT)
- Ross Walker (Thu Aug 07 2008 - 08:29:28 PDT)
- fatima.chami.durham.ac.uk (Thu Aug 07 2008 - 06:41:24 PDT)
AMBER: all & united atoms force field
- Yong Duan (Fri Aug 22 2008 - 17:39:23 PDT)
- fatima.chami.durham.ac.uk (Fri Aug 22 2008 - 13:46:11 PDT)
- Ray Luo (Fri Aug 22 2008 - 10:44:16 PDT)
- fatima.chami.durham.ac.uk (Fri Aug 22 2008 - 06:31:34 PDT)
- cgji (Thu Aug 21 2008 - 15:28:49 PDT)
- fatima.chami.durham.ac.uk (Thu Aug 21 2008 - 15:05:12 PDT)
AMBER: amber 9 on Intel Harpertown
- Ross Walker (Wed Aug 13 2008 - 07:24:47 PDT)
- Geoff Wood (Wed Aug 13 2008 - 02:45:36 PDT)
AMBER: Amber compile
- Shultz, Jack (Tue Aug 19 2008 - 12:25:56 PDT)
- Shultz, Jack (Tue Aug 19 2008 - 11:21:18 PDT)
AMBER: AMBER under cygwin on 64 bit Vista
- Charles Letner, Ph.D. (Sun Aug 31 2008 - 14:30:08 PDT)
AMBER: amber9 hangas after job submission
- Robert Duke (Thu Aug 14 2008 - 05:54:43 PDT)
- Carlos Simmerling (Thu Aug 14 2008 - 03:45:14 PDT)
- Vijay Manickam Achari (Wed Aug 13 2008 - 23:40:03 PDT)
AMBER: bacteriochlorophyll ff
- Anna Karawajczyk (Fri Aug 01 2008 - 03:04:44 PDT)
AMBER: Bennett acceptance ratio with Amber10
- steinbrt.scripps.edu (Wed Aug 27 2008 - 09:28:13 PDT)
- Samuel Genheden (a03samge) (Tue Aug 26 2008 - 23:04:28 PDT)
- steinbrt.scripps.edu (Tue Aug 26 2008 - 06:45:55 PDT)
- Samuel Genheden (a03samge) (Tue Aug 26 2008 - 04:58:13 PDT)
AMBER: Biased MD with Amber 10
- Francesco Pietra (Mon Aug 04 2008 - 11:35:31 PDT)
AMBER: Bonds getting shorter in sander
- Carlos Simmerling (Fri Aug 01 2008 - 06:18:36 PDT)
- Peter Gannett (Fri Aug 01 2008 - 05:47:02 PDT)
AMBER: Compailation problum in Amber 10
- David A. Case (Fri Aug 08 2008 - 15:50:55 PDT)
- Ranga Swamy (Fri Aug 08 2008 - 01:12:56 PDT)
- Ross Walker (Wed Aug 06 2008 - 07:50:05 PDT)
- srinivas sudani (Wed Aug 06 2008 - 02:24:51 PDT)
- srinivas sudani (Sun Aug 03 2008 - 22:41:13 PDT)
- David A. Case (Fri Aug 01 2008 - 12:48:55 PDT)
- srinivas sudani (Thu Jul 31 2008 - 23:59:00 PDT)
AMBER: compilation problem
- Ross Walker (Sat Aug 30 2008 - 11:33:13 PDT)
- john smith (Sat Aug 30 2008 - 04:51:07 PDT)
AMBER: Compile AMBER 9 on TACC Ranger super computer
- Ross Walker (Fri Aug 15 2008 - 10:36:36 PDT)
- jialei (Fri Aug 15 2008 - 09:38:38 PDT)
- Ross Walker (Thu Aug 14 2008 - 17:38:30 PDT)
- jialei (Thu Aug 14 2008 - 17:15:39 PDT)
- David LeBard (Thu Aug 14 2008 - 12:43:52 PDT)
- Ross Walker (Thu Aug 14 2008 - 09:00:02 PDT)
- 张勇 (Thu Aug 14 2008 - 06:32:30 PDT)
- Ross Walker (Wed Aug 13 2008 - 20:39:47 PDT)
- jialei (Wed Aug 13 2008 - 15:26:07 PDT)
AMBER: Compile Error
- Shultz, Jack (Tue Aug 19 2008 - 08:44:25 PDT)
AMBER: constant ph (cpinutil file)
- shubhra srivastava (Tue Aug 26 2008 - 23:46:36 PDT)
AMBER: constph
- shubhra srivastava (Thu Aug 14 2008 - 04:54:57 PDT)
AMBER: conversion from crd to netcdf returns almost identical file!
- Jose Borreguero (Thu Aug 28 2008 - 13:38:50 PDT)
AMBER: coordinate change of pdb structure using xleap
- saurabh agrawal (Wed Aug 27 2008 - 00:23:09 PDT)
- Henrik Öberg (Tue Aug 26 2008 - 23:26:42 PDT)
AMBER: Critical patch for pmemd 10 extra points code
- Robert Duke (Sun Aug 31 2008 - 09:48:56 PDT)
- Carlos Simmerling (Sun Aug 31 2008 - 06:54:33 PDT)
- Robert Duke (Thu Aug 28 2008 - 08:20:59 PDT)
AMBER: Dell 2 Quad Core System Performance
- Ilyas Yildirim (Fri Aug 22 2008 - 18:16:49 PDT)
AMBER: DFTB QMMM parameters ambiguity in AMBER10 docs
- M. L. Dodson (Thu Aug 21 2008 - 10:56:38 PDT)
AMBER: divcon.rst ??
- IN SUK JOUNG (Mon Aug 04 2008 - 17:06:43 PDT)
AMBER: empty frcmod file but missing parameters
- moitrayee.mbu.iisc.ernet.in (Tue Aug 12 2008 - 15:10:03 PDT)
- Alessandro Nascimento (Tue Aug 12 2008 - 15:02:01 PDT)
- moitrayee.mbu.iisc.ernet.in (Tue Aug 12 2008 - 14:20:19 PDT)
AMBER: entropy of released water
- Swarup Gupta (Thu Aug 07 2008 - 05:36:32 PDT)
AMBER: error in parallel amber 9 test
- David A. Case (Sun Aug 03 2008 - 21:28:45 PDT)
- Jaber Jahanbin Sardroodi (Sun Aug 03 2008 - 01:15:19 PDT)
- David A. Case (Sat Aug 02 2008 - 18:37:10 PDT)
- Jaber Jahanbin Sardroodi (Sat Aug 02 2008 - 14:12:07 PDT)
AMBER: Error runing Addles
- Carlos Simmerling (Fri Aug 22 2008 - 05:48:07 PDT)
- Shultz, Jack (Thu Aug 21 2008 - 20:25:17 PDT)
AMBER: Error when compiling and testing AmberTools
- Andreas Svrcek-Seiler (Fri Aug 22 2008 - 02:11:14 PDT)
- Ben Roberts (Thu Aug 21 2008 - 14:46:43 PDT)
AMBER: Force field equation
- Carlos Simmerling (Thu Aug 21 2008 - 05:21:55 PDT)
- Chih-Ying Lin (Wed Aug 20 2008 - 22:16:42 PDT)
- Carlos Simmerling (Wed Aug 20 2008 - 10:53:03 PDT)
- Chih-Ying Lin (Wed Aug 20 2008 - 09:05:39 PDT)
AMBER: frcmod:attn needs revision
- moitrayee.mbu.iisc.ernet.in (Wed Aug 13 2008 - 21:51:50 PDT)
- Junmei Wang (Wed Aug 13 2008 - 12:34:50 PDT)
- moitrayee.mbu.iisc.ernet.in (Wed Aug 13 2008 - 09:55:40 PDT)
- Junmei Wang (Wed Aug 13 2008 - 09:45:11 PDT)
- moitrayee.mbu.iisc.ernet.in (Tue Aug 12 2008 - 15:18:02 PDT)
AMBER: Fwd: Welcome to amber
- Maicon Sartin (Thu Aug 21 2008 - 05:33:08 PDT)
AMBER: general question
- Gigil Toton (Tue Aug 12 2008 - 23:49:12 PDT)
AMBER: generate topology file for alanine scanning (mmpbsa)
- luzhenw1.msu.edu (Thu Aug 14 2008 - 12:32:56 PDT)
AMBER: Glycoprotein once again..........
- Lachele Foley (Lists) (Thu Aug 14 2008 - 06:28:30 PDT)
- dipti lele (Thu Aug 14 2008 - 05:10:10 PDT)
AMBER: glycoprotein setup
- Arturas Ziemys (Tue Aug 12 2008 - 20:35:35 PDT)
AMBER: Gohlke in-house iRED Simulated Order Parameter Script
- Titus, Jamie (bairdje) (Thu Aug 21 2008 - 05:53:09 PDT)
AMBER: GPCR membrane simulation, setting surface tension
- Vlad Cojocaru (Tue Aug 12 2008 - 01:45:08 PDT)
- Fiona McRobb (Mon Aug 11 2008 - 18:42:47 PDT)
AMBER: GPCR membrane simulation, setting surface tension - Message is from an unknown sender
- Fiona McRobb (Tue Aug 12 2008 - 22:09:49 PDT)
AMBER: Help compiling Nab programs for AMBER tools
- M. L. Dodson (Thu Aug 14 2008 - 12:50:51 PDT)
- Ragnarok sdf (Thu Aug 14 2008 - 12:36:04 PDT)
AMBER: help me for filling a nanotube with water??
- Thomas Steinbrecher (Wed Aug 13 2008 - 09:40:22 PDT)
- Markus Kaukonen (Tue Aug 12 2008 - 23:29:48 PDT)
- Jaber Jahanbin Sardroodi (Mon Aug 04 2008 - 18:39:05 PDT)
AMBER: how to choose the appropriate ensemble for a given problem
- Ruchi Sachdeva (Wed Aug 13 2008 - 21:09:28 PDT)
AMBER: How to convert a CHARMM trajectory to AMBER format?
- Jeffrey (Thu Aug 21 2008 - 00:11:55 PDT)
- Jeffrey (Tue Aug 19 2008 - 17:43:58 PDT)
- Ross Walker (Tue Aug 19 2008 - 07:26:25 PDT)
- Wei Huang (Tue Aug 19 2008 - 07:02:22 PDT)
- Jeffrey (Tue Aug 19 2008 - 04:30:35 PDT)
AMBER: IGB=10 in Amber10
- In Hee Park (Tue Aug 19 2008 - 11:55:05 PDT)
AMBER: impropers over bonds between sidechains
- David A. Case (Wed Aug 20 2008 - 10:14:03 PDT)
- Grange Hermitage (Thu Aug 14 2008 - 20:08:49 PDT)
- M. L. Dodson (Thu Aug 14 2008 - 19:29:54 PDT)
- Grange Hermitage (Thu Aug 14 2008 - 18:12:05 PDT)
AMBER: Initial structure from NMR structures
- Ross Walker (Tue Aug 19 2008 - 07:05:43 PDT)
- Siddharth Rastogi (Mon Aug 18 2008 - 23:15:44 PDT)
AMBER: installation amber on suse11.0
- selami ercan (Wed Aug 27 2008 - 11:50:13 PDT)
- Maicon Sartin (Tue Aug 26 2008 - 07:52:01 PDT)
- Ross Walker (Tue Aug 26 2008 - 07:39:31 PDT)
- Cenk \(Jenk\) Andac (Tue Aug 26 2008 - 07:40:30 PDT)
- selami ercan (Tue Aug 26 2008 - 03:57:12 PDT)
AMBER: interaction energies
- Alessandro Nascimento (Fri Aug 15 2008 - 09:18:05 PDT)
- Arturas Ziemys (Thu Aug 14 2008 - 08:21:34 PDT)
AMBER: Is G_disp calculated in MM_PBSA now?
- Ray Luo (Mon Aug 11 2008 - 12:33:14 PDT)
- cgji (Sat Aug 09 2008 - 05:51:55 PDT)
AMBER: Is there a way to cluster frames of a trajectory?
- Carlos Simmerling (Wed Aug 27 2008 - 17:58:27 PDT)
- Sasha Buzko (Wed Aug 27 2008 - 17:57:07 PDT)
- Adrian Roitberg (Wed Aug 27 2008 - 17:56:08 PDT)
- Sasha Buzko (Wed Aug 27 2008 - 17:45:01 PDT)
AMBER: join two units in amber9 or amber10
- taufik.alsarraj.utoronto.ca (Fri Aug 29 2008 - 14:17:58 PDT)
AMBER: latest update on residuegen
- Junmei Wang (Tue Aug 26 2008 - 06:55:09 PDT)
AMBER: LES
- Urszula Uciechowska (Fri Aug 08 2008 - 05:31:56 PDT)
AMBER: LES trajectories
- Urszula Uciechowska (Mon Aug 25 2008 - 01:12:23 PDT)
AMBER: linear interaction energy
- Urszula Uciechowska (Thu Aug 07 2008 - 06:55:18 PDT)
AMBER: MD with NMR restraints
- David A. Case (Wed Aug 20 2008 - 10:07:15 PDT)
- Sally Pias (Wed Aug 13 2008 - 21:25:56 PDT)
AMBER: Membrane simulations
- priya priya (Thu Aug 28 2008 - 01:31:57 PDT)
AMBER: Minimization methods
- teresa.ierano.unina.it (Mon Aug 11 2008 - 09:39:30 PDT)
- teresa.ierano.unina.it (Mon Aug 11 2008 - 09:30:50 PDT)
- M. L. Dodson (Mon Aug 11 2008 - 08:34:05 PDT)
- Ross Walker (Mon Aug 11 2008 - 07:43:47 PDT)
- E.M. (Mon Aug 11 2008 - 05:22:25 PDT)
- teresa.ierano.unina.it (Mon Aug 11 2008 - 05:11:23 PDT)
AMBER: minimization stops or does not write anything
- Robert Duke (Thu Aug 14 2008 - 05:39:01 PDT)
- rebeca.mmb.pcb.ub.es (Thu Aug 14 2008 - 02:01:17 PDT)
AMBER: mm-pbsa / sander.MPI ?
- Arturas Ziemys (Thu Aug 14 2008 - 07:42:02 PDT)
- Miguel Ortiz-Lombardía (Thu Aug 14 2008 - 00:58:54 PDT)
- Arturas Ziemys (Wed Aug 13 2008 - 15:26:56 PDT)
AMBER: MM-PBSA Issue in Amber 10
- Peterson, Matthew W. (Tue Aug 12 2008 - 10:44:29 PDT)
AMBER: MM-PBSA multiple trajectory problem
- Carra, Claudio (JSC-SK)[USRA] (Wed Aug 27 2008 - 07:16:38 PDT)
AMBER: MM_PBSA snapshot statistic calc problem
- Hannes Wallnoefer (Tue Aug 05 2008 - 05:45:48 PDT)
AMBER: mmpbsa
- Urszula Uciechowska (Mon Aug 11 2008 - 01:43:17 PDT)
AMBER: modified parmtop file from ptraj?
- Thomas Cheatham (Wed Aug 13 2008 - 10:43:24 PDT)
- Daniel Cappel (Wed Aug 13 2008 - 06:37:19 PDT)
- Florian Haberl (Wed Aug 13 2008 - 05:47:21 PDT)
- Hannes Wallnoefer (Wed Aug 13 2008 - 05:14:34 PDT)
AMBER: MOIL-View is for SGI. How do we analyze LES trajectories?
- Sasha Buzko (Sat Aug 23 2008 - 13:19:07 PDT)
- Carlos Simmerling (Sat Aug 23 2008 - 05:39:16 PDT)
- Sasha Buzko (Wed Aug 20 2008 - 15:42:01 PDT)
AMBER: MOIL-View: is there a command line version?
- Sasha Buzko (Wed Aug 20 2008 - 11:50:39 PDT)
- Carlos Simmerling (Wed Aug 20 2008 - 11:46:12 PDT)
- Sasha Buzko (Wed Aug 20 2008 - 11:35:24 PDT)
AMBER: mol2, xleap, Segmentation fault
- Cenk \(Jenk\) Andac (Mon Aug 25 2008 - 07:38:28 PDT)
- Anna Karawajczyk (Mon Aug 25 2008 - 06:01:31 PDT)
AMBER: molecular structure
- Carlos Simmerling (Tue Aug 26 2008 - 15:32:51 PDT)
- Chih-Ying Lin (Tue Aug 26 2008 - 15:24:29 PDT)
AMBER: NAB conjgrad returns error?
- NIEL MICHAEL HENRIKSEN (Mon Aug 11 2008 - 16:07:27 PDT)
- Carra, Claudio (JSC-SK)[USRA] (Mon Aug 11 2008 - 15:44:09 PDT)
- David A. Case (Mon Aug 11 2008 - 14:40:49 PDT)
- Carra, Claudio (JSC-SK)[USRA] (Mon Aug 11 2008 - 14:14:12 PDT)
- NIEL MICHAEL HENRIKSEN (Fri Aug 08 2008 - 12:31:13 PDT)
- Andreas Svrcek-Seiler (Fri Aug 08 2008 - 08:48:28 PDT)
- NIEL MICHAEL HENRIKSEN (Fri Aug 08 2008 - 06:50:05 PDT)
- Carra, Claudio (JSC-SK)[USRA] (Thu Aug 07 2008 - 09:19:52 PDT)
- Andreas Svrcek-Seiler (Thu Aug 07 2008 - 08:33:28 PDT)
- Carra, Claudio (JSC-SK)[USRA] (Thu Aug 07 2008 - 08:04:38 PDT)
AMBER: NAB: getseq_from_pdb()
- IN SUK JOUNG (Tue Aug 05 2008 - 17:00:21 PDT)
AMBER: Need help with force field parameters for Lipopolysaccharide (LPS)
- Wenyong Tong (Tue Aug 05 2008 - 12:32:31 PDT)
- Matthew Tessier (Tue Aug 05 2008 - 08:07:22 PDT)
- Wenyong Tong (Tue Aug 05 2008 - 07:51:31 PDT)
- dipti lele (Tue Aug 05 2008 - 03:03:10 PDT)
AMBER: Negative dihedral coefficients in amber99 - Possible?
- Ross Walker (Sun Aug 17 2008 - 22:15:45 PDT)
- Ilyas Yildirim (Sun Aug 17 2008 - 19:33:16 PDT)
AMBER: net charge
- Gigil Toton (Tue Aug 26 2008 - 22:03:19 PDT)
AMBER: new residues in AMOEBA
- Grange Hermitage (Thu Aug 21 2008 - 00:14:59 PDT)
AMBER: NMR average structure
- Carlos Simmerling (Wed Aug 20 2008 - 10:50:28 PDT)
- Gigil Toton (Wed Aug 20 2008 - 10:42:08 PDT)
AMBER: NMR structure as initial structure
- David A. Case (Tue Aug 05 2008 - 17:09:25 PDT)
- Siddharth Rastogi (Mon Aug 04 2008 - 23:40:54 PDT)
AMBER: Not integral charge increasing with number of lipids
- Ross Walker (Thu Aug 07 2008 - 08:24:28 PDT)
- rebeca.mmb.pcb.ub.es (Thu Aug 07 2008 - 03:18:01 PDT)
AMBER: output file format in SANDER.MPI & PMEMD
- Ross Walker (Thu Aug 28 2008 - 10:09:38 PDT)
- fatima.chami.durham.ac.uk (Thu Aug 28 2008 - 05:53:42 PDT)
- Robert Duke (Thu Aug 28 2008 - 05:34:44 PDT)
- fatima.chami.durham.ac.uk (Thu Aug 28 2008 - 03:47:17 PDT)
AMBER: parameters
- Thomas Leonard (Thu Aug 07 2008 - 22:45:09 PDT)
AMBER: Parameters for chloride ion in contact with a protein
- Francesco Pietra (Mon Aug 25 2008 - 07:25:13 PDT)
AMBER: PBCAL in MM_PBSA
- Thomas Leonard (Mon Aug 11 2008 - 01:12:51 PDT)
- Ray Luo (Fri Aug 08 2008 - 11:27:17 PDT)
- Hannes Wallnoefer (Fri Aug 08 2008 - 07:19:30 PDT)
AMBER: pdb file ??
- Chih-Ying Lin (Wed Aug 20 2008 - 23:21:47 PDT)
AMBER: PDB files in Amber10
- Scott Brozell (Mon Aug 25 2008 - 14:32:16 PDT)
- Francesco Pietra (Sat Aug 02 2008 - 00:21:58 PDT)
AMBER: pmemd iwrap trouble
- Robert Duke (Thu Aug 28 2008 - 15:05:05 PDT)
- Thomas Cheatham III (Thu Aug 28 2008 - 14:47:51 PDT)
- Lars Skjærven (Thu Aug 28 2008 - 03:38:02 PDT)
- Carlos Simmerling (Wed Aug 27 2008 - 06:26:54 PDT)
- Robert Duke (Tue Aug 26 2008 - 20:17:29 PDT)
- Robert Duke (Tue Aug 26 2008 - 12:49:18 PDT)
- Lars Skjærven (Tue Aug 26 2008 - 11:36:06 PDT)
- Robert Duke (Tue Aug 26 2008 - 09:59:34 PDT)
- Carlos Simmerling (Tue Aug 26 2008 - 09:57:28 PDT)
- Thomas Cheatham III (Tue Aug 26 2008 - 09:48:04 PDT)
- Lars Skjærven (Tue Aug 26 2008 - 09:23:31 PDT)
- Carlos Simmerling (Tue Aug 26 2008 - 07:26:53 PDT)
- Robert Duke (Mon Aug 25 2008 - 21:38:40 PDT)
- Robert Duke (Mon Aug 25 2008 - 21:22:44 PDT)
- Robert Duke (Mon Aug 25 2008 - 20:38:13 PDT)
- Lars Skjærven (Mon Aug 25 2008 - 15:03:14 PDT)
- Carlos Simmerling (Mon Aug 25 2008 - 09:35:53 PDT)
- Robert Duke (Mon Aug 25 2008 - 08:45:03 PDT)
- Lars Skjærven (Mon Aug 25 2008 - 07:58:01 PDT)
- Lars Skjærven (Mon Aug 25 2008 - 06:32:26 PDT)
- Robert Duke (Mon Aug 25 2008 - 05:40:03 PDT)
- Lars Skjærven (Mon Aug 25 2008 - 03:25:09 PDT)
AMBER: Prepgen
- Grange Hermitage (Sun Aug 17 2008 - 20:22:32 PDT)
- Junmei Wang (Fri Aug 15 2008 - 06:52:27 PDT)
- Grange Hermitage (Thu Aug 14 2008 - 23:12:50 PDT)
- Junmei Wang (Tue Aug 12 2008 - 15:30:45 PDT)
- Grange Hermitage (Mon Aug 11 2008 - 00:10:00 PDT)
- Junmei Wang (Tue Aug 05 2008 - 08:50:00 PDT)
- Grange Hermitage (Thu Jul 31 2008 - 20:21:54 PDT)
- Grange Hermitage (Thu Jul 31 2008 - 19:29:45 PDT)
AMBER: Problem in calculation of resp charges using RED III
- FyD (Fri Aug 29 2008 - 08:19:23 PDT)
- moitrayee.mbu.iisc.ernet.in (Fri Aug 29 2008 - 04:41:21 PDT)
- FyD (Fri Aug 29 2008 - 00:50:42 PDT)
- moitrayee.mbu.iisc.ernet.in (Thu Aug 28 2008 - 23:56:24 PDT)
AMBER: Problem loading the leaprc.amoeba force field file in Amber 10.
- David A. Case (Wed Aug 20 2008 - 10:24:17 PDT)
- Zhao, Zhen (zhaozh) (Tue Aug 19 2008 - 13:20:00 PDT)
AMBER: problem with minimization
- Ross Walker (Thu Aug 07 2008 - 08:40:46 PDT)
- Carlos Simmerling (Thu Aug 07 2008 - 08:29:10 PDT)
- luzhenw1.msu.edu (Thu Aug 07 2008 - 08:13:17 PDT)
AMBER: problem with prep file generation
- Junmei Wang (Wed Aug 13 2008 - 09:59:49 PDT)
- aneesh cna (Wed Aug 13 2008 - 05:05:58 PDT)
AMBER: Problem with setting the NMR restraints
- Alex Spasic (Mon Aug 04 2008 - 12:35:20 PDT)
- Carlos Simmerling (Mon Aug 04 2008 - 11:28:36 PDT)
- Alex Spasic (Mon Aug 04 2008 - 09:58:17 PDT)
- David A. Case (Mon Aug 04 2008 - 08:26:51 PDT)
- Alex Spasic (Mon Aug 04 2008 - 07:15:25 PDT)
AMBER: Problem with the prmtop file generated by sleap and leaprc.amoeba in Amber 10.
- Zhao, Zhen (zhaozh) (Mon Aug 25 2008 - 08:04:34 PDT)
AMBER: Problems with sleap and amoeba
- Neil J. Henson (Tue Aug 19 2008 - 17:03:52 PDT)
- Bill Ross (Tue Aug 19 2008 - 16:51:18 PDT)
- Neil J. Henson (Tue Aug 19 2008 - 16:16:17 PDT)
AMBER: Problems with the charge (membrane simulation)
- Ross Walker (Thu Aug 07 2008 - 08:18:12 PDT)
- rebeca.mmb.pcb.ub.es (Wed Aug 06 2008 - 11:20:30 PDT)
AMBER: Proton Parameters
- David A. Case (Wed Aug 20 2008 - 10:12:02 PDT)
- Shultz, Jack (Thu Aug 14 2008 - 13:34:54 PDT)
AMBER: Querry
- dipti lele (Wed Aug 27 2008 - 06:33:45 PDT)
- Carlos Simmerling (Wed Aug 27 2008 - 06:20:55 PDT)
- dipti lele (Wed Aug 27 2008 - 02:07:52 PDT)
- dipti lele (Wed Aug 27 2008 - 02:00:46 PDT)
- dipti lele (Tue Aug 26 2008 - 04:50:32 PDT)
- Carlos Simmerling (Tue Aug 26 2008 - 07:09:25 PDT)
- Lachele Foley (Lists) (Wed Aug 13 2008 - 08:03:49 PDT)
- Ross Walker (Wed Aug 13 2008 - 07:48:19 PDT)
- dipti lele (Wed Aug 13 2008 - 05:15:11 PDT)
AMBER: Querry about simulating a glycopeptide
- Lachele Foley (Lists) (Tue Aug 12 2008 - 07:03:14 PDT)
- dipti lele (Tue Aug 12 2008 - 03:23:24 PDT)
AMBER: Questions about Locally enhanced sampling (LES) and Replica exchange
- Carlos Simmerling (Wed Aug 20 2008 - 10:47:12 PDT)
- xiaonan zhang (Wed Aug 20 2008 - 00:25:43 PDT)
AMBER: questions about previous posts
- David A. Case (Sat Aug 16 2008 - 08:00:38 PDT)
- Ross Walker (Mon Aug 11 2008 - 23:18:49 PDT)
- Naser Alijabbari (Mon Aug 11 2008 - 21:17:40 PDT)
AMBER: RDF output file format
- Bertrand P. S. Russell (Mon Aug 18 2008 - 03:26:08 PDT)
- aneesh cna (Mon Aug 18 2008 - 02:48:45 PDT)
AMBER: RESP charges fitting for polarizable force fields
- Grange Hermitage (Sat Aug 30 2008 - 21:48:37 PDT)
AMBER: respgen -a charge groups function ineffective unless
- Junmei Wang (Wed Aug 27 2008 - 13:55:47 PDT)
- Grange Hermitage (Fri Aug 01 2008 - 22:00:29 PDT)
AMBER: SANDER Parallel
- Maicon Sartin (Thu Aug 21 2008 - 05:36:56 PDT)
AMBER: Set 251 is corrupted, ptraj error...
- Waqas Nasir (Tue Aug 05 2008 - 04:23:47 PDT)
- David A. Case (Mon Aug 04 2008 - 08:31:28 PDT)
- Waqas Nasir (Mon Aug 04 2008 - 07:54:09 PDT)
AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
- Jianyin Shao (Sat Aug 02 2008 - 19:23:53 PDT)
- Jianyin Shao (Fri Aug 01 2008 - 12:43:14 PDT)
AMBER: Silicon parameters
- Junmei Wang (Fri Aug 22 2008 - 13:29:05 PDT)
- Abdul Hameed, MohamedDiwanMo (Wed Aug 20 2008 - 09:15:56 PDT)
AMBER: Simulating protein conformational changes?
- Sasha Buzko (Fri Aug 01 2008 - 15:42:07 PDT)
AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro
- Grange Hermitage (Mon Aug 18 2008 - 17:30:25 PDT)
- Alan (Mon Aug 18 2008 - 02:34:03 PDT)
- Grange Hermitage (Mon Aug 18 2008 - 02:01:38 PDT)
- Alan (Mon Aug 18 2008 - 00:42:35 PDT)
- Grange Hermitage (Sun Aug 17 2008 - 22:04:18 PDT)
- Grange Hermitage (Sun Aug 17 2008 - 19:28:17 PDT)
AMBER: Solvent Accesible Surface Area (SASA) - Confused
- Deepangi Pandit (Fri Aug 29 2008 - 11:45:19 PDT)
AMBER: solvent interaction in active site
- Hakkim Boy (Wed Aug 27 2008 - 19:41:24 PDT)
AMBER: Source FIles of SANDER
- Maicon Sartin (Wed Aug 27 2008 - 05:47:47 PDT)
- Ross Walker (Tue Aug 26 2008 - 16:57:55 PDT)
- Carlos Simmerling (Tue Aug 26 2008 - 16:21:31 PDT)
- Maicon Sartin (Tue Aug 26 2008 - 16:18:49 PDT)
- Bill Ross (Tue Aug 26 2008 - 12:28:34 PDT)
- Carlos Simmerling (Tue Aug 26 2008 - 12:20:40 PDT)
- Maicon Sartin (Tue Aug 26 2008 - 12:17:39 PDT)
AMBER: tan luo radii
- Ray Luo (Tue Aug 26 2008 - 12:12:57 PDT)
- Jacopo Sgrignani (Tue Aug 26 2008 - 02:06:39 PDT)
AMBER: to understand how frcmod.ff99SB works
- Ross Walker (Fri Aug 29 2008 - 08:17:27 PDT)
- Alan (Fri Aug 29 2008 - 02:00:01 PDT)
- Ilyas Yildirim (Thu Aug 28 2008 - 14:58:03 PDT)
- Alan (Thu Aug 28 2008 - 11:36:55 PDT)
- Ross Walker (Thu Aug 28 2008 - 09:59:09 PDT)
- Melinda Layten (Thu Aug 28 2008 - 07:55:40 PDT)
- Alan (Thu Aug 28 2008 - 03:29:18 PDT)
AMBER: Trans proline
- Brent Krueger (Sat Aug 02 2008 - 20:47:16 PDT)
AMBER: Trouble installing Amber 9
- Sampath Koppole (Wed Aug 20 2008 - 03:28:58 PDT)
AMBER: trying ff99SP
- David A. Case (Wed Aug 20 2008 - 11:31:22 PDT)
- Grange Hermitage (Sun Aug 17 2008 - 23:12:33 PDT)
AMBER: united atom force field
- Ray Luo (Tue Aug 26 2008 - 16:11:47 PDT)
- Adrien Delmont (Fri Aug 22 2008 - 12:17:10 PDT)
- Ray Luo (Fri Aug 22 2008 - 10:37:38 PDT)
- Adrien Delmont (Fri Aug 22 2008 - 05:35:06 PDT)
AMBER: unsubscribe
- khuram sb (Mon Aug 18 2008 - 01:56:36 PDT)
AMBER: Using Na+ ions as input to leap?
- Pablo Englebienne (Wed Aug 20 2008 - 10:40:11 PDT)
AMBER: Using Na+ ions as input to leap? - solved
- Pablo Englebienne (Wed Aug 20 2008 - 12:25:25 PDT)
AMBER: Using RDCs for structure refinement
- David A. Case (Tue Aug 12 2008 - 09:36:24 PDT)
- David Witte (Tue Aug 12 2008 - 00:52:53 PDT)
AMBER: value of Pi in Amber
- Scott Brozell (Tue Aug 26 2008 - 15:07:49 PDT)
- Alan (Fri Aug 08 2008 - 03:36:06 PDT)
AMBER: vdw 6-9 potential
- fatima.chami.durham.ac.uk (Tue Aug 26 2008 - 09:03:55 PDT)
- Carlos Simmerling (Sat Aug 23 2008 - 03:51:24 PDT)
- fatima.chami.durham.ac.uk (Sat Aug 23 2008 - 03:34:57 PDT)
- Carlos Simmerling (Fri Aug 22 2008 - 14:02:48 PDT)
- fatima.chami.durham.ac.uk (Fri Aug 22 2008 - 13:56:57 PDT)
AMBER: vlimit exceeded
- Wang,Ying (Sat Aug 30 2008 - 16:14:21 PDT)
- Ross Walker (Sat Aug 30 2008 - 11:41:02 PDT)
- Wang,Ying (Sat Aug 30 2008 - 08:49:03 PDT)
AMBER: Vlimit Exceeded and inhomogeneous system !!!!!!
- Piyush Wanjari (Mon Aug 25 2008 - 15:00:33 PDT)
- Piyush Wanjari (Mon Aug 25 2008 - 12:52:37 PDT)
- David A. Case (Fri Aug 22 2008 - 20:11:14 PDT)
- Piyush Wanjari (Wed Aug 20 2008 - 21:36:20 PDT)
AMBER: wrapping w/ ptraj
- Arturas Ziemys (Fri Aug 29 2008 - 14:57:52 PDT)
AMBER: xleap fails to savemol2
- FyD (Fri Aug 29 2008 - 23:58:21 PDT)
- taufik.alsarraj.utoronto.ca (Fri Aug 29 2008 - 14:28:52 PDT)
- FyD (Fri Aug 29 2008 - 14:14:42 PDT)
- taufik.alsarraj.utoronto.ca (Fri Aug 29 2008 - 10:28:33 PDT)
- FyD (Thu Aug 28 2008 - 21:58:08 PDT)
- taufik.alsarraj.utoronto.ca (Thu Aug 28 2008 - 15:43:07 PDT)
Dell 2 Quad Core System Performance
- Ross Walker (Wed Aug 27 2008 - 16:01:59 PDT)
- Carlos Simmerling (Wed Aug 27 2008 - 15:15:42 PDT)
- Ilyas Yildirim (Wed Aug 27 2008 - 14:04:14 PDT)
entropy of released water
- Swarup Gupta (Thu Aug 07 2008 - 05:40:26 PDT)
Fwd: AMBER: prepare an initial structure in Amber
- Lachele Foley (Lists) (Fri Aug 01 2008 - 07:52:50 PDT)
Personal favor
- Ross Walker (Thu Aug 28 2008 - 09:39:59 PDT)

Amber Archive Aug 2008 by subject