Amber Archive Aug 2008 by author
342 messages
:
Starting
Sun Aug 03 2008 - 06:07:39 PDT,
Ending
Wed Sep 03 2008 - 06:07:13 PDT
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Abdul Hameed, MohamedDiwanMo
AMBER: Silicon parameters
(Wed Aug 20 2008 - 09:15:56 PDT)
Adrian Roitberg
Re: AMBER: Is there a way to cluster frames of a trajectory?
(Wed Aug 27 2008 - 17:56:08 PDT)
Adrien Delmont
Re: AMBER: united atom force field
(Fri Aug 22 2008 - 12:17:10 PDT)
AMBER: united atom force field
(Fri Aug 22 2008 - 05:35:06 PDT)
Alan
Re: AMBER: to understand how frcmod.ff99SB works
(Fri Aug 29 2008 - 02:00:01 PDT)
Re: AMBER: to understand how frcmod.ff99SB works
(Thu Aug 28 2008 - 11:36:55 PDT)
AMBER: to understand how frcmod.ff99SB works
(Thu Aug 28 2008 - 03:29:18 PDT)
Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro
(Mon Aug 18 2008 - 02:34:03 PDT)
Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro
(Mon Aug 18 2008 - 00:42:35 PDT)
AMBER: value of Pi in Amber
(Fri Aug 08 2008 - 03:36:06 PDT)
Alessandro Nascimento
Re: AMBER: interaction energies
(Fri Aug 15 2008 - 09:18:05 PDT)
Re: AMBER: empty frcmod file but missing parameters
(Tue Aug 12 2008 - 15:02:01 PDT)
Alex Spasic
Re: AMBER: Problem with setting the NMR restraints
(Mon Aug 04 2008 - 12:35:20 PDT)
Re: AMBER: Problem with setting the NMR restraints
(Mon Aug 04 2008 - 09:58:17 PDT)
AMBER: Problem with setting the NMR restraints
(Mon Aug 04 2008 - 07:15:25 PDT)
Andreas Svrcek-Seiler
Re: AMBER: Error when compiling and testing AmberTools
(Fri Aug 22 2008 - 02:11:14 PDT)
RE: AMBER: NAB conjgrad returns error?
(Fri Aug 08 2008 - 08:48:28 PDT)
Re: AMBER: NAB conjgrad returns error?
(Thu Aug 07 2008 - 08:33:28 PDT)
aneesh cna
AMBER: RDF output file format
(Mon Aug 18 2008 - 02:48:45 PDT)
AMBER: problem with prep file generation
(Wed Aug 13 2008 - 05:05:58 PDT)
Anna Karawajczyk
AMBER: mol2, xleap, Segmentation fault
(Mon Aug 25 2008 - 06:01:31 PDT)
AMBER: bacteriochlorophyll ff
(Fri Aug 01 2008 - 03:04:44 PDT)
Arturas Ziemys
AMBER: wrapping w/ ptraj
(Fri Aug 29 2008 - 14:57:52 PDT)
AMBER: interaction energies
(Thu Aug 14 2008 - 08:21:34 PDT)
Re: AMBER: mm-pbsa / sander.MPI ?
(Thu Aug 14 2008 - 07:42:02 PDT)
AMBER: mm-pbsa / sander.MPI ?
(Wed Aug 13 2008 - 15:26:56 PDT)
AMBER: glycoprotein setup
(Tue Aug 12 2008 - 20:35:35 PDT)
Ben Roberts
AMBER: Error when compiling and testing AmberTools
(Thu Aug 21 2008 - 14:46:43 PDT)
Bertrand P. S. Russell
Re: AMBER: RDF output file format
(Mon Aug 18 2008 - 03:26:08 PDT)
Bill Ross
Re: AMBER: Source FIles of SANDER
(Tue Aug 26 2008 - 12:28:34 PDT)
Re: AMBER: Problems with sleap and amoeba
(Tue Aug 19 2008 - 16:51:18 PDT)
Brent Krueger
Re: AMBER: Trans proline
(Sat Aug 02 2008 - 20:47:16 PDT)
Carlos Simmerling
Re: AMBER: Critical patch for pmemd 10 extra points code
(Sun Aug 31 2008 - 06:54:33 PDT)
Re: AMBER: Is there a way to cluster frames of a trajectory?
(Wed Aug 27 2008 - 17:58:27 PDT)
Re: AMBER: Re: Dell 2 Quad Core System Performance
(Wed Aug 27 2008 - 15:15:42 PDT)
Re: AMBER: pmemd iwrap trouble
(Wed Aug 27 2008 - 06:26:54 PDT)
Re: AMBER: Querry
(Wed Aug 27 2008 - 06:20:55 PDT)
Re: AMBER: Source FIles of SANDER
(Tue Aug 26 2008 - 16:21:31 PDT)
Re: AMBER: molecular structure
(Tue Aug 26 2008 - 15:32:51 PDT)
Re: AMBER: Source FIles of SANDER
(Tue Aug 26 2008 - 12:20:40 PDT)
Re: AMBER: pmemd iwrap trouble
(Tue Aug 26 2008 - 09:57:28 PDT)
Re: AMBER: pmemd iwrap trouble
(Tue Aug 26 2008 - 07:26:53 PDT)
Re: AMBER: Querry
(Tue Aug 26 2008 - 07:09:25 PDT)
Re: AMBER: pmemd iwrap trouble
(Mon Aug 25 2008 - 09:35:53 PDT)
Re: AMBER: MOIL-View is for SGI. How do we analyze LES trajectories?
(Sat Aug 23 2008 - 05:39:16 PDT)
Re: AMBER: vdw 6-9 potential
(Sat Aug 23 2008 - 03:51:24 PDT)
Re: AMBER: vdw 6-9 potential
(Fri Aug 22 2008 - 14:02:48 PDT)
Re: AMBER: Error runing Addles
(Fri Aug 22 2008 - 05:48:07 PDT)
Re: AMBER: Force field equation
(Thu Aug 21 2008 - 05:21:55 PDT)
Re: AMBER: MOIL-View: is there a command line version?
(Wed Aug 20 2008 - 11:46:12 PDT)
Re: AMBER: Force field equation
(Wed Aug 20 2008 - 10:53:03 PDT)
Re: AMBER: NMR average structure
(Wed Aug 20 2008 - 10:50:28 PDT)
Re: AMBER: Questions about Locally enhanced sampling (LES) and Replica exchange
(Wed Aug 20 2008 - 10:47:12 PDT)
Re: AMBER: amber9 hangas after job submission
(Thu Aug 14 2008 - 03:45:14 PDT)
Re: AMBER: aggregation or cluster detection
(Thu Aug 07 2008 - 08:38:52 PDT)
Re: AMBER: problem with minimization
(Thu Aug 07 2008 - 08:29:10 PDT)
Re: AMBER: addles
(Tue Aug 05 2008 - 04:02:47 PDT)
Re: AMBER: Problem with setting the NMR restraints
(Mon Aug 04 2008 - 11:28:36 PDT)
Re: AMBER: Bonds getting shorter in sander
(Fri Aug 01 2008 - 06:18:36 PDT)
Carra, Claudio (JSC-SK)[USRA]
AMBER: MM-PBSA multiple trajectory problem
(Wed Aug 27 2008 - 07:16:38 PDT)
RE: AMBER: NAB conjgrad returns error?
(Mon Aug 11 2008 - 15:44:09 PDT)
RE: AMBER: NAB conjgrad returns error?
(Mon Aug 11 2008 - 14:14:12 PDT)
RE: AMBER: NAB conjgrad returns error?
(Thu Aug 07 2008 - 09:19:52 PDT)
AMBER: NAB conjgrad returns error?
(Thu Aug 07 2008 - 08:04:38 PDT)
Cenk \(Jenk\) Andac
Re: AMBER: installation amber on suse11.0
(Tue Aug 26 2008 - 07:40:30 PDT)
Re: AMBER: mol2, xleap, Segmentation fault
(Mon Aug 25 2008 - 07:38:28 PDT)
cgji
Re: AMBER: all & united atoms force field
(Thu Aug 21 2008 - 15:28:49 PDT)
AMBER: Is G_disp calculated in MM_PBSA now?
(Sat Aug 09 2008 - 05:51:55 PDT)
Charles Letner, Ph.D.
AMBER: AMBER under cygwin on 64 bit Vista
(Sun Aug 31 2008 - 14:30:08 PDT)
Chih-Ying Lin
AMBER: molecular structure
(Tue Aug 26 2008 - 15:24:29 PDT)
AMBER: pdb file ??
(Wed Aug 20 2008 - 23:21:47 PDT)
Re: AMBER: Force field equation
(Wed Aug 20 2008 - 22:16:42 PDT)
AMBER: Force field equation
(Wed Aug 20 2008 - 09:05:39 PDT)
Daniel Cappel
Re: AMBER: modified parmtop file from ptraj?
(Wed Aug 13 2008 - 06:37:19 PDT)
David A. Case
Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!!
(Fri Aug 22 2008 - 20:11:14 PDT)
Re: AMBER: trying ff99SP
(Wed Aug 20 2008 - 11:31:22 PDT)
Re: AMBER: Problem loading the leaprc.amoeba force field file in Amber 10.
(Wed Aug 20 2008 - 10:24:17 PDT)
Re: AMBER: impropers over bonds between sidechains
(Wed Aug 20 2008 - 10:14:03 PDT)
Re: AMBER: Proton Parameters
(Wed Aug 20 2008 - 10:12:02 PDT)
Re: AMBER: MD with NMR restraints
(Wed Aug 20 2008 - 10:07:15 PDT)
Re: AMBER: questions about previous posts
(Sat Aug 16 2008 - 08:00:38 PDT)
Re: AMBER: Using RDCs for structure refinement
(Tue Aug 12 2008 - 09:36:24 PDT)
Re: AMBER: NAB conjgrad returns error?
(Mon Aug 11 2008 - 14:40:49 PDT)
Re: AMBER: Compailation problum in Amber 10
(Fri Aug 08 2008 - 15:50:55 PDT)
Re: AMBER: NMR structure as initial structure
(Tue Aug 05 2008 - 17:09:25 PDT)
Re: AMBER: Set 251 is corrupted, ptraj error...
(Mon Aug 04 2008 - 08:31:28 PDT)
Re: AMBER: Problem with setting the NMR restraints
(Mon Aug 04 2008 - 08:26:51 PDT)
Re: AMBER: error in parallel amber 9 test
(Sun Aug 03 2008 - 21:28:45 PDT)
Re: AMBER: error in parallel amber 9 test
(Sat Aug 02 2008 - 18:37:10 PDT)
Re: AMBER: Compailation problum in Amber 10
(Fri Aug 01 2008 - 12:48:55 PDT)
David LeBard
Re: AMBER: Compile AMBER 9 on TACC Ranger super computer
(Thu Aug 14 2008 - 12:43:52 PDT)
David Witte
AMBER: Using RDCs for structure refinement
(Tue Aug 12 2008 - 00:52:53 PDT)
Deepangi Pandit
AMBER: Solvent Accesible Surface Area (SASA) - Confused
(Fri Aug 29 2008 - 11:45:19 PDT)
dipti lele
Re: AMBER: Querry
(Wed Aug 27 2008 - 06:33:45 PDT)
AMBER: querry
(Wed Aug 27 2008 - 02:07:52 PDT)
Re: AMBER: Querry
(Wed Aug 27 2008 - 02:00:46 PDT)
AMBER: Querry
(Tue Aug 26 2008 - 04:50:32 PDT)
AMBER: Glycoprotein once again..........
(Thu Aug 14 2008 - 05:10:10 PDT)
AMBER: Querry
(Wed Aug 13 2008 - 05:15:11 PDT)
AMBER: Querry about simulating a glycopeptide
(Tue Aug 12 2008 - 03:23:24 PDT)
AMBER: Need help with force field parameters for Lipopolysaccharide (LPS)
(Tue Aug 05 2008 - 03:03:10 PDT)
E.M.
Re: AMBER: Minimization methods
(Mon Aug 11 2008 - 05:22:25 PDT)
fatima.chami.durham.ac.uk
Re: AMBER: output file format in SANDER.MPI & PMEMD
(Thu Aug 28 2008 - 05:53:42 PDT)
AMBER: output file format in SANDER.MPI & PMEMD
(Thu Aug 28 2008 - 03:47:17 PDT)
Re: AMBER: vdw 6-9 potential
(Tue Aug 26 2008 - 09:03:55 PDT)
Re: AMBER: vdw 6-9 potential
(Sat Aug 23 2008 - 03:34:57 PDT)
AMBER: vdw 6-9 potential
(Fri Aug 22 2008 - 13:56:57 PDT)
Re: AMBER: all & united atoms force field
(Fri Aug 22 2008 - 13:46:11 PDT)
Re: AMBER: all & united atoms force field
(Fri Aug 22 2008 - 06:31:34 PDT)
AMBER: all & united atoms force field
(Thu Aug 21 2008 - 15:05:12 PDT)
AMBER: aggregation or cluster detection
(Thu Aug 07 2008 - 06:41:24 PDT)
Fiona McRobb
RE: [!!!] - Re: AMBER: GPCR membrane simulation, setting surface tension - Message is from an unknown sender
(Tue Aug 12 2008 - 22:09:49 PDT)
AMBER: GPCR membrane simulation, setting surface tension
(Mon Aug 11 2008 - 18:42:47 PDT)
Florian Haberl
Re: AMBER: modified parmtop file from ptraj?
(Wed Aug 13 2008 - 05:47:21 PDT)
Francesco Pietra
AMBER: Parameters for chloride ion in contact with a protein
(Mon Aug 25 2008 - 07:25:13 PDT)
AMBER: Biased MD with Amber 10
(Mon Aug 04 2008 - 11:35:31 PDT)
AMBER: PDB files in Amber10
(Sat Aug 02 2008 - 00:21:58 PDT)
FyD
Re: AMBER: xleap fails to savemol2
(Fri Aug 29 2008 - 23:58:21 PDT)
Re: AMBER: xleap fails to savemol2
(Fri Aug 29 2008 - 14:14:42 PDT)
Re: AMBER: Problem in calculation of resp charges using RED III
(Fri Aug 29 2008 - 08:19:23 PDT)
Re: AMBER: Problem in calculation of resp charges using RED III
(Fri Aug 29 2008 - 00:50:42 PDT)
Re: AMBER: xleap fails to savemol2
(Thu Aug 28 2008 - 21:58:08 PDT)
Geoff Wood
AMBER: amber 9 on Intel Harpertown
(Wed Aug 13 2008 - 02:45:36 PDT)
Gigil Toton
AMBER: net charge
(Tue Aug 26 2008 - 22:03:19 PDT)
AMBER: NMR average structure
(Wed Aug 20 2008 - 10:42:08 PDT)
AMBER: general question
(Tue Aug 12 2008 - 23:49:12 PDT)
Grange Hermitage
AMBER: RESP charges fitting for polarizable force fields
(Sat Aug 30 2008 - 21:48:37 PDT)
AMBER: new residues in AMOEBA
(Thu Aug 21 2008 - 00:14:59 PDT)
Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro
(Mon Aug 18 2008 - 17:30:25 PDT)
Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro
(Mon Aug 18 2008 - 02:01:38 PDT)
AMBER: trying ff99SP
(Sun Aug 17 2008 - 23:12:33 PDT)
Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro
(Sun Aug 17 2008 - 22:04:18 PDT)
Re: AMBER: Prepgen
(Sun Aug 17 2008 - 20:22:32 PDT)
AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro
(Sun Aug 17 2008 - 19:28:17 PDT)
Re: AMBER: Prepgen
(Thu Aug 14 2008 - 23:12:50 PDT)
Re: AMBER: impropers over bonds between sidechains
(Thu Aug 14 2008 - 20:08:49 PDT)
AMBER: impropers over bonds between sidechains
(Thu Aug 14 2008 - 18:12:05 PDT)
Re: AMBER: Prepgen
(Mon Aug 11 2008 - 00:10:00 PDT)
AMBER: respgen -a charge groups function ineffective unless
(Fri Aug 01 2008 - 22:00:29 PDT)
Re: AMBER: Prepgen
(Thu Jul 31 2008 - 20:21:54 PDT)
Re: AMBER: Prepgen
(Thu Jul 31 2008 - 19:29:45 PDT)
Hakkim Boy
AMBER: solvent interaction in active site
(Wed Aug 27 2008 - 19:41:24 PDT)
Hannes Wallnoefer
AMBER: modified parmtop file from ptraj?
(Wed Aug 13 2008 - 05:14:34 PDT)
AMBER: PBCAL in MM_PBSA
(Fri Aug 08 2008 - 07:19:30 PDT)
AMBER: MM_PBSA snapshot statistic calc problem
(Tue Aug 05 2008 - 05:45:48 PDT)
Henrik Öberg
AMBER: coordinate change of pdb structure using xleap
(Tue Aug 26 2008 - 23:26:42 PDT)
Ilyas Yildirim
RE: AMBER: to understand how frcmod.ff99SB works
(Thu Aug 28 2008 - 14:58:03 PDT)
AMBER: Re: Dell 2 Quad Core System Performance
(Wed Aug 27 2008 - 14:04:14 PDT)
AMBER: Dell 2 Quad Core System Performance
(Fri Aug 22 2008 - 18:16:49 PDT)
AMBER: Negative dihedral coefficients in amber99 - Possible?
(Sun Aug 17 2008 - 19:33:16 PDT)
In Hee Park
AMBER: IGB=10 in Amber10
(Tue Aug 19 2008 - 11:55:05 PDT)
IN SUK JOUNG
AMBER: NAB: getseq_from_pdb()
(Tue Aug 05 2008 - 17:00:21 PDT)
AMBER: divcon.rst ??
(Mon Aug 04 2008 - 17:06:43 PDT)
Jaber Jahanbin Sardroodi
AMBER: help me for filling a nanotube with water??
(Mon Aug 04 2008 - 18:39:05 PDT)
Re: AMBER: error in parallel amber 9 test
(Sun Aug 03 2008 - 01:15:19 PDT)
AMBER: error in parallel amber 9 test
(Sat Aug 02 2008 - 14:12:07 PDT)
Jacopo Sgrignani
AMBER: tan luo radii
(Tue Aug 26 2008 - 02:06:39 PDT)
Jeffrey
Re: Re: RE: AMBER: How to convert a CHARMM trajectory to AMBER format?
(Thu Aug 21 2008 - 00:11:55 PDT)
Re: RE: AMBER: How to convert a CHARMM trajectory to AMBER format?
(Tue Aug 19 2008 - 17:43:58 PDT)
AMBER: How to convert a CHARMM trajectory to AMBER format?
(Tue Aug 19 2008 - 04:30:35 PDT)
jialei
RE: AMBER: Compile AMBER 9 on TACC Ranger super computer
(Fri Aug 15 2008 - 09:38:38 PDT)
RE: AMBER: Compile AMBER 9 on TACC Ranger super computer
(Thu Aug 14 2008 - 17:15:39 PDT)
AMBER: Compile AMBER 9 on TACC Ranger super computer
(Wed Aug 13 2008 - 15:26:07 PDT)
Jianyin Shao
Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Sat Aug 02 2008 - 19:23:53 PDT)
Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Fri Aug 01 2008 - 12:43:14 PDT)
john smith
AMBER: compilation problem
(Sat Aug 30 2008 - 04:51:07 PDT)
Jose Borreguero
AMBER: conversion from crd to netcdf returns almost identical file!
(Thu Aug 28 2008 - 13:38:50 PDT)
Junmei Wang
Re: AMBER: respgen -a charge groups function ineffective unless
(Wed Aug 27 2008 - 13:55:47 PDT)
AMBER: latest update on residuegen
(Tue Aug 26 2008 - 06:55:09 PDT)
Re: AMBER: Silicon parameters
(Fri Aug 22 2008 - 13:29:05 PDT)
Re: AMBER: Prepgen
(Fri Aug 15 2008 - 06:52:27 PDT)
Re: AMBER: frcmod:attn needs revision
(Wed Aug 13 2008 - 12:34:50 PDT)
Re: AMBER: problem with prep file generation
(Wed Aug 13 2008 - 09:59:49 PDT)
Re: AMBER: frcmod:attn needs revision
(Wed Aug 13 2008 - 09:45:11 PDT)
Re: AMBER: Prepgen
(Tue Aug 12 2008 - 15:30:45 PDT)
Re: AMBER: Prepgen
(Tue Aug 05 2008 - 08:50:00 PDT)
khuram sb
AMBER: unsubscribe
(Mon Aug 18 2008 - 01:56:36 PDT)
Lachele Foley (Lists)
Re: AMBER: Glycoprotein once again..........
(Thu Aug 14 2008 - 06:28:30 PDT)
Re: AMBER: Querry
(Wed Aug 13 2008 - 08:03:49 PDT)
Re: AMBER: Querry about simulating a glycopeptide
(Tue Aug 12 2008 - 07:03:14 PDT)
Re: AMBER: aggregation or cluster detection
(Thu Aug 07 2008 - 08:44:07 PDT)
Fwd: AMBER: prepare an initial structure in Amber
(Fri Aug 01 2008 - 07:52:50 PDT)
Lars Skjærven
Re: AMBER: pmemd iwrap trouble
(Thu Aug 28 2008 - 03:38:02 PDT)
Re: AMBER: pmemd iwrap trouble
(Tue Aug 26 2008 - 11:36:06 PDT)
Re: AMBER: pmemd iwrap trouble
(Tue Aug 26 2008 - 09:23:31 PDT)
Re: AMBER: pmemd iwrap trouble
(Mon Aug 25 2008 - 15:03:14 PDT)
Re: AMBER: pmemd iwrap trouble
(Mon Aug 25 2008 - 07:58:01 PDT)
Re: AMBER: pmemd iwrap trouble
(Mon Aug 25 2008 - 06:32:26 PDT)
AMBER: pmemd iwrap trouble
(Mon Aug 25 2008 - 03:25:09 PDT)
luzhenw1.msu.edu
AMBER: generate topology file for alanine scanning (mmpbsa)
(Thu Aug 14 2008 - 12:32:56 PDT)
AMBER: problem with minimization
(Thu Aug 07 2008 - 08:13:17 PDT)
M. L. Dodson
AMBER: DFTB QMMM parameters ambiguity in AMBER10 docs
(Thu Aug 21 2008 - 10:56:38 PDT)
Re: AMBER: impropers over bonds between sidechains
(Thu Aug 14 2008 - 19:29:54 PDT)
Re: AMBER: Help compiling Nab programs for AMBER tools
(Thu Aug 14 2008 - 12:50:51 PDT)
Re: AMBER: Minimization methods
(Mon Aug 11 2008 - 08:34:05 PDT)
Maicon Sartin
Re: AMBER: Source FIles of SANDER
(Wed Aug 27 2008 - 05:47:47 PDT)
Re: AMBER: Source FIles of SANDER
(Tue Aug 26 2008 - 16:18:49 PDT)
AMBER: Source FIles of SANDER
(Tue Aug 26 2008 - 12:17:39 PDT)
Re: AMBER: installation amber on suse11.0
(Tue Aug 26 2008 - 07:52:01 PDT)
AMBER: SANDER Parallel
(Thu Aug 21 2008 - 05:36:56 PDT)
AMBER: Fwd: Welcome to amber
(Thu Aug 21 2008 - 05:33:08 PDT)
Markus Kaukonen
Re: AMBER: help me for filling a nanotube with water??
(Tue Aug 12 2008 - 23:29:48 PDT)
Matthew Tessier
RE: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS)
(Tue Aug 05 2008 - 08:07:22 PDT)
Melinda Layten
Re: AMBER: to understand how frcmod.ff99SB works
(Thu Aug 28 2008 - 07:55:40 PDT)
Miguel Ortiz-Lombardía
Re: AMBER: mm-pbsa / sander.MPI ?
(Thu Aug 14 2008 - 00:58:54 PDT)
moitrayee.mbu.iisc.ernet.in
Re: AMBER: Problem in calculation of resp charges using RED III
(Fri Aug 29 2008 - 04:41:21 PDT)
AMBER: Problem in calculation of resp charges using RED III
(Thu Aug 28 2008 - 23:56:24 PDT)
Re: AMBER: frcmod:attn needs revision
(Wed Aug 13 2008 - 21:51:50 PDT)
Re: AMBER: frcmod:attn needs revision
(Wed Aug 13 2008 - 09:55:40 PDT)
AMBER: frcmod:attn needs revision
(Tue Aug 12 2008 - 15:18:02 PDT)
Re: AMBER: empty frcmod file but missing parameters
(Tue Aug 12 2008 - 15:10:03 PDT)
AMBER: empty frcmod file but missing parameters
(Tue Aug 12 2008 - 14:20:19 PDT)
Naser Alijabbari
AMBER: questions about previous posts
(Mon Aug 11 2008 - 21:17:40 PDT)
Neil J. Henson
Re: AMBER: Problems with sleap and amoeba
(Tue Aug 19 2008 - 17:03:52 PDT)
AMBER: Problems with sleap and amoeba
(Tue Aug 19 2008 - 16:16:17 PDT)
NIEL MICHAEL HENRIKSEN
RE: AMBER: NAB conjgrad returns error?
(Mon Aug 11 2008 - 16:07:27 PDT)
RE: AMBER: NAB conjgrad returns error?
(Fri Aug 08 2008 - 12:31:13 PDT)
RE: AMBER: NAB conjgrad returns error?
(Fri Aug 08 2008 - 06:50:05 PDT)
Pablo Englebienne
Re: AMBER: Using Na+ ions as input to leap? - solved
(Wed Aug 20 2008 - 12:25:25 PDT)
AMBER: Using Na+ ions as input to leap?
(Wed Aug 20 2008 - 10:40:11 PDT)
Peter Gannett
AMBER: Bonds getting shorter in sander
(Fri Aug 01 2008 - 05:47:02 PDT)
Peterson, Matthew W.
AMBER: MM-PBSA Issue in Amber 10
(Tue Aug 12 2008 - 10:44:29 PDT)
Piyush Wanjari
Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!!
(Mon Aug 25 2008 - 15:00:33 PDT)
Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!!
(Mon Aug 25 2008 - 12:52:37 PDT)
AMBER: Vlimit Exceeded and inhomogeneous system !!!!!!
(Wed Aug 20 2008 - 21:36:20 PDT)
priya priya
AMBER: Membrane simulations
(Thu Aug 28 2008 - 01:31:57 PDT)
Ragnarok sdf
AMBER: Help compiling Nab programs for AMBER tools
(Thu Aug 14 2008 - 12:36:04 PDT)
Ranga Swamy
RE: AMBER: Compailation problum in Amber 10
(Fri Aug 08 2008 - 01:12:56 PDT)
Ray Luo
RE: AMBER: united atom force field
(Tue Aug 26 2008 - 16:11:47 PDT)
RE: AMBER: tan luo radii
(Tue Aug 26 2008 - 12:12:57 PDT)
Re: AMBER: all & united atoms force field
(Fri Aug 22 2008 - 10:44:16 PDT)
Re: AMBER: united atom force field
(Fri Aug 22 2008 - 10:37:38 PDT)
RE: AMBER: Is G_disp calculated in MM_PBSA now?
(Mon Aug 11 2008 - 12:33:14 PDT)
RE: AMBER: PBCAL in MM_PBSA
(Fri Aug 08 2008 - 11:27:17 PDT)
rebeca.mmb.pcb.ub.es
AMBER: minimization stops or does not write anything
(Thu Aug 14 2008 - 02:01:17 PDT)
AMBER: Not integral charge increasing with number of lipids
(Thu Aug 07 2008 - 03:18:01 PDT)
AMBER: Problems with the charge (membrane simulation)
(Wed Aug 06 2008 - 11:20:30 PDT)
Robert Duke
Re: AMBER: Critical patch for pmemd 10 extra points code
(Sun Aug 31 2008 - 09:48:56 PDT)
Re: AMBER: pmemd iwrap trouble
(Thu Aug 28 2008 - 15:05:05 PDT)
AMBER: Critical patch for pmemd 10 extra points code
(Thu Aug 28 2008 - 08:20:59 PDT)
Re: AMBER: output file format in SANDER.MPI & PMEMD
(Thu Aug 28 2008 - 05:34:44 PDT)
Re: AMBER: pmemd iwrap trouble
(Tue Aug 26 2008 - 20:17:29 PDT)
Re: AMBER: pmemd iwrap trouble
(Tue Aug 26 2008 - 12:49:18 PDT)
Re: AMBER: pmemd iwrap trouble
(Tue Aug 26 2008 - 09:59:34 PDT)
Re: AMBER: pmemd iwrap trouble
(Mon Aug 25 2008 - 21:38:40 PDT)
Re: AMBER: pmemd iwrap trouble
(Mon Aug 25 2008 - 21:22:44 PDT)
Re: AMBER: pmemd iwrap trouble
(Mon Aug 25 2008 - 20:38:13 PDT)
Re: AMBER: pmemd iwrap trouble
(Mon Aug 25 2008 - 08:45:03 PDT)
Re: AMBER: pmemd iwrap trouble
(Mon Aug 25 2008 - 05:40:03 PDT)
Re: AMBER: amber9 hangas after job submission
(Thu Aug 14 2008 - 05:54:43 PDT)
Re: AMBER: minimization stops or does not write anything
(Thu Aug 14 2008 - 05:39:01 PDT)
Ross Walker
RE: AMBER: vlimit exceeded
(Sat Aug 30 2008 - 11:41:02 PDT)
RE: AMBER: compilation problem
(Sat Aug 30 2008 - 11:33:13 PDT)
RE: AMBER: to understand how frcmod.ff99SB works
(Fri Aug 29 2008 - 08:17:27 PDT)
RE: AMBER: output file format in SANDER.MPI & PMEMD
(Thu Aug 28 2008 - 10:09:38 PDT)
RE: AMBER: to understand how frcmod.ff99SB works
(Thu Aug 28 2008 - 09:59:09 PDT)
AMBER: RE: Personal favor
(Thu Aug 28 2008 - 09:39:59 PDT)
RE: AMBER: Re: Dell 2 Quad Core System Performance
(Wed Aug 27 2008 - 16:01:59 PDT)
RE: AMBER: Source FIles of SANDER
(Tue Aug 26 2008 - 16:57:55 PDT)
RE: AMBER: installation amber on suse11.0
(Tue Aug 26 2008 - 07:39:31 PDT)
RE: AMBER: How to convert a CHARMM trajectory to AMBER format?
(Tue Aug 19 2008 - 07:26:25 PDT)
RE: AMBER: Initial structure from NMR structures
(Tue Aug 19 2008 - 07:05:43 PDT)
RE: AMBER: Negative dihedral coefficients in amber99 - Possible?
(Sun Aug 17 2008 - 22:15:45 PDT)
RE: AMBER: Compile AMBER 9 on TACC Ranger super computer
(Fri Aug 15 2008 - 10:36:36 PDT)
RE: AMBER: Compile AMBER 9 on TACC Ranger super computer
(Thu Aug 14 2008 - 17:38:30 PDT)
RE: AMBER: Compile AMBER 9 on TACC Ranger super computer
(Thu Aug 14 2008 - 09:00:02 PDT)
RE: AMBER: Compile AMBER 9 on TACC Ranger super computer
(Wed Aug 13 2008 - 20:39:47 PDT)
RE: AMBER: Querry
(Wed Aug 13 2008 - 07:48:19 PDT)
RE: AMBER: amber 9 on Intel Harpertown
(Wed Aug 13 2008 - 07:24:47 PDT)
RE: AMBER: questions about previous posts
(Mon Aug 11 2008 - 23:18:49 PDT)
RE: AMBER: Minimization methods
(Mon Aug 11 2008 - 07:43:47 PDT)
RE: AMBER: problem with minimization
(Thu Aug 07 2008 - 08:40:46 PDT)
RE: AMBER: aggregation or cluster detection
(Thu Aug 07 2008 - 08:29:28 PDT)
RE: AMBER: Not integral charge increasing with number of lipids
(Thu Aug 07 2008 - 08:24:28 PDT)
RE: AMBER: Problems with the charge (membrane simulation)
(Thu Aug 07 2008 - 08:18:12 PDT)
RE: AMBER: Compailation problum in Amber 10
(Wed Aug 06 2008 - 07:50:05 PDT)
Ruchi Sachdeva
AMBER: how to choose the appropriate ensemble for a given problem
(Wed Aug 13 2008 - 21:09:28 PDT)
Sally Pias
AMBER: MD with NMR restraints
(Wed Aug 13 2008 - 21:25:56 PDT)
Sampath Koppole
AMBER: Trouble installing Amber 9
(Wed Aug 20 2008 - 03:28:58 PDT)
Samuel Genheden (a03samge)
RE: AMBER: Bennett acceptance ratio with Amber10
(Tue Aug 26 2008 - 23:04:28 PDT)
AMBER: Bennett acceptance ratio with Amber10
(Tue Aug 26 2008 - 04:58:13 PDT)
Sasha Buzko
Re: AMBER: Is there a way to cluster frames of a trajectory?
(Wed Aug 27 2008 - 17:57:07 PDT)
AMBER: Is there a way to cluster frames of a trajectory?
(Wed Aug 27 2008 - 17:45:01 PDT)
Re: AMBER: MOIL-View is for SGI. How do we analyze LES trajectories?
(Sat Aug 23 2008 - 13:19:07 PDT)
AMBER: MOIL-View is for SGI. How do we analyze LES trajectories?
(Wed Aug 20 2008 - 15:42:01 PDT)
Re: AMBER: MOIL-View: is there a command line version?
(Wed Aug 20 2008 - 11:50:39 PDT)
AMBER: MOIL-View: is there a command line version?
(Wed Aug 20 2008 - 11:35:24 PDT)
AMBER: Simulating protein conformational changes?
(Fri Aug 01 2008 - 15:42:07 PDT)
saurabh agrawal
Re: AMBER: coordinate change of pdb structure using xleap
(Wed Aug 27 2008 - 00:23:09 PDT)
Scott Brozell
Re: AMBER: value of Pi in Amber
(Tue Aug 26 2008 - 15:07:49 PDT)
Re: AMBER: PDB files in Amber10
(Mon Aug 25 2008 - 14:32:16 PDT)
selami ercan
Re: AMBER: installation amber on suse11.0
(Wed Aug 27 2008 - 11:50:13 PDT)
AMBER: installation amber on suse11.0
(Tue Aug 26 2008 - 03:57:12 PDT)
shubhra srivastava
AMBER: constant ph (cpinutil file)
(Tue Aug 26 2008 - 23:46:36 PDT)
AMBER: constph
(Thu Aug 14 2008 - 04:54:57 PDT)
Shultz, Jack
AMBER: Error runing Addles
(Thu Aug 21 2008 - 20:25:17 PDT)
RE: AMBER: Amber compile
(Tue Aug 19 2008 - 12:25:56 PDT)
AMBER: Amber compile
(Tue Aug 19 2008 - 11:21:18 PDT)
AMBER: Compile Error
(Tue Aug 19 2008 - 08:44:25 PDT)
AMBER: Proton Parameters
(Thu Aug 14 2008 - 13:34:54 PDT)
Siddharth Rastogi
AMBER: Initial structure from NMR structures
(Mon Aug 18 2008 - 23:15:44 PDT)
AMBER: NMR structure as initial structure
(Mon Aug 04 2008 - 23:40:54 PDT)
srinivas sudani
AMBER: Compailation problum in Amber 10
(Wed Aug 06 2008 - 02:24:51 PDT)
Re: AMBER: Compailation problum in Amber 10
(Sun Aug 03 2008 - 22:41:13 PDT)
AMBER: Compailation problum in Amber 10
(Thu Jul 31 2008 - 23:59:00 PDT)
steinbrt.scripps.edu
RE: AMBER: Bennett acceptance ratio with Amber10
(Wed Aug 27 2008 - 09:28:13 PDT)
Re: AMBER: Bennett acceptance ratio with Amber10
(Tue Aug 26 2008 - 06:45:55 PDT)
Swarup Gupta
AMBER: Re: entropy of released water
(Thu Aug 07 2008 - 05:40:26 PDT)
AMBER: entropy of released water
(Thu Aug 07 2008 - 05:36:32 PDT)
taufik.alsarraj.utoronto.ca
Re: AMBER: xleap fails to savemol2
(Fri Aug 29 2008 - 14:28:52 PDT)
AMBER: join two units in amber9 or amber10
(Fri Aug 29 2008 - 14:17:58 PDT)
Re: AMBER: xleap fails to savemol2
(Fri Aug 29 2008 - 10:28:33 PDT)
AMBER: xleap fails to savemol2
(Thu Aug 28 2008 - 15:43:07 PDT)
teresa.ierano.unina.it
Re: AMBER: Minimization methods
(Mon Aug 11 2008 - 09:39:30 PDT)
RE: AMBER: Minimization methods
(Mon Aug 11 2008 - 09:30:50 PDT)
AMBER: Minimization methods
(Mon Aug 11 2008 - 05:11:23 PDT)
Thomas Cheatham
Re: AMBER: modified parmtop file from ptraj?
(Wed Aug 13 2008 - 10:43:24 PDT)
Thomas Cheatham III
Re: AMBER: pmemd iwrap trouble
(Thu Aug 28 2008 - 14:47:51 PDT)
Re: AMBER: pmemd iwrap trouble
(Tue Aug 26 2008 - 09:48:04 PDT)
Thomas Leonard
AMBER: PBCAL in MM_PBSA
(Mon Aug 11 2008 - 01:12:51 PDT)
AMBER: parameters
(Thu Aug 07 2008 - 22:45:09 PDT)
Thomas Steinbrecher
Re: AMBER: help me for filling a nanotube with water??
(Wed Aug 13 2008 - 09:40:22 PDT)
Titus, Jamie (bairdje)
AMBER: Gohlke in-house iRED Simulated Order Parameter Script
(Thu Aug 21 2008 - 05:53:09 PDT)
Urszula Uciechowska
AMBER: LES trajectories
(Mon Aug 25 2008 - 01:12:23 PDT)
AMBER: mmpbsa
(Mon Aug 11 2008 - 01:43:17 PDT)
AMBER: LES
(Fri Aug 08 2008 - 05:31:56 PDT)
AMBER: linear interaction energy
(Thu Aug 07 2008 - 06:55:18 PDT)
AMBER: addles
(Tue Aug 05 2008 - 01:30:20 PDT)
Vijay Manickam Achari
AMBER: amber9 hangas after job submission
(Wed Aug 13 2008 - 23:40:03 PDT)
Vlad Cojocaru
Re: AMBER: GPCR membrane simulation, setting surface tension
(Tue Aug 12 2008 - 01:45:08 PDT)
Wang,Ying
RE: AMBER: vlimit exceeded
(Sat Aug 30 2008 - 16:14:21 PDT)
AMBER: vlimit exceeded
(Sat Aug 30 2008 - 08:49:03 PDT)
Waqas Nasir
Re: AMBER: Set 251 is corrupted, ptraj error...
(Tue Aug 05 2008 - 04:23:47 PDT)
AMBER: Set 251 is corrupted, ptraj error...
(Mon Aug 04 2008 - 07:54:09 PDT)
Wei Huang
Re: AMBER: How to convert a CHARMM trajectory to AMBER format?
(Tue Aug 19 2008 - 07:02:22 PDT)
Wenyong Tong
Re: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS)
(Tue Aug 05 2008 - 12:32:31 PDT)
Re: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS)
(Tue Aug 05 2008 - 07:51:31 PDT)
xiaonan zhang
AMBER: Questions about Locally enhanced sampling (LES) and Replica exchange
(Wed Aug 20 2008 - 00:25:43 PDT)
Yong Duan
RE: AMBER: all & united atoms force field
(Fri Aug 22 2008 - 17:39:23 PDT)
Zhao, Zhen (zhaozh)
AMBER: Problem with the prmtop file generated by sleap and leaprc.amoeba in Amber 10.
(Mon Aug 25 2008 - 08:04:34 PDT)
AMBER: Problem loading the leaprc.amoeba force field file in Amber 10.
(Tue Aug 19 2008 - 13:20:00 PDT)
张勇
Re:AMBER: Compile AMBER 9 on TACC Ranger super computer
(Thu Aug 14 2008 - 06:32:30 PDT)
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Wed Sep 03 2008 - 06:07:13 PDT
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: Fri Nov 22 2024 - 05:53:41 PST
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