Amber Archive Feb 2004 by thread
356 messages
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Starting
Mon Feb 02 2004 - 14:53:00 PST,
Ending
Mon Mar 01 2004 - 22:53:00 PST
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AMBER: DNA
Beale, John
(Mon Feb 02 2004 - 05:31:51 PST)
Re: AMBER: DNA
David A. Case
(Mon Feb 02 2004 - 08:58:26 PST)
AMBER: convert restart to mdcrd?
Karin Schleinkofer
(Mon Feb 02 2004 - 06:39:40 PST)
Re: AMBER: convert restart to mdcrd?
Dr. Yong Duan
(Mon Feb 02 2004 - 08:48:55 PST)
Re: AMBER: convert restart to mdcrd?
Vlad Cojocaru
(Mon Feb 02 2004 - 08:07:12 PST)
Re: AMBER: convert restart to mdcrd?
Vlad Cojocaru
(Mon Feb 02 2004 - 08:07:49 PST)
Re: AMBER: convert restart to mdcrd?
Dr. Yong Duan
(Mon Feb 02 2004 - 09:27:41 PST)
Re: AMBER: convert restart to mdcrd?
Vlad Cojocaru
(Mon Feb 02 2004 - 07:33:35 PST)
Re: AMBER: convert restart to mdcrd?
Teletchéa Stéphane
(Mon Feb 02 2004 - 08:17:30 PST)
AMBER: ptraj & LES
Vlad Cojocaru
(Mon Feb 02 2004 - 08:46:08 PST)
Re: AMBER: ptraj & LES
Michael Trieb
(Mon Feb 02 2004 - 09:11:08 PST)
Re: AMBER: ptraj & LES
Vlad Cojocaru
(Mon Feb 02 2004 - 09:22:09 PST)
AMBER: LEaP- Error reading frcmod parameters.
Miguel de Federico
(Mon Feb 02 2004 - 10:03:00 PST)
Re: AMBER: LEaP- Error reading frcmod parameters.
David A. Case
(Mon Feb 02 2004 - 10:20:43 PST)
Re: AMBER: NVE&polarizable force field
Martina Roeselova
(Mon Feb 02 2004 - 09:33:17 PST)
AMBER: cell dimensions
Dave S Walker
(Mon Feb 02 2004 - 13:46:54 PST)
Re: AMBER: cell dimensions
David A. Case
(Thu Feb 05 2004 - 10:00:41 PST)
Re: AMBER: NVE&polarizable force field
Byungchan Kim
(Tue Feb 03 2004 - 09:54:55 PST)
Re: AMBER: ANAL problem.
David A. Case
(Mon Feb 02 2004 - 10:51:02 PST)
AMBER: TI, angle parameters for nitrogen, frcmod
Carsten Detering
(Mon Feb 02 2004 - 12:38:59 PST)
Re: AMBER: TI, angle parameters for nitrogen, frcmod
David A. Case
(Thu Feb 05 2004 - 09:51:39 PST)
AMBER: nucleic acid bases nonplanar during LES sim
Vlad Cojocaru
(Mon Feb 02 2004 - 13:17:09 PST)
Re: AMBER: nucleic acid bases nonplanar during LES sim
Carlos Simmerling
(Mon Feb 02 2004 - 13:56:00 PST)
AMBER: temperature in DelPhi for MM-PBSA calculation
Qing Zhang
(Mon Feb 02 2004 - 14:54:05 PST)
RE: AMBER: temperature in DelPhi for MM-PBSA calculation
S. Frank Yan
(Mon Feb 02 2004 - 15:18:22 PST)
RE: AMBER: temperature in DelPhi for MM-PBSA calculation
Qing Zhang
(Mon Feb 02 2004 - 16:58:54 PST)
Re: AMBER: temperature in DelPhi for MM-PBSA calculation
rluo.uci.edu
(Mon Feb 02 2004 - 18:45:52 PST)
AMBER: leap - orientation of sequenced residues
Sarah Wittkopp
(Mon Feb 02 2004 - 17:58:33 PST)
Re: AMBER: leap - orientation of sequenced residues
David A. Case
(Tue Feb 03 2004 - 09:44:50 PST)
AMBER: Installing Amber on IBM AIX cluster
Wayne Dawson
(Mon Feb 02 2004 - 22:11:49 PST)
AMBER: xleap & antechamber
L Jin
(Tue Feb 03 2004 - 01:46:54 PST)
Re: AMBER: xleap & antechamber
David A. Case
(Thu Feb 05 2004 - 09:46:02 PST)
AMBER: protonation
Nikolai Smolin
(Tue Feb 03 2004 - 01:50:23 PST)
AMBER: the uses for Amber FFs
a b
(Tue Feb 03 2004 - 06:48:24 PST)
Re: AMBER: the uses for Amber FFs
Vlad Cojocaru
(Tue Feb 03 2004 - 06:56:26 PST)
AMBER: What does this error message mean?
nie beining
(Tue Feb 03 2004 - 07:58:41 PST)
Re: AMBER: What does this error message mean?
David A. Case
(Tue Feb 03 2004 - 08:12:48 PST)
Re: AMBER: What does this error message mean?
Carlos Simmerling
(Tue Feb 03 2004 - 08:30:56 PST)
Re: AMBER: What does this error message mean?
Martina Roeselova
(Tue Feb 03 2004 - 11:55:22 PST)
AMBER: Carnal
Herbert Georg
(Tue Feb 03 2004 - 08:11:28 PST)
Re: AMBER: Carnal
Bill Ross
(Tue Feb 03 2004 - 10:14:02 PST)
Re: AMBER: Carnal
Herbert Georg
(Tue Feb 03 2004 - 11:30:33 PST)
AMBER: Amber on Redhat Enterprise
Mingfeng Yang
(Tue Feb 03 2004 - 10:23:44 PST)
Re: AMBER: What does this error message mean?
Bill Ross
(Tue Feb 03 2004 - 10:40:15 PST)
AMBER: A general question
aini.UMDNJ.EDU
(Tue Feb 03 2004 - 15:49:06 PST)
Re: AMBER: A general question
Carlos Simmerling
(Tue Feb 03 2004 - 16:13:09 PST)
Re: AMBER: A general question
aini.UMDNJ.EDU
(Tue Feb 03 2004 - 17:39:44 PST)
Re: AMBER: questions parm94/99 ff secondary structure
Wayne Dawson
(Thu Feb 05 2004 - 23:50:07 PST)
Re: AMBER: questions parm94/99 ff secondary structure
Carlos Simmerling
(Fri Feb 06 2004 - 04:58:45 PST)
AMBER: NMODE for protein via MM-PBSA-cntd
ML
(Wed Feb 04 2004 - 08:09:57 PST)
Re: AMBER: NMODE for protein via MM-PBSA-cntd
David A. Case
(Wed Feb 04 2004 - 08:32:37 PST)
Re: AMBER: NMODE for protein via MM-PBSA-cntd
ML
(Wed Feb 04 2004 - 09:18:12 PST)
AMBER: rstdip
Martina Roeselova
(Wed Feb 04 2004 - 09:57:18 PST)
Re: AMBER: rstdip
Scott Brozell
(Wed Feb 04 2004 - 10:19:45 PST)
Re: AMBER: sander and mpich (which compilers/mpich work)
Viktor Hornak
(Wed Feb 04 2004 - 11:13:13 PST)
AMBER: carnal
Herbert Georg
(Wed Feb 04 2004 - 11:18:37 PST)
Re: AMBER: carnal
Bill Ross
(Wed Feb 04 2004 - 11:40:31 PST)
AMBER: How to remove Cl- ions
Do Anh Tuan
(Fri Feb 06 2004 - 02:38:41 PST)
Re: AMBER: How to remove Cl- ions
Itziar Maestre Asenjo
(Fri Feb 06 2004 - 02:58:05 PST)
Re: AMBER: How to remove Cl- ions
Vlad Cojocaru
(Fri Feb 06 2004 - 03:09:52 PST)
AMBER: How to remove Cl- ions
Wayne Dawson
(Fri Feb 06 2004 - 03:19:33 PST)
Re: AMBER: carnal
Bill Ross
(Mon Feb 16 2004 - 10:37:54 PST)
Re: AMBER: carnal
Bill Ross
(Tue Feb 24 2004 - 09:49:16 PST)
AMBER: antechamber + mopac error
Carsten Detering
(Wed Feb 04 2004 - 18:57:48 PST)
RE: AMBER: antechamber + mopac error
Meg McCarrick
(Thu Feb 05 2004 - 09:12:42 PST)
Re: AMBER: antechamber + mopac error
David A. Case
(Thu Feb 05 2004 - 09:21:11 PST)
AMBER: ptraj
Julien Pecher
(Thu Feb 05 2004 - 00:46:09 PST)
Re: AMBER: ptraj
Bill Ross
(Thu Feb 05 2004 - 01:43:59 PST)
AMBER: PMEMD and nmropt=1
aldo jongejan
(Thu Feb 05 2004 - 03:52:29 PST)
Re: AMBER: PMEMD and nmropt=1
Robert Duke
(Thu Feb 05 2004 - 04:39:58 PST)
RE: AMBER: PMEMD and nmropt=1
Kristina Furse
(Thu Feb 05 2004 - 13:19:52 PST)
Re: AMBER: PMEMD and nmropt=1
Robert Duke
(Thu Feb 05 2004 - 13:45:07 PST)
Re: AMBER: PMEMD and nmropt=1
David A. Case
(Thu Feb 05 2004 - 17:29:41 PST)
Re: AMBER: Re: ANAL problem
David A. Case
(Thu Feb 05 2004 - 09:36:05 PST)
Re: AMBER: Re: ANAL problem
Bill Ross
(Thu Feb 05 2004 - 10:07:58 PST)
AMBER: antechamber error in test / differences in prmtop files
Carsten Detering
(Thu Feb 05 2004 - 12:07:07 PST)
Re: AMBER: antechamber error in test / differences in prmtop files
David A. Case
(Thu Feb 05 2004 - 13:11:53 PST)
AMBER: ptraj and dipoles
Herbert Georg
(Thu Feb 05 2004 - 13:40:24 PST)
Re: AMBER: ptraj and dipoles
David A. Case
(Thu Feb 05 2004 - 23:11:50 PST)
Re: AMBER: ptraj and dipoles
Herbert Georg
(Fri Feb 06 2004 - 03:47:12 PST)
AMBER: ptraj and dipoles....
Herbert Georg
(Fri Feb 06 2004 - 13:12:10 PST)
AMBER: MCSS
Chen, Ya
(Thu Feb 05 2004 - 20:33:48 PST)
Re: AMBER: MCSS
David A. Case
(Thu Feb 05 2004 - 23:12:47 PST)
AMBER: water as a "ligand" in GBSA and MM-PBSA?
Giulio Rastelli
(Fri Feb 06 2004 - 09:41:50 PST)
AMBER: How to remove Cl- ions
Do Anh Tuan
(Fri Feb 06 2004 - 05:24:10 PST)
Re: AMBER: How to remove Cl- ions
Bill Ross
(Fri Feb 06 2004 - 08:35:27 PST)
AMBER: off-subject ROCKS/Qbank
James W. Caldwell
(Fri Feb 06 2004 - 12:03:09 PST)
Fwd: Re: AMBER: Lattice structures in xleap
Brandon Tefft
(Fri Feb 06 2004 - 13:27:50 PST)
Re: Fwd: Re: AMBER: Lattice structures in xleap
David A. Case
(Fri Feb 06 2004 - 13:54:07 PST)
Re: Fwd: Re: AMBER: Lattice structures in xleap
Bill Ross
(Fri Feb 06 2004 - 14:21:12 PST)
AMBER: antechamber + mopac +scf failed
Carsten Detering
(Fri Feb 06 2004 - 16:11:22 PST)
AMBER: antechamber + mopac + MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED
Carsten Detering
(Fri Feb 06 2004 - 17:50:46 PST)
Re: AMBER: antechamber + mopac + MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED
David A. Case
(Sat Feb 07 2004 - 08:33:48 PST)
AMBER: adding ions to nucleic acids
a b
(Sun Feb 08 2004 - 02:47:19 PST)
Re: AMBER: adding ions to nucleic acids
Vlad Cojocaru
(Sun Feb 08 2004 - 04:25:55 PST)
AMBER: question about the average structure from ptraj
aini.UMDNJ.EDU
(Sun Feb 08 2004 - 11:33:23 PST)
Re: AMBER: question about the average structure from ptraj
Thomas E. Cheatham, III
(Sun Feb 08 2004 - 11:49:23 PST)
Re: AMBER: adding ions to nucleic acids
Bill Ross
(Sun Feb 08 2004 - 11:40:50 PST)
Re: AMBER: adding ions to nucleic acids
Dr. Yong Duan
(Tue Feb 10 2004 - 21:54:58 PST)
Re: AMBER: question about the average structure from ptraj
Bill Ross
(Sun Feb 08 2004 - 11:47:11 PST)
AMBER: dipole moment in ptraj
Herbert Georg
(Sun Feb 08 2004 - 10:42:07 PST)
Re: AMBER: dipole moment in ptraj
Thomas E. Cheatham, III
(Sun Feb 08 2004 - 15:00:55 PST)
AMBER: Aldo's PMEMD bug
Robert Duke
(Mon Feb 09 2004 - 05:53:43 PST)
Re: AMBER: Aldo's PMEMD bug
aldo jongejan
(Mon Feb 09 2004 - 07:44:39 PST)
AMBER: antechamber error
jwfang
(Mon Feb 09 2004 - 07:50:17 PST)
Re: AMBER: antechamber error
David A. Case
(Mon Feb 09 2004 - 08:22:07 PST)
Re: AMBER: antechamber error
Carsten Detering
(Mon Feb 09 2004 - 09:38:41 PST)
RE: AMBER: antechamber error
Fang, Jianwen
(Mon Feb 09 2004 - 10:00:28 PST)
AMBER: antechamber + FAILED TO ACHIEVE SCF
Carsten Detering
(Mon Feb 09 2004 - 11:17:41 PST)
Re: AMBER: antechamber + FAILED TO ACHIEVE SCF
Junmei Wang
(Mon Feb 09 2004 - 11:27:02 PST)
Re: AMBER: antechamber + FAILED TO ACHIEVE SCF
Carsten Detering
(Mon Feb 09 2004 - 14:02:10 PST)
Re: AMBER: antechamber + FAILED TO ACHIEVE SCF
David A. Case
(Mon Feb 09 2004 - 14:17:49 PST)
AMBER: Nmode convergence
ML
(Mon Feb 09 2004 - 23:36:27 PST)
Re: AMBER: Nmode convergence
ML
(Tue Feb 10 2004 - 07:26:12 PST)
Re: AMBER: Nmode convergence
David A. Case
(Tue Feb 10 2004 - 08:34:17 PST)
Re: AMBER: Nmode convergence
ML
(Wed Feb 11 2004 - 00:14:31 PST)
AMBER: Temperature in Nmode
ML
(Tue Feb 10 2004 - 07:25:12 PST)
Re: AMBER: Temperature in Nmode
David A. Case
(Tue Feb 10 2004 - 08:42:06 PST)
Re: AMBER: Temperature in Nmode
ML
(Tue Feb 10 2004 - 12:46:19 PST)
AMBER: minimization output
L Jin
(Tue Feb 10 2004 - 08:36:25 PST)
Re: AMBER: minimization output
David A. Case
(Tue Feb 10 2004 - 13:05:59 PST)
Re: AMBER: minimization output
L Jin
(Fri Feb 13 2004 - 01:49:52 PST)
Re: AMBER: minimization output
Anna Schrey
(Fri Feb 20 2004 - 01:07:40 PST)
Re: AMBER: minimization output
L Jin
(Fri Feb 20 2004 - 02:36:35 PST)
AMBER: LES question
Lishan Yao
(Tue Feb 10 2004 - 12:47:20 PST)
Re: AMBER: LES question
Vlad Cojocaru
(Tue Feb 10 2004 - 13:01:12 PST)
Re: AMBER: LES question
Lishan Yao
(Tue Feb 10 2004 - 13:02:18 PST)
Re: AMBER: LES question
xiaolin cheng
(Tue Feb 10 2004 - 16:14:31 PST)
Re: AMBER: LES question
Carlos Simmerling
(Wed Feb 11 2004 - 05:48:48 PST)
Re: AMBER: LES question
Lishan Yao
(Wed Feb 11 2004 - 06:16:01 PST)
Re: AMBER: LES question
Carlos Simmerling
(Wed Feb 11 2004 - 09:55:27 PST)
Re: AMBER: LES question
Lishan Yao
(Wed Feb 11 2004 - 11:20:54 PST)
Re: AMBER: LES question
Carlos Simmerling
(Wed Feb 11 2004 - 11:43:58 PST)
Re: AMBER: LES question
Lishan Yao
(Wed Feb 11 2004 - 11:52:09 PST)
Re: AMBER: LES question
Carlos Simmerling
(Wed Feb 11 2004 - 12:03:44 PST)
Re: AMBER: LES question
Lishan Yao
(Thu Feb 12 2004 - 05:59:02 PST)
AMBER: Nitrogen vdw type
Terry Downing
(Tue Feb 10 2004 - 14:56:37 PST)
AMBER: Installing AMBER on SGI Octane 2-CPU - erfcfun.c compile prob.
Joseph E. Maxwell
(Tue Feb 10 2004 - 15:36:26 PST)
Re: AMBER: Installing AMBER on SGI Octane 2-CPU - erfcfun.c compile prob.
David A. Case
(Tue Feb 10 2004 - 15:54:45 PST)
AMBER: Box of mixed solvant
FyD
(Tue Feb 10 2004 - 20:18:42 PST)
Re: AMBER: Box of mixed solvant
Dr. Yong Duan
(Tue Feb 10 2004 - 22:09:28 PST)
AMBER: atom type for GBSA
aini.UMDNJ.EDU
(Wed Feb 11 2004 - 07:13:04 PST)
Re: AMBER: atom type for GBSA
David A. Case
(Wed Feb 11 2004 - 09:33:04 PST)
AMBER: GBSA frequency update
Sergio E. Wong
(Wed Feb 11 2004 - 15:29:10 PST)
Re: AMBER: GBSA frequency update
David A. Case
(Wed Feb 11 2004 - 22:09:34 PST)
AMBER: Run calculations for protein in Amber
Małgorzata Jarończyk
(Thu Feb 12 2004 - 01:18:20 PST)
Re: AMBER: Run calculations for protein in Amber
Carlos Simmerling
(Thu Feb 12 2004 - 05:18:32 PST)
AMBER: ptraj
Karin Schleinkofer
(Thu Feb 12 2004 - 02:57:47 PST)
Re: AMBER: ptraj
Vlad Cojocaru
(Thu Feb 12 2004 - 03:45:55 PST)
Re: AMBER: ptraj
Thomas E. Cheatham, III
(Thu Feb 12 2004 - 10:03:36 PST)
Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function
Małgorzata Jarończyk
(Thu Feb 12 2004 - 06:28:59 PST)
Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function
Vlad Cojocaru
(Thu Feb 12 2004 - 06:34:31 PST)
Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function
David A. Case
(Thu Feb 12 2004 - 08:41:16 PST)
AMBER: TER in amber
Lishan Yao
(Thu Feb 12 2004 - 07:04:03 PST)
Re: AMBER: TER in amber
Vlad Cojocaru
(Thu Feb 12 2004 - 07:56:04 PST)
Re: AMBER: TER in amber
Lishan Yao
(Thu Feb 12 2004 - 08:17:02 PST)
Re: AMBER: TER in amber
Vlad Cojocaru
(Fri Feb 13 2004 - 00:35:41 PST)
Re: AMBER: TER in amber
David A. Case
(Thu Feb 12 2004 - 08:56:45 PST)
Re: AMBER: TER in amber
Lishan Yao
(Thu Feb 12 2004 - 10:08:29 PST)
Re: AMBER: TER in amber
Lishan Yao
(Thu Feb 12 2004 - 09:12:45 PST)
AMBER: MM-PBSA: molecular charges and active site water
Anselm Horn
(Thu Feb 12 2004 - 07:23:05 PST)
Re: AMBER: MM-PBSA: molecular charges and active site water
David A. Case
(Thu Feb 12 2004 - 20:06:56 PST)
Re: AMBER: MM-PBSA: molecular charges and active site water
ML
(Thu Feb 12 2004 - 23:30:23 PST)
AMBER: center of mass in CARNAL
Herbert Georg
(Thu Feb 12 2004 - 08:15:17 PST)
AMBER: neutrality of charge in AMBER 7
Sichun Yang
(Thu Feb 12 2004 - 12:51:51 PST)
Re: AMBER: neutrality of charge in AMBER 7
David A. Case
(Sat Feb 14 2004 - 12:10:22 PST)
AMBER: Re: To David Case
Małgorzata Jarończyk
(Fri Feb 13 2004 - 03:25:52 PST)
AMBER: minimizating complex-protein with AMBER
susan.costantini.unina2.it
(Sun Feb 15 2004 - 01:27:00 PST)
Re: AMBER: minimizating complex-protein with AMBER
David A. Case
(Sun Feb 15 2004 - 21:14:02 PST)
AMBER: problem with tleap in Amber
donna j
(Sun Feb 15 2004 - 18:44:25 PST)
Re: AMBER: problem with tleap in Amber
David A. Case
(Sun Feb 15 2004 - 21:10:31 PST)
AMBER: MM-PBSA:??Decomposition of receptor energies??
ML
(Mon Feb 16 2004 - 01:18:17 PST)
Re: AMBER: MM-PBSA:??Decomposition of receptor energies??
Holger Gohlke
(Mon Feb 16 2004 - 02:09:07 PST)
AMBER: SIGSEGV
John
(Mon Feb 16 2004 - 02:43:36 PST)
Re: AMBER: SIGSEGV
David A. Case
(Mon Feb 16 2004 - 08:30:18 PST)
AMBER:
John
(Tue Feb 17 2004 - 02:05:22 PST)
Re: AMBER: MM-PBSA:??Decomposition of receptor energies??
ML
(Mon Feb 16 2004 - 07:59:04 PST)
Re: AMBER: MM-PBSA:??Decomposition of receptor energies??
Holger Gohlke
(Mon Feb 16 2004 - 23:24:25 PST)
AMBER: TIP4P
Nikolai Smolin
(Mon Feb 16 2004 - 02:58:56 PST)
Re: AMBER: TIP4P
David A. Case
(Mon Feb 16 2004 - 08:36:37 PST)
AMBER: IFC COMPILER
Obdulia Rabal
(Mon Feb 16 2004 - 04:54:00 PST)
Re: AMBER: IFC COMPILER
Robert Duke
(Mon Feb 16 2004 - 05:18:03 PST)
AMBER: carnal
Julien Pecher
(Mon Feb 16 2004 - 05:17:33 PST)
AMBER: DIELC
L Jin
(Mon Feb 16 2004 - 05:51:35 PST)
AMBER: bad crd file
John
(Mon Feb 16 2004 - 07:30:26 PST)
AMBER: image in ptraj
Lishan Yao
(Mon Feb 16 2004 - 08:11:25 PST)
AMBER: TIP4P extended
Nikolai Smolin
(Mon Feb 16 2004 - 09:06:30 PST)
Re: AMBER: TIP4P extended
Sarah Wittkopp
(Mon Feb 16 2004 - 09:21:15 PST)
Re: AMBER: TIP4P extended
David A. Case
(Mon Feb 16 2004 - 09:37:32 PST)
AMBER: TIP4P extended
Nikolai Smolin
(Mon Feb 16 2004 - 09:10:19 PST)
Re: AMBER: bad crd file
Bill Ross
(Mon Feb 16 2004 - 10:51:57 PST)
AMBER: problem with tleap in Amber
donna j
(Sun Feb 15 2004 - 19:01:27 PST)
AMBER: saveamberparm warning in leap?
opitz.che.udel.edu
(Mon Feb 16 2004 - 13:24:45 PST)
Re: AMBER: saveamberparm warning in leap?
David A. Case
(Mon Feb 16 2004 - 17:04:17 PST)
AMBER: multiple messages on the amber reflector
David A. Case
(Mon Feb 16 2004 - 15:33:40 PST)
AMBER: moil-view question
S. Frank Yan
(Mon Feb 16 2004 - 18:43:57 PST)
Re: AMBER: moil-view question
Carlos Simmerling
(Tue Feb 17 2004 - 05:38:59 PST)
Re: AMBER: moil-view question
Teletchéa Stéphane
(Tue Feb 17 2004 - 05:49:31 PST)
AMBER: flexible water potential
Herbert Georg
(Tue Feb 17 2004 - 03:22:12 PST)
AMBER: Close contact warnings
L Jin
(Tue Feb 17 2004 - 06:29:57 PST)
Re: AMBER: Close contact warnings
David A. Case
(Tue Feb 17 2004 - 08:39:22 PST)
Re: AMBER: Close contact warnings
L Jin
(Tue Feb 17 2004 - 10:14:37 PST)
Re: AMBER: Close contact warnings
David A. Case
(Tue Feb 17 2004 - 10:37:06 PST)
Re: AMBER: Close contact warnings
L Jin
(Wed Feb 18 2004 - 02:14:55 PST)
Re: AMBER: Close contact warnings
Michael George Lerner
(Wed Feb 18 2004 - 05:58:50 PST)
Re: AMBER: Close contact warnings
L Jin
(Wed Feb 18 2004 - 08:55:55 PST)
Re: AMBER: Close contact warnings
David A. Case
(Wed Feb 18 2004 - 11:34:24 PST)
Re: AMBER: Close contact warnings
Bill Ross
(Wed Feb 18 2004 - 10:20:38 PST)
Re: AMBER: Close contact warnings
L Jin
(Wed Feb 18 2004 - 10:56:49 PST)
RE: AMBER: Close contact warnings
Yong Duan
(Wed Feb 18 2004 - 11:07:36 PST)
RE: AMBER: Close contact warnings
L Jin
(Thu Feb 19 2004 - 07:11:54 PST)
Re: AMBER: Close contact warnings
David A. Case
(Thu Feb 19 2004 - 08:30:15 PST)
AMBER: prep files for modified bases
Wen Li
(Thu Feb 19 2004 - 08:58:01 PST)
Re: AMBER: prep files for modified bases
David A. Case
(Thu Feb 19 2004 - 12:23:41 PST)
Re: AMBER: Close contact warnings
Bill Ross
(Wed Feb 18 2004 - 11:29:19 PST)
RE: AMBER: Close contact warnings
Bill Ross
(Thu Feb 19 2004 - 11:25:33 PST)
AMBER: Build a H+ ion in Leap?
Xin Chen
(Thu Feb 19 2004 - 11:40:40 PST)
AMBER: RESP charges for protein fragment
Tom Turner
(Tue Feb 17 2004 - 08:20:15 PST)
AMBER: How to add H+ ion in leap?
xinchen
(Tue Feb 17 2004 - 11:46:10 PST)
Re: AMBER: center of mass in CARNAL
Bill Ross
(Tue Feb 17 2004 - 12:25:43 PST)
Re: AMBER: How to add H+ ion in leap?
Bill Ross
(Tue Feb 17 2004 - 12:29:17 PST)
Re: AMBER: How to add H+ ion in leap?
xinchen
(Tue Feb 17 2004 - 12:43:18 PST)
Re: AMBER: How to add H+ ion in leap?
Bill Ross
(Tue Feb 17 2004 - 13:09:01 PST)
AMBER: (no subject)
ThuZar Lwin
(Tue Feb 17 2004 - 12:52:40 PST)
Re: AMBER: (no subject)
Bill Ross
(Tue Feb 17 2004 - 13:17:39 PST)
Re: AMBER: (no subject)
ThuZar Lwin
(Tue Feb 17 2004 - 13:33:30 PST)
AMBER: multiple messages on the amber reflector
Amber Administration
(Tue Feb 17 2004 - 14:27:52 PST)
AMBER: contributed parameters (modified base - PSU)
Shau Grossman
(Tue Feb 17 2004 - 18:14:16 PST)
RE: AMBER: contributed parameters (modified base - PSU)
S. Frank Yan
(Tue Feb 17 2004 - 18:32:56 PST)
Re: AMBER: contributed parameters
FyD
(Wed Feb 18 2004 - 09:12:04 PST)
Re: AMBER: contributed parameters
Shau Grossman
(Thu Feb 19 2004 - 18:55:46 PST)
AMBER: ions94.lib file
Wen Li
(Fri Feb 20 2004 - 09:10:06 PST)
Re: AMBER: contributed parameters
FyD
(Fri Feb 20 2004 - 09:08:34 PST)
Re: AMBER: contributed parameters
Shau Grossman
(Fri Feb 20 2004 - 13:46:04 PST)
Re: AMBER: contributed parameters
FyD
(Fri Feb 20 2004 - 16:05:48 PST)
AMBER: R.E.D.
Shau Grossman
(Mon Feb 23 2004 - 17:20:44 PST)
Re: AMBER: R.E.D.
FyD
(Mon Feb 23 2004 - 17:42:13 PST)
Re: AMBER: R.E.D.
Shau Grossman
(Mon Feb 23 2004 - 18:13:43 PST)
Re: AMBER: R.E.D.
FyD
(Tue Feb 24 2004 - 08:16:57 PST)
AMBER: Segmentation fault in SaveAmberParm
xinchen
(Tue Feb 17 2004 - 19:31:35 PST)
Re: AMBER: Segmentation fault in SaveAmberParm
Xin Chen
(Wed Feb 18 2004 - 11:12:53 PST)
AMBER: histidine and its various forms
Stern, Julie
(Wed Feb 18 2004 - 06:38:31 PST)
Re: AMBER: histidine and its various forms
David A. Case
(Wed Feb 18 2004 - 07:58:44 PST)
Re: AMBER: histidine and its various forms
Peter Oelschlaeger
(Wed Feb 18 2004 - 10:10:49 PST)
AMBER: sander + ewald bomb
Carsten Detering
(Wed Feb 18 2004 - 11:20:51 PST)
Re: AMBER: sander + ewald bomb
Michael Crowley
(Wed Feb 18 2004 - 13:13:42 PST)
Re: AMBER: sander + ewald bomb
David A. Case
(Wed Feb 18 2004 - 14:00:40 PST)
AMBER: GLYCAM web site
Scott Brozell
(Wed Feb 18 2004 - 12:00:39 PST)
AMBER: MD simulations with 2 molecules
Joey Harriman
(Wed Feb 18 2004 - 12:32:47 PST)
Re: AMBER: MD simulations with 2 molecules
David A. Case
(Wed Feb 18 2004 - 14:15:04 PST)
AMBER: check unit + saveamberparm
Carsten Detering
(Wed Feb 18 2004 - 18:21:58 PST)
re: AMBER: check unit + saveamberparm
S. Frank Yan
(Fri Feb 20 2004 - 16:17:41 PST)
AMBER: tmd question
hj zou
(Wed Feb 18 2004 - 18:58:45 PST)
Re: AMBER: tmd question
Carlos Simmerling
(Thu Feb 19 2004 - 08:17:51 PST)
AMBER: mm_pbsa question
hj zou
(Wed Feb 18 2004 - 19:22:00 PST)
AMBER: pmf calculation using gibbs.
Myunggi Yi
(Wed Feb 18 2004 - 21:22:46 PST)
Re: AMBER: pmf calculation using gibbs.
David A. Case
(Wed Feb 18 2004 - 20:45:57 PST)
Re: AMBER: pmf calculation using gibbs.
Myunggi Yi
(Thu Feb 19 2004 - 07:13:30 PST)
Re: AMBER: pmf calculation using gibbs.
David A. Case
(Thu Feb 19 2004 - 08:27:33 PST)
Re: AMBER: compiling software(RESP) on MAC G5
Scott Brozell
(Wed Feb 18 2004 - 21:36:06 PST)
Re: AMBER: compiling software(RESP) on MAC G5
FyD
(Thu Feb 19 2004 - 08:27:54 PST)
Re: AMBER: compiling software(RESP) on MAC G5
James W. Caldwell
(Thu Feb 19 2004 - 10:50:28 PST)
Re: AMBER: compiling software(RESP) on MAC G5
David A. Case
(Thu Feb 19 2004 - 12:21:39 PST)
AMBER: how to add force field parameters
Ioana Cozmuta
(Thu Feb 19 2004 - 12:27:02 PST)
Re: AMBER: compiling software(RESP) on MAC G5
Lifeng Tian.PantherServer
(Thu Feb 19 2004 - 12:41:05 PST)
AMBER: LCPO parameters in gbsa
Giulio Rastelli
(Thu Feb 19 2004 - 08:53:56 PST)
Re: AMBER: LCPO parameters in gbsa
David A. Case
(Mon Feb 23 2004 - 10:51:46 PST)
AMBER: distance-aromatic ring
John
(Thu Feb 19 2004 - 03:03:56 PST)
AMBER: LES
Petr Jeřábek
(Thu Feb 19 2004 - 10:10:50 PST)
Re: AMBER: LES
Carlos Simmerling
(Thu Feb 19 2004 - 12:26:21 PST)
Re: AMBER: LES
Petr Jeřábek
(Thu Feb 19 2004 - 13:08:38 PST)
Re: AMBER: LES
Carlos Simmerling
(Thu Feb 19 2004 - 13:11:58 PST)
Re: AMBER: LES
Viktor Hornak
(Thu Feb 19 2004 - 13:30:32 PST)
Re: AMBER: LES
Petr Jeřábek
(Thu Feb 19 2004 - 14:10:00 PST)
Re: AMBER: LES
Carlos Simmerling
(Thu Feb 19 2004 - 14:13:07 PST)
Re: AMBER: distance-aromatic ring
Bill Ross
(Thu Feb 19 2004 - 11:41:32 PST)
Re: AMBER: Build a H+ ion in Leap?
Bill Ross
(Thu Feb 19 2004 - 12:00:38 PST)
Re: AMBER: Build a H+ ion in Leap?
xinchen
(Thu Feb 19 2004 - 12:19:20 PST)
Re: AMBER: Build a H+ ion in Leap?
Bill Ross
(Thu Feb 19 2004 - 13:22:08 PST)
Re: AMBER: sander output
Dave S Walker
(Thu Feb 19 2004 - 15:55:59 PST)
Re: AMBER: sander output
David A. Case
(Thu Feb 19 2004 - 21:54:32 PST)
Re: AMBER: sander output
Dave S Walker
(Fri Feb 20 2004 - 13:47:24 PST)
AMBER: The charge given by xleap from amber 5
Ben Cossins
(Fri Feb 20 2004 - 04:25:55 PST)
AMBER: LES methodology question
Vlad Cojocaru
(Fri Feb 20 2004 - 04:12:14 PST)
Re: AMBER: LES methodology question
Carlos Simmerling
(Fri Feb 20 2004 - 05:01:06 PST)
AMBER: Defining residues
opitz.che.udel.edu
(Sat Feb 21 2004 - 20:34:56 PST)
Re: AMBER: Defining residues
David A. Case
(Mon Feb 23 2004 - 08:49:58 PST)
Re: AMBER: Defining residues
Bill Ross
(Mon Feb 23 2004 - 10:04:33 PST)
Re: AMBER: Defining residues
opitz.che.udel.edu
(Mon Feb 23 2004 - 11:02:58 PST)
Re: AMBER: Defining residues
John Bushnell
(Mon Feb 23 2004 - 12:44:44 PST)
Re: AMBER: Defining residues
Bill Ross
(Mon Feb 23 2004 - 12:14:46 PST)
Re: AMBER: Defining residues
opitz.che.udel.edu
(Mon Feb 23 2004 - 13:35:44 PST)
Re: AMBER: Defining residues
John Bushnell
(Mon Feb 23 2004 - 14:19:48 PST)
Re: AMBER: Defining residues
opitz.che.udel.edu
(Mon Feb 23 2004 - 13:47:51 PST)
Re: AMBER: Defining residues
Bill Ross
(Mon Feb 23 2004 - 14:39:48 PST)
Re: AMBER: Defining residues
John Bushnell
(Mon Feb 23 2004 - 15:39:46 PST)
AMBER: xleap don't recognize my residue/atom
scopio
(Sun Feb 22 2004 - 03:18:42 PST)
Re: AMBER: xleap don't recognize my residue/atom
Rhonda Torres
(Sun Feb 22 2004 - 14:23:59 PST)
AMBER: Can anybody help me with CHARMM
Gabbar Daaku
(Sun Feb 22 2004 - 19:13:09 PST)
Re: AMBER: Can anybody help me with CHARMM
Tru Huynh
(Wed Feb 25 2004 - 05:36:18 PST)
Re: AMBER: Can anybody help me with CHARMM
Piotr Cieplak
(Sun Feb 22 2004 - 19:49:21 PST)
AMBER: How to add ACE and NME groups?
Małgorzata Jarończyk
(Mon Feb 23 2004 - 01:47:00 PST)
Re: AMBER: How to add ACE and NME groups?
David A. Case
(Mon Feb 23 2004 - 08:47:05 PST)
Re: AMBER: How to add ACE and NME groups?
Ben Cossins
(Tue Feb 24 2004 - 08:47:43 PST)
AMBER: protein - fractional native contacts
uddhavesh bhaskar sonavane
(Mon Feb 23 2004 - 03:50:06 PST)
AMBER: pka calculation
hj zou
(Mon Feb 23 2004 - 05:33:00 PST)
AMBER: Thermostat comparison ?
MD Tyka, Biochemistry
(Mon Feb 23 2004 - 09:41:56 PST)
AMBER: how to use prep file
Fang, Jianwen
(Mon Feb 23 2004 - 11:15:19 PST)
RE: AMBER: how to use prep file
Kristina Furse
(Mon Feb 23 2004 - 12:14:20 PST)
Re: AMBER: how to use prep file
David A. Case
(Mon Feb 23 2004 - 12:19:30 PST)
RE: AMBER: how to use prep file
Bill Ross
(Mon Feb 23 2004 - 12:30:37 PST)
AMBER: problem with frcmod file
donna j
(Mon Feb 23 2004 - 13:47:12 PST)
Re: AMBER: problem with frcmod file
David A. Case
(Mon Feb 23 2004 - 14:43:59 PST)
Re: AMBER: problem with frcmod file
donna j
(Thu Feb 26 2004 - 10:23:25 PST)
Re: AMBER: problem with frcmod file
James W. Caldwell
(Thu Feb 26 2004 - 10:45:44 PST)
Re: AMBER: problem with frcmod file
donna j
(Sun Feb 29 2004 - 11:43:24 PST)
Re: AMBER: problem with frcmod file
Bill Ross
(Mon Feb 23 2004 - 14:44:08 PST)
AMBER: Can you write me how can I add the ACE and NMe groups in the Xleap?
Małgorzata Jarończyk
(Tue Feb 24 2004 - 06:59:46 PST)
AMBER: carnal
Youyi Peng
(Tue Feb 24 2004 - 08:36:11 PST)
AMBER: add Na+
L Jin
(Tue Feb 24 2004 - 10:23:55 PST)
RE: AMBER: add Na+
Ross Walker
(Tue Feb 24 2004 - 10:42:28 PST)
RE: AMBER: add Na+
L Jin
(Tue Feb 24 2004 - 11:29:36 PST)
Re: AMBER: add Na+
David A. Case
(Tue Feb 24 2004 - 11:35:06 PST)
RE: AMBER: add Na+
Bill Ross
(Tue Feb 24 2004 - 11:07:07 PST)
RE: AMBER: add Na+
Bill Ross
(Tue Feb 24 2004 - 11:33:34 PST)
RE: AMBER: add Na+
L Jin
(Wed Feb 25 2004 - 02:33:02 PST)
RE: AMBER: add Na+
Bill Ross
(Wed Feb 25 2004 - 10:31:43 PST)
AMBER: Star like (branching) molecule
opitz.che.udel.edu
(Tue Feb 24 2004 - 14:54:45 PST)
Re: AMBER: Star like (branching) molecule
John Bushnell
(Tue Feb 24 2004 - 15:33:45 PST)
Re: AMBER: Star like (branching) molecule
Bill Ross
(Tue Feb 24 2004 - 15:40:13 PST)
Re: AMBER: Star like (branching) molecule
Bill Ross
(Tue Feb 24 2004 - 15:51:10 PST)
AMBER: PGA
Beale, John
(Wed Feb 25 2004 - 05:09:46 PST)
AMBER: NMR restraints-Floating point exception
John
(Wed Feb 25 2004 - 06:44:52 PST)
Re: AMBER: NMR restraints-Floating point exception
David A. Case
(Wed Feb 25 2004 - 08:17:46 PST)
RE: AMBER: NMR restraints-Floating point exception
John
(Wed Feb 25 2004 - 10:19:25 PST)
AMBER: pmf calculation using gibbs
Myunggi Yi
(Wed Feb 25 2004 - 08:47:25 PST)
Re: AMBER: pmf calculation using gibbs
David Smith
(Thu Feb 26 2004 - 00:57:02 PST)
AMBER: Errors when running tleap
Ann P
(Wed Feb 25 2004 - 13:13:53 PST)
RE: AMBER: Errors when running tleap
Ann P
(Thu Feb 26 2004 - 11:21:03 PST)
RE: AMBER: Errors when running tleap
Bill Ross
(Thu Feb 26 2004 - 11:47:05 PST)
Re: AMBER: Errors when running tleap
Bill Ross
(Wed Feb 25 2004 - 13:31:54 PST)
AMBER: averaged structure with unknown elements
Youyi Peng
(Wed Feb 25 2004 - 13:32:54 PST)
Re: AMBER: averaged structure with unknown elements
David A. Case
(Wed Feb 25 2004 - 14:15:25 PST)
Re: AMBER: averaged structure with unknown elements
Bill Ross
(Wed Feb 25 2004 - 13:49:40 PST)
AMBER: mmpbsa qustion
hj zou
(Wed Feb 25 2004 - 17:23:37 PST)
Re: AMBER: mmpbsa qustion
Holger Gohlke
(Wed Feb 25 2004 - 23:29:06 PST)
Re: AMBER: mmpbsa qustion
James W. Caldwell
(Thu Feb 26 2004 - 10:06:13 PST)
AMBER: size.h error
Emmanuel Giudice
(Thu Feb 26 2004 - 13:15:20 PST)
Re: AMBER: size.h error
Surjit Dixit
(Thu Feb 26 2004 - 13:53:20 PST)
Re: AMBER: size.h error
David A. Case
(Thu Feb 26 2004 - 14:48:29 PST)
AMBER: sander + vlimit exceed...
Carsten Detering
(Thu Feb 26 2004 - 15:16:31 PST)
AMBER: pka calculation
hj zou
(Fri Feb 27 2004 - 18:42:34 PST)
Re: AMBER: pka calculation
Florian Barth
(Sat Feb 28 2004 - 07:46:04 PST)
AMBER: PB in mm-pbsa
Sue Heavner
(Sat Feb 28 2004 - 08:30:05 PST)
Re: AMBER: PB in mm-pbsa
Holger Gohlke
(Sun Feb 29 2004 - 06:02:29 PST)
AMBER: Problems with xleap
Javier Perez Miron
(Thu Feb 26 2004 - 17:18:11 PST)
Last message date
:
Mon Mar 01 2004 - 22:53:00 PST
Archived on
: Wed Dec 25 2024 - 05:53:21 PST
356 messages
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