Amber Archive Nov 2008 by author
354 messages
:
Starting
Sun Nov 02 2008 - 05:09:57 PST,
Ending
Fri Dec 05 2008 - 18:12:45 PST
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Adrian Roitberg
Re: AMBER: Chloride anion ligands leave the protein during MD
(Fri Nov 14 2008 - 06:00:33 PST)
Re: AMBER: Problem with evaporating water over longer simulation times
(Wed Nov 12 2008 - 17:06:38 PST)
Alan
Re: AMBER: antechamber and gaff for a homodimer
(Thu Nov 27 2008 - 04:27:31 PST)
Re: AMBER: AdoMet parameterization with antechamber
(Mon Nov 24 2008 - 02:46:52 PST)
Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)
(Thu Nov 20 2008 - 04:13:09 PST)
Re: AMBER: compiling ambertools with intel compilers
(Thu Nov 20 2008 - 04:10:58 PST)
Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)
(Thu Nov 20 2008 - 03:48:56 PST)
AMBER: compiling ambertools with intel compilers
(Thu Nov 20 2008 - 02:27:26 PST)
Alessandro Nascimento
Re: AMBER: gigabit ethernet cards and switches
(Thu Nov 06 2008 - 11:28:46 PST)
AMBER: gigabit ethernet cards and switches
(Thu Nov 06 2008 - 08:51:43 PST)
Andreas Svrcek-Seiler
Re: AMBER: High ESURF
(Mon Nov 17 2008 - 00:24:02 PST)
Andrei Neamtu
AMBER: compiling amber 10
(Fri Nov 21 2008 - 23:26:58 PST)
Arturas Ziemys
AMBER: molsurf fails
(Tue Nov 25 2008 - 07:27:27 PST)
Re: AMBER: problem
(Tue Nov 18 2008 - 07:07:19 PST)
RE: AMBER: problem
(Mon Nov 17 2008 - 20:36:25 PST)
AMBER: problem
(Sun Nov 16 2008 - 21:07:38 PST)
AMBER: MM-PBSA and trajectory input
(Thu Nov 13 2008 - 09:22:36 PST)
Ashish Sangwai
Re: AMBER: Restraints
(Thu Nov 13 2008 - 11:11:45 PST)
AMBER: using "EP" for dummy atom
(Thu Nov 06 2008 - 17:24:23 PST)
babak minoofar
AMBER: N(CN2)- ion
(Fri Nov 28 2008 - 05:12:26 PST)
Balazs JOJART
Re: AMBER: Electrostatic Energy Components
(Mon Nov 24 2008 - 04:19:42 PST)
Barbault Florent
Re: AMBER: AMBER forfield choose
(Thu Nov 20 2008 - 08:21:17 PST)
Re: AMBER: AMBER forfield choose
(Thu Nov 20 2008 - 06:45:20 PST)
AMBER: problem with cartesian restraints with NTP simulations
(Wed Nov 19 2008 - 06:50:13 PST)
Bill Ross
Re: AMBER: load opls force field
(Thu Nov 13 2008 - 12:32:19 PST)
Re: AMBER: Extracting periodic box size deviation
(Thu Nov 06 2008 - 17:42:35 PST)
Campbell, Patrick
AMBER: Question on AMBER MD Implications
(Sat Nov 01 2008 - 03:01:17 PDT)
Carlos Simmerling
Re: AMBER: Questions on TIP4P model?
(Fri Nov 28 2008 - 12:03:14 PST)
Re: AMBER: seeking help regrading Zinc protein GBSA minimization
(Fri Nov 28 2008 - 04:33:16 PST)
Re: AMBER: Heating up
(Fri Nov 28 2008 - 04:30:29 PST)
Re: AMBER: GB versus explicit medium
(Mon Nov 24 2008 - 03:08:40 PST)
Re: AMBER: Electrostatic Energy Components
(Sat Nov 22 2008 - 09:42:53 PST)
Re: AMBER: Electrostatic Energy Components
(Sat Nov 22 2008 - 09:41:48 PST)
Re: AMBER: Electrostatic Energy Components
(Fri Nov 21 2008 - 15:46:10 PST)
Re: AMBER: ptraj center problem
(Fri Nov 21 2008 - 10:42:17 PST)
Re: AMBER: AMBER forfield choose
(Thu Nov 20 2008 - 08:21:51 PST)
Re: AMBER: AMBER forfield choose
(Thu Nov 20 2008 - 07:51:18 PST)
Re: AMBER: PB Radii
(Mon Nov 17 2008 - 03:30:41 PST)
Re: AMBER: Trajectory file ended and unit 24 error on open inptraj
(Sun Nov 16 2008 - 04:42:22 PST)
Re: AMBER: Trajectory file ended and unit 24 error on open inptraj
(Sat Nov 15 2008 - 07:44:32 PST)
Re: AMBER: Sander *.top and *.crd file from PDB file
(Fri Nov 14 2008 - 13:00:30 PST)
Re: AMBER: Newbie question: partial minimization in implicit solvent
(Wed Nov 12 2008 - 12:47:56 PST)
Re: AMBER: changing pdb structure
(Tue Nov 11 2008 - 03:35:42 PST)
Re: AMBER: changing pdb structure
(Mon Nov 10 2008 - 12:37:32 PST)
Re: AMBER: problem with group input and NMR restaints
(Wed Nov 05 2008 - 12:39:29 PST)
Re: AMBER: problem with group input and NMR restaints
(Wed Nov 05 2008 - 10:13:29 PST)
Re: AMBER: problem with group input and NMR restaints
(Wed Nov 05 2008 - 08:53:09 PST)
Re: AMBER: problem with group input and NMR restaints
(Tue Nov 04 2008 - 09:53:48 PST)
Re: AMBER: problem with group input and NMR restaints
(Tue Nov 04 2008 - 08:41:22 PST)
Re: AMBER: problem with group input and NMR restaints
(Tue Nov 04 2008 - 07:35:46 PST)
Re: AMBER: Minimisation and heating under GB conditions
(Mon Nov 03 2008 - 10:52:23 PST)
Re: AMBER: Minimisation and heating under GB conditions
(Mon Nov 03 2008 - 06:45:22 PST)
Re: AMBER: Minimisation and heating under GB conditions
(Mon Nov 03 2008 - 03:29:25 PST)
Catein Catherine
AMBER: temperature error in md calculation
(Wed Nov 05 2008 - 00:11:41 PST)
RE: AMBER: error message of xleap
(Mon Nov 03 2008 - 01:52:24 PST)
CHAMI F.
AMBER: Choline chloride salt
(Wed Nov 26 2008 - 06:49:45 PST)
AMBER: subroutine Work : Jarynski work theorem
(Wed Nov 26 2008 - 04:21:07 PST)
AMBER: subroutine for torsional potential
(Fri Nov 14 2008 - 06:16:37 PST)
Chih-Ying Lin
AMBER: Br - ion defined ?
(Wed Nov 05 2008 - 09:20:36 PST)
Chin, Keith B
RE: AMBER: Questions on TIP4P model?
(Sat Nov 29 2008 - 15:43:21 PST)
AMBER: Questions on TIP4P model?
(Fri Nov 28 2008 - 11:20:38 PST)
RE: AMBER: How to manually adjust periodic boundary conditions (PBC)
(Wed Nov 19 2008 - 17:15:17 PST)
AMBER: How to manually adjust periodic boundary conditions (PBC)
(Wed Nov 19 2008 - 11:58:41 PST)
AMBER:
(Tue Nov 18 2008 - 15:39:26 PST)
AMBER: How to create *.top & *.crd file with hexagonal lattice
(Sun Nov 16 2008 - 17:02:05 PST)
RE: AMBER: Sander *.top and *.crd file from PDB file
(Fri Nov 14 2008 - 12:55:57 PST)
AMBER: Sander *.top and *.crd file from PDB file
(Fri Nov 14 2008 - 11:43:41 PST)
Chris C.
AMBER: Problem running NEB in AMBER10
(Wed Nov 26 2008 - 10:38:17 PST)
CJ Dickson
AMBER: Extracting periodic box size deviation
(Thu Nov 06 2008 - 15:29:20 PST)
Dave Rogers
Re: AMBER: ptraj and netcdf with AmberTools1.2 ?
(Wed Nov 05 2008 - 13:34:21 PST)
David A. Case
Re: AMBER: Questions on TIP4P model?
(Sat Nov 29 2008 - 11:21:01 PST)
Re: AMBER: Gradual releasing of position restraints
(Wed Nov 26 2008 - 09:00:41 PST)
Re: AMBER: Referencing AMBER
(Wed Nov 26 2008 - 08:25:20 PST)
Re: AMBER: Test failure with Amber 10
(Wed Nov 26 2008 - 04:46:41 PST)
Re: AMBER: using packmol file in Amber
(Tue Nov 25 2008 - 11:45:29 PST)
Re: AMBER: molsurf fails
(Tue Nov 25 2008 - 11:26:14 PST)
Re: AMBER: Fully QM periodic runs
(Tue Nov 25 2008 - 03:56:51 PST)
Re: Re: AMBER: AdoMet parameterization with antechamber
(Mon Nov 24 2008 - 09:19:54 PST)
Re: AMBER: Electrostatic Energy Components
(Mon Nov 24 2008 - 04:14:13 PST)
Re: AMBER: question - gaff and leaprc.ff03ua
(Sun Nov 23 2008 - 13:49:37 PST)
Re: AMBER: AdoMet parameterization with antechamber
(Sun Nov 23 2008 - 13:13:23 PST)
Re: AMBER: Electrostatic Energy Components
(Sat Nov 22 2008 - 12:37:51 PST)
Re: AMBER: compiling amber 10
(Sat Nov 22 2008 - 12:33:54 PST)
Re: AMBER: QM/MM simulation
(Sat Nov 22 2008 - 06:53:50 PST)
Re: AMBER: compiling ambertools with intel compilers
(Fri Nov 21 2008 - 09:44:58 PST)
Re: AMBER: Problems for use manganese molecules
(Fri Nov 21 2008 - 04:46:22 PST)
Re: AMBER: How to manually adjust periodic boundary conditions (PBC)
(Thu Nov 20 2008 - 12:52:57 PST)
Re: AMBER: compiling ambertools with intel compilers
(Thu Nov 20 2008 - 12:50:27 PST)
Re: AMBER: CG and HC atoms partial charges in AMBER
(Thu Nov 20 2008 - 07:56:15 PST)
Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)
(Thu Nov 20 2008 - 05:38:37 PST)
Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)
(Thu Nov 20 2008 - 05:36:48 PST)
Re: AMBER: compiling ambertools with intel compilers
(Thu Nov 20 2008 - 04:04:22 PST)
Re: AMBER: How to manually adjust periodic boundary conditions (PBC)
(Wed Nov 19 2008 - 15:35:33 PST)
Re: AMBER: question - gaff and leaprc.ff03ua
(Wed Nov 19 2008 - 07:08:02 PST)
Re: AMBER: problem with cartesian restraints with NTP simulations
(Wed Nov 19 2008 - 07:02:56 PST)
Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)
(Wed Nov 19 2008 - 06:35:45 PST)
Re: AMBER: AMBER10 compiling SANDER parallel problem
(Tue Nov 18 2008 - 13:25:23 PST)
Re: AMBER: segmentation fault when restarting periodic structure
(Tue Nov 18 2008 - 06:20:41 PST)
Re: AMBER: How to create *.top & *.crd file with hexagonal lattice
(Tue Nov 18 2008 - 06:05:12 PST)
Re: AMBER: problem
(Tue Nov 18 2008 - 04:15:57 PST)
Re: AMBER: SPCFW temperature oscillations
(Tue Nov 18 2008 - 04:13:16 PST)
Re: AMBER: AMBER10 installation question
(Tue Nov 18 2008 - 04:05:07 PST)
Re: AMBER: velocity units?
(Mon Nov 17 2008 - 08:53:19 PST)
Re: AMBER: AMBER question: perturbed charge twice the unperturbed
(Thu Nov 13 2008 - 12:39:41 PST)
Re: AMBER: load opls force field
(Thu Nov 13 2008 - 04:06:40 PST)
Re: AMBER: PB Radii
(Thu Nov 13 2008 - 04:01:57 PST)
Re: AMBER: ff02 in nmode gives error "too many dihedrals" ?
(Wed Nov 12 2008 - 07:13:45 PST)
Re: AMBER: Amber 9 installation problems
(Tue Nov 11 2008 - 15:22:54 PST)
Re: AMBER: test sander error in amber7
(Tue Nov 11 2008 - 04:15:51 PST)
Re: AMBER: Amber 9 installation problems
(Mon Nov 10 2008 - 09:32:39 PST)
Re: AMBER: looks like I have problem with "make clean" command
(Mon Nov 10 2008 - 04:39:26 PST)
Re: AMBER: problem with zMatrix in tleap
(Sun Nov 09 2008 - 09:17:02 PST)
Re: AMBER: AMBER question: perturbed charge twice the unperturbed
(Sun Nov 09 2008 - 09:16:52 PST)
Re: AMBER: AMBER : Inconsistent MD length and no of angles after ptraj
(Fri Nov 07 2008 - 21:33:48 PST)
Re: AMBER: ptraj and netcdf with AmberTools1.2 ?
(Thu Nov 06 2008 - 04:08:00 PST)
Re: AMBER: temperature error in md calculation
(Wed Nov 05 2008 - 06:10:41 PST)
Re: AMBER: Minimisation and heating under GB conditions
(Mon Nov 03 2008 - 06:01:59 PST)
Diddo Diddens
AMBER: segmentation fault when restarting periodic structure
(Fri Nov 14 2008 - 04:47:23 PST)
Dmitri Nilov
AMBER: Gradual releasing of position restraints
(Tue Nov 25 2008 - 06:23:02 PST)
AMBER: Equilibration protocol for large protein
(Tue Nov 18 2008 - 08:33:26 PST)
drugdesign
Re: AMBER: Amber 9 installation problems
(Thu Nov 13 2008 - 08:25:34 PST)
Re: AMBER: Amber 9 installation problems
(Wed Nov 12 2008 - 11:09:47 PST)
Re: AMBER: Amber 9 installation problems
(Tue Nov 11 2008 - 23:36:51 PST)
Re: AMBER: Amber 9 installation problems
(Tue Nov 11 2008 - 06:13:32 PST)
AMBER: Amber 9 installation problems
(Mon Nov 10 2008 - 03:27:39 PST)
AMBER: looks like I have problem with "make clean" command
(Sun Nov 09 2008 - 23:27:22 PST)
E.M.
Re: AMBER: AMBER question: perturbed charge twice the unperturbed
(Sun Nov 09 2008 - 15:08:05 PST)
Edward M
AMBER: AMBER question: perturbed charge twice the unperturbed
(Sat Nov 08 2008 - 21:36:54 PST)
Francesco Pietra
Re: AMBER: Heating up
(Fri Nov 28 2008 - 07:57:49 PST)
Re: AMBER: Setting GROUP for pmemd
(Fri Nov 28 2008 - 02:12:07 PST)
AMBER: Heating up
(Thu Nov 27 2008 - 10:29:30 PST)
Re: AMBER: RE: About restart amber
(Tue Nov 25 2008 - 13:47:35 PST)
Re: AMBER: RE: About restart amber
(Tue Nov 25 2008 - 12:59:35 PST)
Re: AMBER: RE: About restart amber
(Tue Nov 25 2008 - 00:00:38 PST)
Re: AMBER: RE: About restart amber
(Mon Nov 24 2008 - 13:22:44 PST)
Re: AMBER: GB versus explicit medium
(Mon Nov 24 2008 - 07:33:43 PST)
AMBER: GB versus explicit medium
(Mon Nov 24 2008 - 01:39:58 PST)
Re: AMBER: RE: About restart amber
(Sat Nov 22 2008 - 08:03:02 PST)
Re: AMBER: compiling ambertools with intel compilers
(Thu Nov 20 2008 - 10:44:21 PST)
Re: AMBER: compiling ambertools with intel compilers
(Thu Nov 20 2008 - 08:38:29 PST)
Re: AMBER: RESTRAINTS: no valid redirection found
(Mon Nov 17 2008 - 13:30:54 PST)
Re: AMBER: RESTRAINTS: no valid redirection found
(Mon Nov 17 2008 - 11:21:01 PST)
Re: AMBER: RESTRAINTS: no valid redirection found
(Mon Nov 17 2008 - 10:00:25 PST)
Fwd: AMBER: RESTRAINTS: no valid redirection found
(Mon Nov 17 2008 - 09:35:04 PST)
AMBER: RESTRAINTS: no valid redirection found
(Mon Nov 17 2008 - 09:15:17 PST)
Re: AMBER: Chloride anion ligands leave the protein during MD
(Sun Nov 16 2008 - 03:17:00 PST)
AMBER: Chloride anion ligands leave the protein during MD
(Thu Nov 13 2008 - 07:06:06 PST)
Re: AMBER: Minimisation and heating under GB conditions
(Mon Nov 03 2008 - 23:27:55 PST)
Re: AMBER: Minimisation and heating under GB conditions
(Mon Nov 03 2008 - 10:07:14 PST)
Re: AMBER: Minimisation and heating under GB conditions
(Mon Nov 03 2008 - 06:17:34 PST)
Re: AMBER: Minimisation and heating under GB conditions
(Mon Nov 03 2008 - 06:08:42 PST)
AMBER: Minimisation and heating under GB conditions
(Mon Nov 03 2008 - 00:58:58 PST)
Francois Theillet
AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters
(Fri Nov 07 2008 - 07:24:36 PST)
FyD
Re: AMBER: RED vIII-lack of charges in mol2
(Sat Nov 29 2008 - 08:23:34 PST)
Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ?
(Fri Nov 28 2008 - 23:30:19 PST)
Re: AMBER: antechamber and gaff for a homodimer
(Thu Nov 27 2008 - 08:02:55 PST)
Re: AMBER: problem
(Sun Nov 16 2008 - 23:40:33 PST)
Re: AMBER: organic solvents
(Fri Nov 14 2008 - 23:56:30 PST)
Gert Kiss
AMBER: normal-vector of a plane with 'corrplane'
(Thu Nov 27 2008 - 12:28:46 PST)
guardiani.fi.infn.it
AMBER: Electrostatic Energy Components
(Fri Nov 21 2008 - 11:29:08 PST)
Guillermo Mulliert Carlín
Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ?
(Thu Nov 27 2008 - 23:20:30 PST)
Gustavo Seabra
Re: AMBER: QM/MM simulation
(Sat Nov 22 2008 - 11:19:22 PST)
Re: AMBER: ptraj closest command
(Mon Nov 17 2008 - 08:51:42 PST)
Re: AMBER: Trajectory file ended and unit 24 error on open inptraj
(Sun Nov 16 2008 - 08:05:42 PST)
Re: AMBER: Sander *.top and *.crd file from PDB file
(Fri Nov 14 2008 - 12:30:21 PST)
Re: AMBER: Chloride anion ligands leave the protein during MD
(Fri Nov 14 2008 - 05:40:45 PST)
Re: AMBER: Problem with evaporating water over longer simulation times
(Wed Nov 12 2008 - 11:48:01 PST)
Re: AMBER: Steered MD and Jarzynski in pulling simulations
(Sun Nov 09 2008 - 18:36:38 PST)
Hazard, E. Starr
AMBER: AMBER10 failing to compile PMEMD
(Sat Nov 22 2008 - 14:06:03 PST)
AMBER: AMBER10 compiling SANDER parallel problem
(Tue Nov 18 2008 - 12:48:31 PST)
hfox1.nd.edu
RE: AMBER: Fully QM periodic runs
(Mon Nov 24 2008 - 13:28:36 PST)
Holger Gohlke
Re: AMBER: mm_pbsa.pl and Amber10
(Mon Nov 10 2008 - 09:12:16 PST)
Ilyas Yildirim
RE: AMBER: Electrostatic Energy Components
(Fri Nov 21 2008 - 16:12:44 PST)
RE: AMBER: Electrostatic Energy Components
(Fri Nov 21 2008 - 14:11:14 PST)
j00323240.students.jsums.edu
AMBER: problem with AMOEBA
(Wed Nov 26 2008 - 11:07:13 PST)
Jacob Kongsted
AMBER: ff02 in nmode gives error "too many dihedrals" ?
(Mon Nov 10 2008 - 01:16:36 PST)
Jeffrey
Re: RE: Re: Re: Re: AMBER: AdoMet parameterization with antechamber
(Thu Nov 27 2008 - 07:30:33 PST)
Re: Re: Re: Re: AMBER: AdoMet parameterization with antechamber
(Wed Nov 26 2008 - 06:44:27 PST)
Re: Re: Re: AMBER: AdoMet parameterization with antechamber
(Tue Nov 25 2008 - 08:14:44 PST)
Re: Re: AMBER: AdoMet parameterization with antechamber
(Mon Nov 24 2008 - 08:19:41 PST)
AMBER: AdoMet parameterization with antechamber
(Sun Nov 23 2008 - 07:55:30 PST)
Re: Re: AMBER: AMBER10 installation question
(Wed Nov 19 2008 - 05:27:13 PST)
AMBER: AMBER10 installation question
(Mon Nov 17 2008 - 19:20:14 PST)
Jeremy Harris
AMBER: pmemd
(Thu Nov 20 2008 - 08:27:14 PST)
Jesse Jun
AMBER: Ptraj Normal Mode Analysis
(Fri Nov 14 2008 - 13:19:31 PST)
Jianyin Shao
Re: AMBER: question about ptraj
(Thu Nov 13 2008 - 15:38:44 PST)
Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps
(Fri Nov 07 2008 - 08:24:03 PST)
Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps
(Thu Nov 06 2008 - 14:48:47 PST)
Jiri Sponer
Re: AMBER: Chloride anion ligands leave the protein during MD
(Fri Nov 14 2008 - 06:19:33 PST)
jitrayut jitonnom
Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ?
(Fri Nov 28 2008 - 15:34:43 PST)
AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ?
(Thu Nov 27 2008 - 17:26:54 PST)
Joachim Reichelt
AMBER: MOLYBDENUM
(Wed Nov 19 2008 - 06:14:31 PST)
Jochen Heil
AMBER: Your "bellymask-patch"
(Thu Nov 13 2008 - 05:45:30 PST)
AMBER: Newbie question: partial minimization in implicit solvent
(Wed Nov 12 2008 - 09:48:38 PST)
John Chodera
AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)
(Tue Nov 18 2008 - 11:58:22 PST)
John Finke
Re: AMBER: Problems compiling leap on Altix Cluster
(Mon Nov 03 2008 - 15:43:09 PST)
AMBER: Problems compiling leap on Altix Cluster
(Mon Nov 03 2008 - 12:51:54 PST)
Jojart Balazs
Re: AMBER: Electrostatic Energy Components
(Sun Nov 23 2008 - 00:34:01 PST)
Re: AMBER: Electrostatic Energy Components
(Fri Nov 21 2008 - 23:53:46 PST)
Jose Borreguero
AMBER: velocity units?
(Mon Nov 17 2008 - 08:14:35 PST)
Joseph Nachman
AMBER: Referencing AMBER
(Wed Nov 26 2008 - 08:01:57 PST)
AMBER: Restraints
(Thu Nov 13 2008 - 10:59:23 PST)
Junmei Wang
Re: AMBER: Electrostatic Energy Components
(Sun Nov 23 2008 - 19:36:38 PST)
Kevin Parkes
RE: AMBER: Test failure with Amber 10
(Wed Nov 26 2008 - 06:36:36 PST)
AMBER: Test failure with Amber 10
(Wed Nov 26 2008 - 02:33:35 PST)
Lachele Foley (Lists)
Re: AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters
(Fri Nov 07 2008 - 13:25:18 PST)
Re: AMBER: Glycam
(Thu Nov 06 2008 - 07:01:48 PST)
Larry Layne
Re: AMBER: MM_PBSA binding error
(Tue Nov 04 2008 - 05:51:22 PST)
Lili Peng
Re: AMBER: Force field for Gd3+ (metal ion)?
(Thu Nov 20 2008 - 16:00:29 PST)
Re: AMBER: xLeap error
(Mon Nov 10 2008 - 13:49:53 PST)
AMBER: xLeap error
(Mon Nov 10 2008 - 12:45:58 PST)
AMBER: Force field for Gd (gadolinium)?
(Thu Nov 06 2008 - 01:05:26 PST)
M. L. Dodson
Re: AMBER: GB versus explicit medium
(Mon Nov 24 2008 - 07:43:52 PST)
Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps
(Mon Nov 10 2008 - 10:23:17 PST)
Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps
(Fri Nov 07 2008 - 15:15:06 PST)
Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps
(Thu Nov 06 2008 - 15:49:49 PST)
AMBER: ptraj new mask parser: differences from ambmask and core dumps
(Thu Nov 06 2008 - 10:31:07 PST)
Re: AMBER: Steered MD and Jarzynski in pulling simulations
(Wed Nov 05 2008 - 07:04:23 PST)
Marcelo Puiatti
AMBER: organic solvents
(Fri Nov 14 2008 - 15:20:30 PST)
Margaret Johnson
AMBER: PMEMD with AMOEBA parms including a lone pair site
(Tue Nov 18 2008 - 18:29:04 PST)
Mark M Huntress
AMBER: resp charges in parameterization
(Wed Nov 12 2008 - 08:24:55 PST)
Mark Williamson
Re: AMBER: organic solvents
(Fri Nov 14 2008 - 15:28:10 PST)
Re: AMBER: xLeap error
(Mon Nov 10 2008 - 13:58:27 PST)
Marudachalam S
AMBER: Amber on linux
(Wed Nov 19 2008 - 09:58:10 PST)
Matthew Tessier
RE: AMBER: CG and HC atoms partial charges in AMBER
(Thu Nov 20 2008 - 09:09:16 PST)
RE: AMBER: CG and HC atoms partial charges in AMBER
(Thu Nov 20 2008 - 08:40:43 PST)
RE: AMBER: CG and HC atoms partial charges in AMBER
(Thu Nov 20 2008 - 08:15:56 PST)
Mengjuei Hsieh
Re: AMBER: gigabit ethernet cards and switches
(Thu Nov 06 2008 - 18:39:23 PST)
mori.cerm.unifi.it
Re: AMBER: AMBER forfield choose
(Thu Nov 20 2008 - 07:09:28 PST)
Naser Alijabbari
AMBER: SPCFW temperature oscillations
(Mon Nov 17 2008 - 20:19:12 PST)
AMBER: process_mdout modify
(Mon Nov 03 2008 - 22:20:07 PST)
Navnit Kumar Mishra
Re: AMBER: About antechamber and GAFF [UPDATED]
(Wed Nov 26 2008 - 05:04:20 PST)
Neha Gandhi
AMBER: RED vIII-lack of charges in mol2
(Sat Nov 29 2008 - 06:24:30 PST)
AMBER: Glycam
(Wed Nov 05 2008 - 20:02:01 PST)
Nina Fischer
AMBER: cis - trans isomerization
(Thu Nov 27 2008 - 06:39:21 PST)
oguz gurbulak
AMBER: using packmol file in Amber
(Tue Nov 25 2008 - 07:49:19 PST)
Re: AMBER: question - gaff and leaprc.ff03ua
(Sun Nov 23 2008 - 08:43:48 PST)
AMBER: question - gaff and leaprc.ff03ua
(Wed Nov 19 2008 - 05:56:17 PST)
AMBER: load opls force field
(Thu Nov 13 2008 - 02:38:11 PST)
parul sharma
AMBER: AMBER : Inconsistent MD length and no of angles after ptraj
(Fri Nov 07 2008 - 01:52:07 PST)
Patrick McCarren
Re: AMBER: Optimal compiling of amber on XT3
(Sat Nov 01 2008 - 00:13:08 PDT)
Prem Prakash Pathak
AMBER:
(Mon Nov 03 2008 - 19:20:09 PST)
priya priya
Re: AMBER: problem with group input and NMR restaints
(Wed Nov 05 2008 - 12:00:48 PST)
Re: AMBER: problem with group input and NMR restaints
(Wed Nov 05 2008 - 09:22:33 PST)
Re: AMBER: problem with group input and NMR restaints
(Wed Nov 05 2008 - 08:05:05 PST)
Re: AMBER: problem with group input and NMR restaints
(Tue Nov 04 2008 - 09:38:37 PST)
RE: AMBER: problem with group input and NMR restaints
(Tue Nov 04 2008 - 08:16:34 PST)
AMBER: problem with group input and NMR restaints
(Tue Nov 04 2008 - 07:20:09 PST)
rai001.student.ucr.edu
Re: AMBER: question about ptraj
(Thu Nov 13 2008 - 15:56:49 PST)
AMBER: question about ptraj
(Wed Nov 12 2008 - 22:30:48 PST)
Ray Luo
RE: AMBER: MM_PBSA binding error
(Tue Nov 04 2008 - 11:18:54 PST)
rebeca
Re: AMBER: antechamber and gaff for a homodimer
(Thu Nov 27 2008 - 05:33:19 PST)
AMBER: antechamber and gaff for a homodimer
(Thu Nov 27 2008 - 03:12:23 PST)
robaldo.dna.uba.ar
Re: AMBER: ptraj center problem
(Fri Nov 21 2008 - 12:04:56 PST)
AMBER: ptraj center problem
(Fri Nov 21 2008 - 09:31:27 PST)
Robert Duke
Re: AMBER: Question fot Amber 10 Benchmarks
(Thu Nov 27 2008 - 06:37:20 PST)
Re: AMBER: Test failure with Amber 10
(Wed Nov 26 2008 - 09:28:14 PST)
Re: AMBER: RE: About restart amber
(Tue Nov 25 2008 - 13:55:15 PST)
Re: AMBER: RE: About restart amber
(Tue Nov 25 2008 - 13:23:09 PST)
Re: AMBER: RE: About restart amber
(Tue Nov 25 2008 - 06:27:16 PST)
Re: AMBER: Ewald troubles when running very big boxes
(Mon Nov 24 2008 - 18:09:23 PST)
Re: AMBER: AMBER10 failing to compile PMEMD
(Sat Nov 22 2008 - 14:42:50 PST)
Re: AMBER: pmemd
(Thu Nov 20 2008 - 08:40:36 PST)
Re: AMBER: PMEMD with AMOEBA parms including a lone pair site
(Tue Nov 18 2008 - 18:50:14 PST)
Re: AMBER: SPCFW temperature oscillations
(Tue Nov 18 2008 - 05:16:27 PST)
Re: AMBER: RESTRAINTS: no valid redirection found
(Mon Nov 17 2008 - 11:58:18 PST)
Re: AMBER: RESTRAINTS: no valid redirection found
(Mon Nov 17 2008 - 09:34:50 PST)
Ross Walker
RE: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ?
(Fri Nov 28 2008 - 18:11:49 PST)
RE: AMBER: Question fot Amber 10 Benchmarks
(Thu Nov 27 2008 - 08:57:06 PST)
RE: AMBER: Problem running NEB in AMBER10
(Wed Nov 26 2008 - 11:04:55 PST)
RE: Re: Re: Re: AMBER: AdoMet parameterization with antechamber
(Wed Nov 26 2008 - 09:28:51 PST)
RE: AMBER: About antechamber and GAFF [UPDATED]
(Wed Nov 26 2008 - 08:39:30 PST)
RE: AMBER: Test failure with Amber 10
(Wed Nov 26 2008 - 08:30:42 PST)
RE: AMBER: Fully QM periodic runs
(Tue Nov 25 2008 - 08:54:24 PST)
RE: AMBER: Gradual releasing of position restraints
(Tue Nov 25 2008 - 08:48:13 PST)
RE: AMBER: Electrostatic Energy Components
(Sat Nov 22 2008 - 09:21:22 PST)
RE: AMBER: RE: About restart amber
(Sat Nov 22 2008 - 09:18:57 PST)
RE: AMBER: QM/MM simulation
(Sat Nov 22 2008 - 08:59:49 PST)
RE: AMBER: Electrostatic Energy Components
(Fri Nov 21 2008 - 16:20:56 PST)
RE: AMBER: Electrostatic Energy Components
(Fri Nov 21 2008 - 14:33:30 PST)
AMBER: RE: About restart amber
(Fri Nov 21 2008 - 13:45:16 PST)
RE: AMBER: Electrostatic Energy Components
(Fri Nov 21 2008 - 13:36:20 PST)
RE: AMBER: pmemd
(Thu Nov 20 2008 - 08:36:51 PST)
RE: AMBER: Restraints
(Thu Nov 13 2008 - 11:11:53 PST)
RE: AMBER: Your "bellymask-patch"
(Thu Nov 13 2008 - 10:17:58 PST)
RE: AMBER: Amber 9 installation problems
(Wed Nov 12 2008 - 13:16:03 PST)
RE: AMBER: Newbie question: partial minimization in implicit solvent
(Wed Nov 12 2008 - 13:00:39 PST)
RE: AMBER: Amber 9 installation problems
(Wed Nov 12 2008 - 07:21:59 PST)
AMBER: RE: problems about TMD in your tutorial
(Mon Nov 10 2008 - 00:20:18 PST)
RE: AMBER: using "EP" for dummy atom
(Thu Nov 06 2008 - 18:05:22 PST)
AMBER: RE: problems about TMD in your tutorial
(Thu Nov 06 2008 - 11:32:58 PST)
AMBER: RE: Problem with the NEB tutorial
(Thu Nov 06 2008 - 11:24:30 PST)
RE: AMBER: gigabit ethernet cards and switches
(Thu Nov 06 2008 - 10:37:04 PST)
AMBER: RE: QUERRY?
(Thu Nov 06 2008 - 10:37:04 PST)
AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query
(Thu Nov 06 2008 - 10:37:04 PST)
AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query
(Thu Nov 06 2008 - 00:18:22 PST)
RE: AMBER: AMBER10: QMMM parallel test error
(Wed Nov 05 2008 - 17:41:27 PST)
RE: AMBER: problem with group input and NMR restaints
(Tue Nov 04 2008 - 07:46:17 PST)
RE: AMBER: process_mdout modify
(Tue Nov 04 2008 - 07:41:33 PST)
RE: AMBER: Problems compiling leap on Altix Cluster
(Mon Nov 03 2008 - 16:06:07 PST)
RE: AMBER: Problems compiling leap on Altix Cluster
(Mon Nov 03 2008 - 13:47:06 PST)
RE: AMBER: error message of xleap
(Mon Nov 03 2008 - 09:05:54 PST)
Ryan Pavlovicz
AMBER: NMR optimization with group averages (IGR1 / IGR2)
(Fri Nov 14 2008 - 07:59:36 PST)
S.Sundar Raman
AMBER: seeking help regrading Zinc protein GBSA minimization
(Thu Nov 27 2008 - 04:32:08 PST)
Saiful Islam
Re: AMBER: test sander error in amber7
(Mon Nov 10 2008 - 23:36:30 PST)
AMBER: test sander error in amber7
(Mon Nov 10 2008 - 05:43:45 PST)
Samuel Genheden
AMBER: Steered MD and Jarzynski in pulling simulations
(Wed Nov 05 2008 - 06:48:33 PST)
Sasha Buzko
Re: AMBER: Problem with evaporating water over longer simulation times
(Wed Nov 12 2008 - 16:53:06 PST)
Re: AMBER: Problem with evaporating water over longer simulation times
(Wed Nov 12 2008 - 12:56:16 PST)
AMBER: Problem with evaporating water over longer simulation times
(Wed Nov 12 2008 - 11:14:00 PST)
saurabh agrawal
AMBER: nonbonded parameters for titanium
(Mon Nov 24 2008 - 08:57:56 PST)
Sergey Samsonov
AMBER: Problems of MM/MM-GBSA calculations
(Thu Nov 27 2008 - 02:53:53 PST)
Shozeb Haider
Re: AMBER: Amber 9 installation problems
(Mon Nov 10 2008 - 08:37:54 PST)
Siddharth Rastogi
AMBER: High ESURF
(Mon Nov 17 2008 - 00:07:57 PST)
Re: AMBER: Trajectory file ended and unit 24 error on open inptraj
(Sat Nov 15 2008 - 22:18:59 PST)
AMBER: Trajectory file ended and unit 24 error on open inptraj
(Sat Nov 15 2008 - 07:33:10 PST)
AMBER: how to remove counter ions ( K+ / Cl- ions) using rdparm?
(Fri Nov 14 2008 - 06:02:34 PST)
steinbrt.rci.rutgers.edu
AMBER: Ewald troubles when running very big boxes
(Mon Nov 24 2008 - 12:50:50 PST)
Re: AMBER: Amber on linux
(Wed Nov 19 2008 - 11:47:45 PST)
AMBER: ptraj closest command
(Mon Nov 17 2008 - 08:14:11 PST)
Re: AMBER: subroutine for torsional potential
(Fri Nov 14 2008 - 06:49:25 PST)
Re: AMBER: Problem with evaporating water over longer simulation times
(Wed Nov 12 2008 - 11:57:33 PST)
Re: AMBER: resp charges in parameterization
(Wed Nov 12 2008 - 08:44:17 PST)
Stephan.Reiling.sanofi-aventis.com
AMBER: mm_pbsa.pl and Amber10
(Mon Nov 10 2008 - 08:05:27 PST)
Stephane Abel
Re: AMBER: About antechamber and GAFF [UPDATED]
(Thu Nov 27 2008 - 03:33:56 PST)
AMBER: About antechamber and GAFF [UPDATED]
(Wed Nov 26 2008 - 03:21:52 PST)
AMBER: About antechamber and GAFF
(Wed Nov 26 2008 - 03:02:00 PST)
Re: AMBER: CG and HC atoms partial charges in AMBER
(Thu Nov 20 2008 - 09:07:07 PST)
Re: AMBER: CG and HC atoms partial charges in AMBER
(Thu Nov 20 2008 - 08:51:25 PST)
Re: AMBER: CG and HC atoms partial charges in AMBER
(Thu Nov 20 2008 - 08:26:10 PST)
AMBER: CG and HC atoms partial charges in AMBER
(Thu Nov 20 2008 - 07:40:17 PST)
Su Nwe
AMBER: unsubscribe amber
(Mon Nov 24 2008 - 23:12:02 PST)
Swarup Gupta
Re: AMBER: PB Radii
(Mon Nov 17 2008 - 03:24:42 PST)
Re: AMBER: PB Radii
(Sat Nov 15 2008 - 19:44:25 PST)
AMBER: PB Radii
(Wed Nov 12 2008 - 23:06:34 PST)
sychen
Re[2]: AMBER: Question fot Amber 10 Benchmarks
(Thu Nov 27 2008 - 18:18:00 PST)
AMBER: Question fot Amber 10 Benchmarks
(Wed Nov 26 2008 - 23:50:11 PST)
Syed Tarique Moin
Re: AMBER: QM/MM simulation
(Sat Nov 22 2008 - 07:11:12 PST)
AMBER: QM/MM simulation
(Sat Nov 22 2008 - 00:00:36 PST)
Taufik Al-Sarraj
Re: AMBER: changing pdb structure
(Mon Nov 24 2008 - 15:37:24 PST)
Re: AMBER: changing pdb structure
(Mon Nov 10 2008 - 13:10:23 PST)
Re: AMBER: changing pdb structure
(Mon Nov 10 2008 - 12:31:39 PST)
AMBER: coot mutation
(Thu Nov 06 2008 - 12:19:00 PST)
Thomas Patko
Re: AMBER: compiling ambertools with intel compilers
(Thu Nov 20 2008 - 14:15:58 PST)
tri nam Vo
AMBER: Running Amber8 - Sander
(Sun Nov 23 2008 - 22:28:31 PST)
vallespardojl.chem.leidenuniv.nl
AMBER: Problems for use manganese molecules
(Fri Nov 21 2008 - 01:06:37 PST)
Wang,Ying
Re: AMBER: AMBER forfield choose
(Thu Nov 20 2008 - 07:17:45 PST)
Re: AMBER: AMBER forfield choose
(Thu Nov 20 2008 - 07:05:28 PST)
AMBER: AMBER forfield choose
(Thu Nov 20 2008 - 06:32:24 PST)
Wei Huang
Re: Re: AMBER: AdoMet parameterization with antechamber
(Mon Nov 24 2008 - 08:41:12 PST)
Wenyong Tong
Re: AMBER: About antechamber and GAFF [UPDATED]
(Wed Nov 26 2008 - 09:13:34 PST)
Yang, Ping
RE: AMBER: AMBER10: QMMM parallel test error
(Wed Nov 05 2008 - 19:57:29 PST)
AMBER: AMBER10: QMMM parallel test error
(Wed Nov 05 2008 - 15:44:27 PST)
Ye Mei
AMBER: Is there an easy way to calculate the electric field at the center of a group of atoms
(Thu Nov 27 2008 - 07:12:51 PST)
Last message date
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Fri Dec 05 2008 - 18:12:45 PST
Archived on
: Mon Dec 23 2024 - 05:53:40 PST
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