AMBER Archive (2008) - Nov 2008 By Author

Starting: Sat Nov 01 2008 - 02:13:08 CDT
Ending: Sat Nov 29 2008 - 17:43:21 CST

• Adrian Roitberg
  • Re: AMBER: Chloride anion ligands leave the protein during MD (Fri Nov 14 2008 - 08:00:33 CST)
  • Re: AMBER: Problem with evaporating water over longer simulation times (Wed Nov 12 2008 - 19:06:38 CST)
• Alan
  • Re: AMBER: antechamber and gaff for a homodimer (Thu Nov 27 2008 - 06:27:31 CST)
  • Re: AMBER: AdoMet parameterization with antechamber (Mon Nov 24 2008 - 04:46:52 CST)
  • Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) (Thu Nov 20 2008 - 06:13:09 CST)
  • Re: AMBER: compiling ambertools with intel compilers (Thu Nov 20 2008 - 06:10:58 CST)
  • Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) (Thu Nov 20 2008 - 05:48:56 CST)
  • AMBER: compiling ambertools with intel compilers (Thu Nov 20 2008 - 04:27:26 CST)
• Alessandro Nascimento
  • Re: AMBER: gigabit ethernet cards and switches (Thu Nov 06 2008 - 13:28:46 CST)
  • AMBER: gigabit ethernet cards and switches (Thu Nov 06 2008 - 10:51:43 CST)
• Andreas Svrcek-Seiler
  • Re: AMBER: High ESURF (Mon Nov 17 2008 - 02:24:02 CST)
• Andrei Neamtu
  • AMBER: compiling amber 10 (Sat Nov 22 2008 - 01:26:58 CST)
• Arturas Ziemys
  • AMBER: molsurf fails (Tue Nov 25 2008 - 09:27:27 CST)
  • Re: AMBER: problem (Tue Nov 18 2008 - 09:07:19 CST)
  • RE: AMBER: problem (Mon Nov 17 2008 - 22:36:25 CST)
  • AMBER: problem (Sun Nov 16 2008 - 23:07:38 CST)
  • AMBER: MM-PBSA and trajectory input (Thu Nov 13 2008 - 11:22:36 CST)
• Ashish Sangwai
  • Re: AMBER: Restraints (Thu Nov 13 2008 - 13:11:45 CST)
  • AMBER: using "EP" for dummy atom (Thu Nov 06 2008 - 19:24:23 CST)
• babak minoofar
  • AMBER: N(CN2)- ion (Fri Nov 28 2008 - 07:12:26 CST)
• Balazs JOJART
  • Re: AMBER: Electrostatic Energy Components (Mon Nov 24 2008 - 06:19:42 CST)
• Barbault Florent
  • Re: AMBER: AMBER forfield choose (Thu Nov 20 2008 - 08:45:20 CST)
  • Re: AMBER: AMBER forfield choose (Thu Nov 20 2008 - 10:21:17 CST)
  • AMBER: problem with cartesian restraints with NTP simulations (Wed Nov 19 2008 - 08:50:13 CST)
• Bill Ross
  • Re: AMBER: load opls force field (Thu Nov 13 2008 - 14:32:19 CST)
  • Re: AMBER: Extracting periodic box size deviation (Thu Nov 06 2008 - 19:42:35 CST)
• Campbell, Patrick
  • AMBER: Question on AMBER MD Implications (Sat Nov 01 2008 - 05:01:17 CDT)
• Carlos Simmerling
  • Re: AMBER: Questions on TIP4P model? (Fri Nov 28 2008 - 14:03:14 CST)
  • Re: AMBER: seeking help regrading Zinc protein GBSA minimization (Fri Nov 28 2008 - 06:33:16 CST)
  • Re: AMBER: Heating up (Fri Nov 28 2008 - 06:30:29 CST)
  • Re: AMBER: GB versus explicit medium (Mon Nov 24 2008 - 05:08:40 CST)
  • Re: AMBER: Electrostatic Energy Components (Sat Nov 22 2008 - 11:42:53 CST)
  • Re: AMBER: Electrostatic Energy Components (Sat Nov 22 2008 - 11:41:48 CST)
  • Re: AMBER: Electrostatic Energy Components (Fri Nov 21 2008 - 17:46:10 CST)
  • Re: AMBER: ptraj center problem (Fri Nov 21 2008 - 12:42:17 CST)
  • Re: AMBER: AMBER forfield choose (Thu Nov 20 2008 - 10:21:51 CST)
  • Re: AMBER: AMBER forfield choose (Thu Nov 20 2008 - 09:51:18 CST)
  • Re: AMBER: PB Radii (Mon Nov 17 2008 - 05:30:41 CST)
  • Re: AMBER: Trajectory file ended and unit 24 error on open inptraj (Sun Nov 16 2008 - 06:42:22 CST)
  • Re: AMBER: Trajectory file ended and unit 24 error on open inptraj (Sat Nov 15 2008 - 09:44:32 CST)
  • Re: AMBER: Sander *.top and *.crd file from PDB file (Fri Nov 14 2008 - 15:00:30 CST)
  • Re: AMBER: Newbie question: partial minimization in implicit solvent (Wed Nov 12 2008 - 14:47:56 CST)
  • Re: AMBER: changing pdb structure (Tue Nov 11 2008 - 05:35:42 CST)
  • Re: AMBER: changing pdb structure (Mon Nov 10 2008 - 14:37:32 CST)
  • Re: AMBER: problem with group input and NMR restaints (Wed Nov 05 2008 - 14:39:29 CST)
  • Re: AMBER: problem with group input and NMR restaints (Wed Nov 05 2008 - 12:13:29 CST)
  • Re: AMBER: problem with group input and NMR restaints (Wed Nov 05 2008 - 10:53:09 CST)
  • Re: AMBER: problem with group input and NMR restaints (Tue Nov 04 2008 - 11:53:48 CST)
  • Re: AMBER: problem with group input and NMR restaints (Tue Nov 04 2008 - 10:41:22 CST)
  • Re: AMBER: problem with group input and NMR restaints (Tue Nov 04 2008 - 09:35:46 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 12:52:23 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 08:45:22 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 05:29:25 CST)
• Catein Catherine
  • AMBER: temperature error in md calculation (Wed Nov 05 2008 - 02:11:41 CST)
  • RE: AMBER: error message of xleap (Mon Nov 03 2008 - 03:52:24 CST)
• CHAMI F.
  • AMBER: Choline chloride salt (Wed Nov 26 2008 - 08:49:45 CST)
  • AMBER: subroutine Work : Jarynski work theorem (Wed Nov 26 2008 - 06:21:07 CST)
  • AMBER: subroutine for torsional potential (Fri Nov 14 2008 - 08:16:37 CST)
• Chih-Ying Lin
  • AMBER: Br - ion defined ? (Wed Nov 05 2008 - 11:20:36 CST)
• Chin, Keith B
  • RE: AMBER: Questions on TIP4P model? (Sat Nov 29 2008 - 17:43:21 CST)
  • AMBER: Questions on TIP4P model? (Fri Nov 28 2008 - 13:20:38 CST)
  • RE: AMBER: How to manually adjust periodic boundary conditions (PBC) (Wed Nov 19 2008 - 19:15:17 CST)
  • AMBER: How to manually adjust periodic boundary conditions (PBC) (Wed Nov 19 2008 - 13:58:41 CST)
  • AMBER: (Tue Nov 18 2008 - 17:39:26 CST)
  • AMBER: How to create *.top & *.crd file with hexagonal lattice (Sun Nov 16 2008 - 19:02:05 CST)
  • RE: AMBER: Sander *.top and *.crd file from PDB file (Fri Nov 14 2008 - 14:55:57 CST)
  • AMBER: Sander *.top and *.crd file from PDB file (Fri Nov 14 2008 - 13:43:41 CST)
• Chris C.
  • AMBER: Problem running NEB in AMBER10 (Wed Nov 26 2008 - 12:38:17 CST)
• CJ Dickson
  • AMBER: Extracting periodic box size deviation (Thu Nov 06 2008 - 17:29:20 CST)
• Dave Rogers
  • Re: AMBER: ptraj and netcdf with AmberTools1.2 ? (Wed Nov 05 2008 - 15:34:21 CST)
• David A. Case
  • Re: AMBER: Questions on TIP4P model? (Sat Nov 29 2008 - 13:21:01 CST)
  • Re: AMBER: Gradual releasing of position restraints (Wed Nov 26 2008 - 11:00:41 CST)
  • Re: AMBER: Referencing AMBER (Wed Nov 26 2008 - 10:25:20 CST)
  • Re: AMBER: Test failure with Amber 10 (Wed Nov 26 2008 - 06:46:41 CST)
  • Re: AMBER: using packmol file in Amber (Tue Nov 25 2008 - 13:45:29 CST)
  • Re: AMBER: molsurf fails (Tue Nov 25 2008 - 13:26:14 CST)
  • Re: AMBER: Fully QM periodic runs (Tue Nov 25 2008 - 05:56:51 CST)
  • Re: Re: AMBER: AdoMet parameterization with antechamber (Mon Nov 24 2008 - 11:19:54 CST)
  • Re: AMBER: Electrostatic Energy Components (Mon Nov 24 2008 - 06:14:13 CST)
  • Re: AMBER: question - gaff and leaprc.ff03ua (Sun Nov 23 2008 - 15:49:37 CST)
  • Re: AMBER: AdoMet parameterization with antechamber (Sun Nov 23 2008 - 15:13:23 CST)
  • Re: AMBER: Electrostatic Energy Components (Sat Nov 22 2008 - 14:37:51 CST)
  • Re: AMBER: compiling amber 10 (Sat Nov 22 2008 - 14:33:54 CST)
  • Re: AMBER: QM/MM simulation (Sat Nov 22 2008 - 08:53:50 CST)
  • Re: AMBER: compiling ambertools with intel compilers (Fri Nov 21 2008 - 11:44:58 CST)
  • Re: AMBER: Problems for use manganese molecules (Fri Nov 21 2008 - 06:46:22 CST)
  • Re: AMBER: How to manually adjust periodic boundary conditions (PBC) (Thu Nov 20 2008 - 14:52:57 CST)
  • Re: AMBER: compiling ambertools with intel compilers (Thu Nov 20 2008 - 14:50:27 CST)
  • Re: AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 09:56:15 CST)
  • Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) (Thu Nov 20 2008 - 07:38:37 CST)
  • Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) (Thu Nov 20 2008 - 07:36:48 CST)
  • Re: AMBER: compiling ambertools with intel compilers (Thu Nov 20 2008 - 06:04:22 CST)
  • Re: AMBER: How to manually adjust periodic boundary conditions (PBC) (Wed Nov 19 2008 - 17:35:33 CST)
  • Re: AMBER: question - gaff and leaprc.ff03ua (Wed Nov 19 2008 - 09:08:02 CST)
  • Re: AMBER: problem with cartesian restraints with NTP simulations (Wed Nov 19 2008 - 09:02:56 CST)
  • Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) (Wed Nov 19 2008 - 08:35:45 CST)
  • Re: AMBER: AMBER10 compiling SANDER parallel problem (Tue Nov 18 2008 - 15:25:23 CST)
  • Re: AMBER: segmentation fault when restarting periodic structure (Tue Nov 18 2008 - 08:20:41 CST)
  • Re: AMBER: How to create *.top & *.crd file with hexagonal lattice (Tue Nov 18 2008 - 08:05:12 CST)
  • Re: AMBER: problem (Tue Nov 18 2008 - 06:15:57 CST)
  • Re: AMBER: SPCFW temperature oscillations (Tue Nov 18 2008 - 06:13:16 CST)
  • Re: AMBER: AMBER10 installation question (Tue Nov 18 2008 - 06:05:07 CST)
  • Re: AMBER: velocity units? (Mon Nov 17 2008 - 10:53:19 CST)
  • Re: AMBER: AMBER question: perturbed charge twice the unperturbed (Thu Nov 13 2008 - 14:39:41 CST)
  • Re: AMBER: load opls force field (Thu Nov 13 2008 - 06:06:40 CST)
  • Re: AMBER: PB Radii (Thu Nov 13 2008 - 06:01:57 CST)
  • Re: AMBER: ff02 in nmode gives error "too many dihedrals" ? (Wed Nov 12 2008 - 09:13:45 CST)
  • Re: AMBER: Amber 9 installation problems (Tue Nov 11 2008 - 17:22:54 CST)
  • Re: AMBER: test sander error in amber7 (Tue Nov 11 2008 - 06:15:51 CST)
  • Re: AMBER: Amber 9 installation problems (Mon Nov 10 2008 - 11:32:39 CST)
  • Re: AMBER: looks like I have problem with "make clean" command (Mon Nov 10 2008 - 06:39:26 CST)
  • Re: AMBER: AMBER question: perturbed charge twice the unperturbed (Sun Nov 09 2008 - 11:16:52 CST)
  • Re: AMBER: problem with zMatrix in tleap (Sun Nov 09 2008 - 11:17:02 CST)
  • Re: AMBER: AMBER : Inconsistent MD length and no of angles after ptraj (Fri Nov 07 2008 - 23:33:48 CST)
  • Re: AMBER: ptraj and netcdf with AmberTools1.2 ? (Thu Nov 06 2008 - 06:08:00 CST)
  • Re: AMBER: temperature error in md calculation (Wed Nov 05 2008 - 08:10:41 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 08:01:59 CST)
• Diddo Diddens
  • AMBER: segmentation fault when restarting periodic structure (Fri Nov 14 2008 - 06:47:23 CST)
• Dmitri Nilov
  • AMBER: Gradual releasing of position restraints (Tue Nov 25 2008 - 08:23:02 CST)
  • AMBER: Equilibration protocol for large protein (Tue Nov 18 2008 - 10:33:26 CST)
• drugdesign
  • Re: AMBER: Amber 9 installation problems (Thu Nov 13 2008 - 10:25:34 CST)
  • Re: AMBER: Amber 9 installation problems (Wed Nov 12 2008 - 13:09:47 CST)
  • Re: AMBER: Amber 9 installation problems (Wed Nov 12 2008 - 01:36:51 CST)
  • Re: AMBER: Amber 9 installation problems (Tue Nov 11 2008 - 08:13:32 CST)
  • AMBER: Amber 9 installation problems (Mon Nov 10 2008 - 05:27:39 CST)
  • AMBER: looks like I have problem with "make clean" command (Mon Nov 10 2008 - 01:27:22 CST)
• E.M.
  • Re: AMBER: AMBER question: perturbed charge twice the unperturbed (Sun Nov 09 2008 - 17:08:05 CST)
• Edward M
  • AMBER: AMBER question: perturbed charge twice the unperturbed (Sat Nov 08 2008 - 23:36:54 CST)
• Francesco Pietra
  • Re: AMBER: Heating up (Fri Nov 28 2008 - 09:57:49 CST)
  • Re: AMBER: Setting GROUP for pmemd (Fri Nov 28 2008 - 04:12:07 CST)
  • Re: AMBER: Setting GROUP for pmemd (Fri Nov 28 2008 - 04:12:07 CST)
  • AMBER: Heating up (Thu Nov 27 2008 - 12:29:30 CST)
  • Re: AMBER: RE: About restart amber (Tue Nov 25 2008 - 15:47:35 CST)
  • Re: AMBER: RE: About restart amber (Tue Nov 25 2008 - 14:59:35 CST)
  • Re: AMBER: RE: About restart amber (Tue Nov 25 2008 - 02:00:38 CST)
  • Re: AMBER: RE: About restart amber (Mon Nov 24 2008 - 15:22:44 CST)
  • Re: AMBER: GB versus explicit medium (Mon Nov 24 2008 - 09:33:43 CST)
  • AMBER: GB versus explicit medium (Mon Nov 24 2008 - 03:39:58 CST)
  • Re: AMBER: RE: About restart amber (Sat Nov 22 2008 - 10:03:02 CST)
  • Re: AMBER: compiling ambertools with intel compilers (Thu Nov 20 2008 - 12:44:21 CST)
  • Re: AMBER: compiling ambertools with intel compilers (Thu Nov 20 2008 - 10:38:29 CST)
  • Re: AMBER: RESTRAINTS: no valid redirection found (Mon Nov 17 2008 - 15:30:54 CST)
  • Re: AMBER: RESTRAINTS: no valid redirection found (Mon Nov 17 2008 - 13:21:01 CST)
  • Re: AMBER: RESTRAINTS: no valid redirection found (Mon Nov 17 2008 - 12:00:25 CST)
  • Fwd: AMBER: RESTRAINTS: no valid redirection found (Mon Nov 17 2008 - 11:35:04 CST)
  • AMBER: RESTRAINTS: no valid redirection found (Mon Nov 17 2008 - 11:15:17 CST)
  • Re: AMBER: Chloride anion ligands leave the protein during MD (Sun Nov 16 2008 - 05:17:00 CST)
  • AMBER: Chloride anion ligands leave the protein during MD (Thu Nov 13 2008 - 09:06:06 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Tue Nov 04 2008 - 01:27:55 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 12:07:14 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 08:17:34 CST)
  • Re: AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 08:08:42 CST)
  • AMBER: Minimisation and heating under GB conditions (Mon Nov 03 2008 - 02:58:58 CST)
• Francois Theillet
  • AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters (Fri Nov 07 2008 - 09:24:36 CST)
• FyD
  • Re: AMBER: RED vIII-lack of charges in mol2 (Sat Nov 29 2008 - 10:23:34 CST)
  • Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? (Sat Nov 29 2008 - 01:30:19 CST)
  • Re: AMBER: antechamber and gaff for a homodimer (Thu Nov 27 2008 - 10:02:55 CST)
  • Re: AMBER: problem (Mon Nov 17 2008 - 01:40:33 CST)
  • Re: AMBER: organic solvents (Sat Nov 15 2008 - 01:56:30 CST)
• Gert Kiss
  • AMBER: normal-vector of a plane with 'corrplane' (Thu Nov 27 2008 - 14:28:46 CST)
• guardiani_at_fi.infn.it
  • AMBER: Electrostatic Energy Components (Fri Nov 21 2008 - 13:29:08 CST)
• Guillermo Mulliert Carlín
  • Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? (Fri Nov 28 2008 - 01:20:30 CST)
• Gustavo Seabra
  • Re: AMBER: QM/MM simulation (Sat Nov 22 2008 - 13:19:22 CST)
  • Re: AMBER: ptraj closest command (Mon Nov 17 2008 - 10:51:42 CST)
  • Re: AMBER: Trajectory file ended and unit 24 error on open inptraj (Sun Nov 16 2008 - 10:05:42 CST)
  • Re: AMBER: Sander *.top and *.crd file from PDB file (Fri Nov 14 2008 - 14:30:21 CST)
  • Re: AMBER: Chloride anion ligands leave the protein during MD (Fri Nov 14 2008 - 07:40:45 CST)
  • Re: AMBER: Problem with evaporating water over longer simulation times (Wed Nov 12 2008 - 13:48:01 CST)
  • Re: AMBER: Steered MD and Jarzynski in pulling simulations (Sun Nov 09 2008 - 20:36:38 CST)
• Hazard, E. Starr
  • AMBER: AMBER10 failing to compile PMEMD (Sat Nov 22 2008 - 16:06:03 CST)
  • AMBER: AMBER10 compiling SANDER parallel problem (Tue Nov 18 2008 - 14:48:31 CST)
• hfox1_at_nd.edu
  • RE: AMBER: Fully QM periodic runs (Mon Nov 24 2008 - 15:28:36 CST)
• Holger Gohlke
  • Re: AMBER: mm_pbsa.pl and Amber10 (Mon Nov 10 2008 - 11:12:16 CST)
• Ilyas Yildirim
  • RE: AMBER: Electrostatic Energy Components (Fri Nov 21 2008 - 18:12:44 CST)
  • RE: AMBER: Electrostatic Energy Components (Fri Nov 21 2008 - 16:11:14 CST)
• j00323240_at_students.jsums.edu
  • AMBER: problem with AMOEBA (Wed Nov 26 2008 - 13:07:13 CST)
• Jacob Kongsted
  • AMBER: ff02 in nmode gives error "too many dihedrals" ? (Mon Nov 10 2008 - 03:16:36 CST)
• Jeffrey
  • Re: RE: Re: Re: Re: AMBER: AdoMet parameterization with antechamber (Thu Nov 27 2008 - 09:30:33 CST)
  • Re: Re: Re: Re: AMBER: AdoMet parameterization with antechamber (Wed Nov 26 2008 - 08:44:27 CST)
  • Re: Re: Re: AMBER: AdoMet parameterization with antechamber (Tue Nov 25 2008 - 10:14:44 CST)
  • Re: Re: AMBER: AdoMet parameterization with antechamber (Mon Nov 24 2008 - 10:19:41 CST)
  • AMBER: AdoMet parameterization with antechamber (Sun Nov 23 2008 - 09:55:30 CST)
  • Re: Re: AMBER: AMBER10 installation question (Wed Nov 19 2008 - 07:27:13 CST)
  • AMBER: AMBER10 installation question (Mon Nov 17 2008 - 21:20:14 CST)
• Jeremy Harris
  • AMBER: pmemd (Thu Nov 20 2008 - 10:27:14 CST)
• Jesse Jun
  • AMBER: Ptraj Normal Mode Analysis (Fri Nov 14 2008 - 15:19:31 CST)
• Jianyin Shao
  • Re: AMBER: question about ptraj (Thu Nov 13 2008 - 17:38:44 CST)
  • Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps (Fri Nov 07 2008 - 10:24:03 CST)
  • Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps (Thu Nov 06 2008 - 16:48:47 CST)
• Jiri Sponer
  • Re: AMBER: Chloride anion ligands leave the protein during MD (Fri Nov 14 2008 - 08:19:33 CST)
• jitrayut jitonnom
  • Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? (Fri Nov 28 2008 - 17:34:43 CST)
  • AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? (Thu Nov 27 2008 - 19:26:54 CST)
• Joachim Reichelt
  • AMBER: MOLYBDENUM (Wed Nov 19 2008 - 08:14:31 CST)
• Jochen Heil
  • AMBER: Your "bellymask-patch" (Thu Nov 13 2008 - 07:45:30 CST)
  • AMBER: Newbie question: partial minimization in implicit solvent (Wed Nov 12 2008 - 11:48:38 CST)
• John Chodera
  • AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) (Tue Nov 18 2008 - 13:58:22 CST)
• John Finke
  • Re: AMBER: Problems compiling leap on Altix Cluster (Mon Nov 03 2008 - 17:43:09 CST)
  • AMBER: Problems compiling leap on Altix Cluster (Mon Nov 03 2008 - 14:51:54 CST)
• Jojart Balazs
  • Re: AMBER: Electrostatic Energy Components (Sun Nov 23 2008 - 02:34:01 CST)
  • Re: AMBER: Electrostatic Energy Components (Sat Nov 22 2008 - 01:53:46 CST)
• Jose Borreguero
  • AMBER: velocity units? (Mon Nov 17 2008 - 10:14:35 CST)
• Joseph Nachman
  • AMBER: Referencing AMBER (Wed Nov 26 2008 - 10:01:57 CST)
  • AMBER: Restraints (Thu Nov 13 2008 - 12:59:23 CST)
• Junmei Wang
  • Re: AMBER: Electrostatic Energy Components (Sun Nov 23 2008 - 21:36:38 CST)
• Kevin Parkes
  • RE: AMBER: Test failure with Amber 10 (Wed Nov 26 2008 - 08:36:36 CST)
  • AMBER: Test failure with Amber 10 (Wed Nov 26 2008 - 04:33:35 CST)
• Lachele Foley (Lists)
  • Re: AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters (Fri Nov 07 2008 - 15:25:18 CST)
  • Re: AMBER: Glycam (Thu Nov 06 2008 - 09:01:48 CST)
• Larry Layne
  • Re: AMBER: MM_PBSA binding error (Tue Nov 04 2008 - 07:51:22 CST)
• Lili Peng
  • Re: AMBER: Force field for Gd3+ (metal ion)? (Thu Nov 20 2008 - 18:00:29 CST)
  • Re: AMBER: xLeap error (Mon Nov 10 2008 - 15:49:53 CST)
  • AMBER: xLeap error (Mon Nov 10 2008 - 14:45:58 CST)
  • AMBER: Force field for Gd (gadolinium)? (Thu Nov 06 2008 - 03:05:26 CST)
• M. L. Dodson
  • Re: AMBER: GB versus explicit medium (Mon Nov 24 2008 - 09:43:52 CST)
  • Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps (Mon Nov 10 2008 - 12:23:17 CST)
  • Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps (Fri Nov 07 2008 - 17:15:06 CST)
  • Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps (Thu Nov 06 2008 - 17:49:49 CST)
  • AMBER: ptraj new mask parser: differences from ambmask and core dumps (Thu Nov 06 2008 - 12:31:07 CST)
  • Re: AMBER: Steered MD and Jarzynski in pulling simulations (Wed Nov 05 2008 - 09:04:23 CST)
• Marcelo Puiatti
  • AMBER: organic solvents (Fri Nov 14 2008 - 17:20:30 CST)
• Margaret Johnson
  • AMBER: PMEMD with AMOEBA parms including a lone pair site (Tue Nov 18 2008 - 20:29:04 CST)
• Mark M Huntress
  • AMBER: resp charges in parameterization (Wed Nov 12 2008 - 10:24:55 CST)
• Mark Williamson
  • Re: AMBER: organic solvents (Fri Nov 14 2008 - 17:28:10 CST)
  • Re: AMBER: xLeap error (Mon Nov 10 2008 - 15:58:27 CST)
• Marudachalam S
  • AMBER: Amber on linux (Wed Nov 19 2008 - 11:58:10 CST)
• Matthew Tessier
  • RE: AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 11:09:16 CST)
  • RE: AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 10:40:43 CST)
  • RE: AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 10:15:56 CST)
• Mengjuei Hsieh
  • Re: AMBER: gigabit ethernet cards and switches (Thu Nov 06 2008 - 20:39:23 CST)
• mori_at_cerm.unifi.it
  • Re: AMBER: AMBER forfield choose (Thu Nov 20 2008 - 09:09:28 CST)
• Naser Alijabbari
  • AMBER: SPCFW temperature oscillations (Mon Nov 17 2008 - 22:19:12 CST)
  • AMBER: process_mdout modify (Tue Nov 04 2008 - 00:20:07 CST)
• Navnit Kumar Mishra
  • Re: AMBER: About antechamber and GAFF [UPDATED] (Wed Nov 26 2008 - 07:04:20 CST)
• Neha Gandhi
  • AMBER: RED vIII-lack of charges in mol2 (Sat Nov 29 2008 - 08:24:30 CST)
  • AMBER: Glycam (Wed Nov 05 2008 - 22:02:01 CST)
• Nina Fischer
  • AMBER: cis - trans isomerization (Thu Nov 27 2008 - 08:39:21 CST)
• oguz gurbulak
  • AMBER: using packmol file in Amber (Tue Nov 25 2008 - 09:49:19 CST)
  • Re: AMBER: question - gaff and leaprc.ff03ua (Sun Nov 23 2008 - 10:43:48 CST)
  • AMBER: question - gaff and leaprc.ff03ua (Wed Nov 19 2008 - 07:56:17 CST)
  • AMBER: load opls force field (Thu Nov 13 2008 - 04:38:11 CST)
• parul sharma
  • AMBER: AMBER : Inconsistent MD length and no of angles after ptraj (Fri Nov 07 2008 - 03:52:07 CST)
• Patrick McCarren
  • Re: AMBER: Optimal compiling of amber on XT3 (Sat Nov 01 2008 - 02:13:08 CDT)
• Prem Prakash Pathak
  • AMBER: (Mon Nov 03 2008 - 21:20:09 CST)
• priya priya
  • Re: AMBER: problem with group input and NMR restaints (Wed Nov 05 2008 - 14:00:48 CST)
  • Re: AMBER: problem with group input and NMR restaints (Wed Nov 05 2008 - 11:22:33 CST)
  • Re: AMBER: problem with group input and NMR restaints (Wed Nov 05 2008 - 10:05:05 CST)
  • Re: AMBER: problem with group input and NMR restaints (Tue Nov 04 2008 - 11:38:37 CST)
  • RE: AMBER: problem with group input and NMR restaints (Tue Nov 04 2008 - 10:16:34 CST)
  • AMBER: problem with group input and NMR restaints (Tue Nov 04 2008 - 09:20:09 CST)
• rai001_at_student.ucr.edu
  • Re: AMBER: question about ptraj (Thu Nov 13 2008 - 17:56:49 CST)
  • AMBER: question about ptraj (Thu Nov 13 2008 - 00:30:48 CST)
• Ray Luo
  • RE: AMBER: MM_PBSA binding error (Tue Nov 04 2008 - 13:18:54 CST)
• rebeca
  • Re: AMBER: antechamber and gaff for a homodimer (Thu Nov 27 2008 - 07:33:19 CST)
  • AMBER: antechamber and gaff for a homodimer (Thu Nov 27 2008 - 05:12:23 CST)
• robaldo_at_dna.uba.ar
  • Re: AMBER: ptraj center problem (Fri Nov 21 2008 - 14:04:56 CST)
  • AMBER: ptraj center problem (Fri Nov 21 2008 - 11:31:27 CST)
• Robert Duke
  • Re: AMBER: Question fot Amber 10 Benchmarks (Thu Nov 27 2008 - 08:37:20 CST)
  • Re: AMBER: Test failure with Amber 10 (Wed Nov 26 2008 - 11:28:14 CST)
  • Re: AMBER: RE: About restart amber (Tue Nov 25 2008 - 15:55:15 CST)
  • Re: AMBER: RE: About restart amber (Tue Nov 25 2008 - 15:23:09 CST)
  • Re: AMBER: RE: About restart amber (Tue Nov 25 2008 - 08:27:16 CST)
  • Re: AMBER: Ewald troubles when running very big boxes (Mon Nov 24 2008 - 20:09:23 CST)
  • Re: AMBER: AMBER10 failing to compile PMEMD (Sat Nov 22 2008 - 16:42:50 CST)
  • Re: AMBER: pmemd (Thu Nov 20 2008 - 10:40:36 CST)
  • Re: AMBER: PMEMD with AMOEBA parms including a lone pair site (Tue Nov 18 2008 - 20:50:14 CST)
  • Re: AMBER: SPCFW temperature oscillations (Tue Nov 18 2008 - 07:16:27 CST)
  • Re: AMBER: RESTRAINTS: no valid redirection found (Mon Nov 17 2008 - 13:58:18 CST)
  • Re: AMBER: RESTRAINTS: no valid redirection found (Mon Nov 17 2008 - 11:34:50 CST)
• Ross Walker
  • RE: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? (Fri Nov 28 2008 - 20:11:49 CST)
  • RE: AMBER: Question fot Amber 10 Benchmarks (Thu Nov 27 2008 - 10:57:06 CST)
  • RE: AMBER: Problem running NEB in AMBER10 (Wed Nov 26 2008 - 13:04:55 CST)
  • RE: Re: Re: Re: AMBER: AdoMet parameterization with antechamber (Wed Nov 26 2008 - 11:28:51 CST)
  • RE: AMBER: About antechamber and GAFF [UPDATED] (Wed Nov 26 2008 - 10:39:30 CST)
  • RE: AMBER: Test failure with Amber 10 (Wed Nov 26 2008 - 10:30:42 CST)
  • RE: AMBER: Fully QM periodic runs (Tue Nov 25 2008 - 10:54:24 CST)
  • RE: AMBER: Gradual releasing of position restraints (Tue Nov 25 2008 - 10:48:13 CST)
  • RE: AMBER: Electrostatic Energy Components (Sat Nov 22 2008 - 11:21:22 CST)
  • RE: AMBER: RE: About restart amber (Sat Nov 22 2008 - 11:18:57 CST)
  • RE: AMBER: QM/MM simulation (Sat Nov 22 2008 - 10:59:49 CST)
  • RE: AMBER: Electrostatic Energy Components (Fri Nov 21 2008 - 18:20:56 CST)
  • RE: AMBER: Electrostatic Energy Components (Fri Nov 21 2008 - 16:33:30 CST)
  • AMBER: RE: About restart amber (Fri Nov 21 2008 - 15:45:16 CST)
  • RE: AMBER: Electrostatic Energy Components (Fri Nov 21 2008 - 15:36:20 CST)
  • RE: AMBER: pmemd (Thu Nov 20 2008 - 10:36:51 CST)
  • RE: AMBER: Restraints (Thu Nov 13 2008 - 13:11:53 CST)
  • RE: AMBER: Your "bellymask-patch" (Thu Nov 13 2008 - 12:17:58 CST)
  • RE: AMBER: Amber 9 installation problems (Wed Nov 12 2008 - 15:16:03 CST)
  • RE: AMBER: Newbie question: partial minimization in implicit solvent (Wed Nov 12 2008 - 15:00:39 CST)
  • RE: AMBER: Amber 9 installation problems (Wed Nov 12 2008 - 09:21:59 CST)
  • AMBER: RE: problems about TMD in your tutorial (Mon Nov 10 2008 - 02:20:18 CST)
  • RE: AMBER: using "EP" for dummy atom (Thu Nov 06 2008 - 20:05:22 CST)
  • AMBER: RE: problems about TMD in your tutorial (Thu Nov 06 2008 - 13:32:58 CST)
  • AMBER: RE: Problem with the NEB tutorial (Thu Nov 06 2008 - 13:24:30 CST)
  • RE: AMBER: gigabit ethernet cards and switches (Thu Nov 06 2008 - 12:37:04 CST)
  • AMBER: RE: QUERRY? (Thu Nov 06 2008 - 12:37:04 CST)
  • AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query (Thu Nov 06 2008 - 12:37:04 CST)
  • AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query (Thu Nov 06 2008 - 02:18:22 CST)
  • RE: AMBER: AMBER10: QMMM parallel test error (Wed Nov 05 2008 - 19:41:27 CST)
  • RE: AMBER: problem with group input and NMR restaints (Tue Nov 04 2008 - 09:46:17 CST)
  • RE: AMBER: process_mdout modify (Tue Nov 04 2008 - 09:41:33 CST)
  • RE: AMBER: Problems compiling leap on Altix Cluster (Mon Nov 03 2008 - 18:06:07 CST)
  • RE: AMBER: Problems compiling leap on Altix Cluster (Mon Nov 03 2008 - 15:47:06 CST)
  • RE: AMBER: error message of xleap (Mon Nov 03 2008 - 11:05:54 CST)
• Ryan Pavlovicz
  • AMBER: NMR optimization with group averages (IGR1 / IGR2) (Fri Nov 14 2008 - 09:59:36 CST)
• S.Sundar Raman
  • AMBER: seeking help regrading Zinc protein GBSA minimization (Thu Nov 27 2008 - 06:32:08 CST)
• Saiful Islam
  • Re: AMBER: test sander error in amber7 (Tue Nov 11 2008 - 01:36:30 CST)
  • AMBER: test sander error in amber7 (Mon Nov 10 2008 - 07:43:45 CST)
• Samuel Genheden
  • AMBER: Steered MD and Jarzynski in pulling simulations (Wed Nov 05 2008 - 08:48:33 CST)
• Sasha Buzko
  • Re: AMBER: Problem with evaporating water over longer simulation times (Wed Nov 12 2008 - 18:53:06 CST)
  • Re: AMBER: Problem with evaporating water over longer simulation times (Wed Nov 12 2008 - 14:56:16 CST)
  • AMBER: Problem with evaporating water over longer simulation times (Wed Nov 12 2008 - 13:14:00 CST)
• saurabh agrawal
  • AMBER: nonbonded parameters for titanium (Mon Nov 24 2008 - 10:57:56 CST)
• Sergey Samsonov
  • AMBER: Problems of MM/MM-GBSA calculations (Thu Nov 27 2008 - 04:53:53 CST)
• Shozeb Haider
  • Re: AMBER: Amber 9 installation problems (Mon Nov 10 2008 - 10:37:54 CST)
• Siddharth Rastogi
  • AMBER: High ESURF (Mon Nov 17 2008 - 02:07:57 CST)
  • Re: AMBER: Trajectory file ended and unit 24 error on open inptraj (Sun Nov 16 2008 - 00:18:59 CST)
  • AMBER: Trajectory file ended and unit 24 error on open inptraj (Sat Nov 15 2008 - 09:33:10 CST)
  • AMBER: how to remove counter ions ( K+ / Cl- ions) using rdparm? (Fri Nov 14 2008 - 08:02:34 CST)
• steinbrt_at_rci.rutgers.edu
  • AMBER: Ewald troubles when running very big boxes (Mon Nov 24 2008 - 14:50:50 CST)
  • Re: AMBER: Amber on linux (Wed Nov 19 2008 - 13:47:45 CST)
  • AMBER: ptraj closest command (Mon Nov 17 2008 - 10:14:11 CST)
  • Re: AMBER: subroutine for torsional potential (Fri Nov 14 2008 - 08:49:25 CST)
  • Re: AMBER: Problem with evaporating water over longer simulation times (Wed Nov 12 2008 - 13:57:33 CST)
  • Re: AMBER: Problem with evaporating water over longer simulation times (Wed Nov 12 2008 - 13:57:33 CST)
  • Re: AMBER: resp charges in parameterization (Wed Nov 12 2008 - 10:44:17 CST)
• Stephan.Reiling_at_sanofi-aventis.com
  • AMBER: mm_pbsa.pl and Amber10 (Mon Nov 10 2008 - 10:05:27 CST)
• Stephane Abel
  • Re: AMBER: About antechamber and GAFF [UPDATED] (Thu Nov 27 2008 - 05:33:56 CST)
  • AMBER: About antechamber and GAFF [UPDATED] (Wed Nov 26 2008 - 05:21:52 CST)
  • AMBER: About antechamber and GAFF (Wed Nov 26 2008 - 05:02:00 CST)
  • Re: AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 11:07:07 CST)
  • Re: AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 10:51:25 CST)
  • Re: AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 10:26:10 CST)
  • AMBER: CG and HC atoms partial charges in AMBER (Thu Nov 20 2008 - 09:40:17 CST)
• Su Nwe
  • AMBER: unsubscribe amber (Tue Nov 25 2008 - 01:12:02 CST)
• Swarup Gupta
  • Re: AMBER: PB Radii (Mon Nov 17 2008 - 05:24:42 CST)
  • Re: AMBER: PB Radii (Sat Nov 15 2008 - 21:44:25 CST)
  • AMBER: PB Radii (Thu Nov 13 2008 - 01:06:34 CST)
• sychen
  • Re[2]: AMBER: Question fot Amber 10 Benchmarks (Thu Nov 27 2008 - 20:18:00 CST)
  • AMBER: Question fot Amber 10 Benchmarks (Thu Nov 27 2008 - 01:50:11 CST)
• Syed Tarique Moin
  • Re: AMBER: QM/MM simulation (Sat Nov 22 2008 - 09:11:12 CST)
  • AMBER: QM/MM simulation (Sat Nov 22 2008 - 02:00:36 CST)
• Taufik Al-Sarraj
  • Re: AMBER: changing pdb structure (Mon Nov 24 2008 - 17:37:24 CST)
  • Re: AMBER: changing pdb structure (Mon Nov 10 2008 - 15:10:23 CST)
  • Re: AMBER: changing pdb structure (Mon Nov 10 2008 - 14:31:39 CST)
  • AMBER: coot mutation (Thu Nov 06 2008 - 14:19:00 CST)
• Thomas Patko
  • Re: AMBER: compiling ambertools with intel compilers (Thu Nov 20 2008 - 16:15:58 CST)
• tri nam Vo
  • AMBER: Running Amber8 - Sander (Mon Nov 24 2008 - 00:28:31 CST)
• vallespardojl_at_chem.leidenuniv.nl
  • AMBER: Problems for use manganese molecules (Fri Nov 21 2008 - 03:06:37 CST)
• Wang,Ying
  • AMBER: AMBER forfield choose (Thu Nov 20 2008 - 08:32:24 CST)
  • Re: AMBER: AMBER forfield choose (Thu Nov 20 2008 - 09:17:45 CST)
  • Re: AMBER: AMBER forfield choose (Thu Nov 20 2008 - 09:05:28 CST)
• Wei Huang
  • Re: Re: AMBER: AdoMet parameterization with antechamber (Mon Nov 24 2008 - 10:41:12 CST)
• Wenyong Tong
  • Re: AMBER: About antechamber and GAFF [UPDATED] (Wed Nov 26 2008 - 11:13:34 CST)
• Yang, Ping
  • RE: AMBER: AMBER10: QMMM parallel test error (Wed Nov 05 2008 - 21:57:29 CST)
  • AMBER: AMBER10: QMMM parallel test error (Wed Nov 05 2008 - 17:44:27 CST)
• 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 - 09:12:51 CST)

Last message date: Wed Dec 31 2008 - 22:47:27 CST
Archived on: Thu Jan 08 2009 - 16:01:50 CST