Amber Archive Dec 2008: by author

ABEL Stephane 175950
- AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III (Tue Dec 16 2008 - 03:28:56 PST)
- AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems (Fri Dec 12 2008 - 09:33:44 PST)
- AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems (Fri Dec 12 2008 - 08:41:19 PST)
- AMBER: tutorial A1, file missing readit.f (Thu Dec 11 2008 - 04:22:41 PST)
Adrian Roitberg
- Re: AMBER: Switching function in NAMD (Tue Dec 23 2008 - 11:56:58 PST)
- Re: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 08:40:23 PST)
- Re: AMBER: Calculating the dielectrostatic constant from simulation? (Mon Dec 15 2008 - 05:44:09 PST)
- Re: AMBER: Constant pH dynamics (Tue Dec 09 2008 - 08:24:17 PST)
Alessandro Nascimento
- AMBER: SMD-related questions (Mon Dec 29 2008 - 05:07:05 PST)
- Re: AMBER: Pulling using restraintmask (Thu Dec 11 2008 - 12:58:51 PST)
Alexander Metz
- AMBER: LINMIN error in geometrically constrained minimization . MM-PB/SA conditions (Thu Dec 04 2008 - 09:04:03 PST)
amit
- RE: AMBER: amber 9 compilation error with mvapich and intel compilers (Mon Dec 22 2008 - 10:15:34 PST)
- Re: AMBER: amber 9 compilation error with mvapich and intel compilers (Mon Dec 22 2008 - 09:12:41 PST)
Amit Bajaj
- Re: AMBER: amber 9 compilation error with mvapich and intel compilers (Sun Dec 21 2008 - 21:41:35 PST)
- AMBER: amber 9 compilation error with mvapich and intel compilers (Sat Dec 20 2008 - 06:17:03 PST)
Andrew Ring
- AMBER: Playstation 3 Benchmarks (Mon Dec 22 2008 - 16:40:44 PST)
aneesh cna
- AMBER: mdout file details (Mon Dec 29 2008 - 22:20:40 PST)
Anselm Horn
- Re: AMBER: prep files ATP-MG++ and for phosphorylated threonine (Tue Dec 09 2008 - 02:06:17 PST)
Atro Tossavainen
- Re: AMBER: AMBER 10 PMEMD / SGI_MIPS (Tue Dec 16 2008 - 04:17:48 PST)
- Re: AMBER: AMBER 10 PMEMD / SGI_MIPS (Mon Dec 15 2008 - 06:40:41 PST)
- Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Mon Dec 15 2008 - 06:27:05 PST)
- AMBER: AMBER 10 PMEMD / SGI_MIPS (Mon Dec 15 2008 - 04:51:16 PST)
- Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Mon Dec 15 2008 - 03:12:53 PST)
- Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Mon Dec 15 2008 - 02:06:51 PST)
- Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Mon Dec 15 2008 - 01:36:09 PST)
- Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Sun Dec 14 2008 - 12:11:53 PST)
- Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Sat Dec 13 2008 - 14:12:30 PST)
- AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Sat Dec 13 2008 - 13:18:45 PST)
babak minoofar
- Re: AMBER: N(CN2)- ion (Fri Dec 12 2008 - 01:29:54 PST)
- Re: AMBER: N(CN2)- ion (Thu Dec 04 2008 - 08:00:58 PST)
balaji nagarajan
- AMBER: (Mon Dec 22 2008 - 05:36:38 PST)
- RE: AMBER: Error: tutorial one for md simulation of DNA (Sun Dec 21 2008 - 20:06:55 PST)
- AMBER: reg.concentration of ions (Fri Dec 12 2008 - 08:34:49 PST)
- RE: AMBER: reg.building ions (Fri Dec 12 2008 - 04:14:57 PST)
- AMBER: reg.building ions (Fri Dec 12 2008 - 02:40:07 PST)
- AMBER: reg-antichamber run (Wed Dec 10 2008 - 09:08:17 PST)
- AMBER: parallel installation (Tue Dec 09 2008 - 19:56:20 PST)
- RE: AMBER: reg-adding ions (Mon Dec 08 2008 - 20:32:14 PST)
- AMBER: reg-adding ions (Mon Dec 08 2008 - 00:20:05 PST)
- RE: AMBER: regad-tutorial-dna-polyAT (Sun Dec 07 2008 - 22:40:39 PST)
- AMBER: regad-tutorial-dna-polyAT (Sun Dec 07 2008 - 20:45:10 PST)
- RE: AMBER: reg unstability of structure in md (Thu Dec 04 2008 - 20:32:21 PST)
- AMBER: reg unstability of structure in md (Wed Dec 03 2008 - 20:17:51 PST)
- RE: AMBER: reg.dnasaveparm&tcrd (Mon Dec 01 2008 - 08:56:44 PST)
- RE: AMBER: reg.dnasaveparm&tcrd (Mon Dec 01 2008 - 08:51:00 PST)
- AMBER: reg.dnasaveparm&tcrd (Mon Dec 01 2008 - 06:05:52 PST)
Barbault Florent
- Re: AMBER: MM/GBSA Error during deccomposition (Wed Dec 03 2008 - 12:32:14 PST)
Beale, John
- AMBER: RMS plot (Wed Dec 31 2008 - 11:11:39 PST)
- AMBER: (Wed Dec 24 2008 - 05:19:48 PST)
- AMBER: Constant pH dynamics (Tue Dec 09 2008 - 04:51:39 PST)
Ben Eisenbraun
- AMBER: Building Amber 10 with Intel MKL and compiler mini howto (Wed Dec 10 2008 - 09:45:04 PST)
Bill K
- Re: AMBER: How do you evaluate forces on a fixed atom? (Tue Dec 02 2008 - 17:54:35 PST)
- AMBER: How do you evaluate forces on a fixed atom? (Mon Dec 01 2008 - 10:45:42 PST)
Brent Krueger
- Re: AMBER: RESP GAUSSIAN AMBER (Sun Dec 14 2008 - 18:52:14 PST)
Carlos Simmerling
- Re: AMBER: distance restraint between non-bonded molecules (Fri Dec 19 2008 - 07:24:09 PST)
- Re: AMBER: restraintmask - reference file is not working (Thu Dec 18 2008 - 04:14:27 PST)
- Re: AMBER: distance restraint between non-bonded molecules (Thu Dec 18 2008 - 03:45:13 PST)
- Re: AMBER: restraintmask - reference file is not working (Wed Dec 17 2008 - 11:51:35 PST)
- Re: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 07:12:32 PST)
- Re: AMBER: restraintmask - reference file is not working (Wed Dec 17 2008 - 05:19:25 PST)
- Re: AMBER: restraintmask - reference file is not working (Tue Dec 16 2008 - 17:05:03 PST)
- Re: AMBER: restraintmask - reference file is not working (Tue Dec 16 2008 - 16:38:14 PST)
- Re: AMBER: problem with toturial A3 (MM-PBSA) (Tue Dec 16 2008 - 05:57:42 PST)
- Re: AMBER: ff99 (PK/IDIVF) (Tue Dec 16 2008 - 04:01:32 PST)
- Re: AMBER: ff99 (PK/IDIVF) (Sun Dec 14 2008 - 10:38:23 PST)
- Re: AMBER: problem with toturial A3 (MM-PBSA) (Sat Dec 13 2008 - 07:35:13 PST)
- Re: AMBER: ff99 (PK/IDIVF) (Fri Dec 12 2008 - 06:05:11 PST)
- Re: AMBER: DNA: GB solvent with salt (Fri Dec 12 2008 - 03:33:14 PST)
- Re: AMBER: Distorted ring... (Thu Dec 11 2008 - 04:15:57 PST)
- Re: AMBER: reg unstability of structure in md (Fri Dec 05 2008 - 03:41:40 PST)
- Re: AMBER: reg unstability of structure in md (Thu Dec 04 2008 - 03:28:12 PST)
- Re: AMBER: seeking help regrading Zinc protein GBSA minimization (Mon Dec 01 2008 - 03:16:02 PST)
Carra, Claudio (JSC-SK)[USRA]
- AMBER: mwcovar limit? (Mon Dec 29 2008 - 14:31:27 PST)
Catein Catherine
- RE: AMBER: Error: tutorial one for md simulation of DNA (Sun Dec 21 2008 - 21:12:32 PST)
- AMBER: Error: tutorial one for md simulation of DNA (Sun Dec 21 2008 - 19:33:41 PST)
- AMBER: DNA: GB solvent with salt (Fri Dec 12 2008 - 01:31:13 PST)
Cenk \(Jenk\) Andac
- Re: AMBER: FAD RESP charges and parameters (Tue Dec 30 2008 - 08:03:17 PST)
- Re: AMBER: FAD RESP charges and parameters (Tue Dec 30 2008 - 04:28:41 PST)
- AMBER: FAD RESP charges and parameters (Mon Dec 29 2008 - 14:51:49 PST)
CHAMI F.
- AMBER: building new ions (Mon Dec 15 2008 - 05:50:50 PST)
- AMBER: building new ions (Fri Dec 12 2008 - 04:23:20 PST)
chengtao.sjtu.edu.cn
- Re: AMBER: pressure component (Tue Dec 16 2008 - 00:42:00 PST)
- AMBER: pressure component (Mon Dec 15 2008 - 00:17:21 PST)
Chris C.
- Re: AMBER: Problem running NEB in AMBER10 (Wed Dec 03 2008 - 10:29:48 PST)
Cristina Sisu
- Re: AMBER: MM/GBSA Error during deccomposition (Thu Dec 04 2008 - 03:27:48 PST)
D.J. Cole
- AMBER: Hydroxide ion in POL3 water (Thu Dec 18 2008 - 04:13:58 PST)
Daniel Emery
- AMBER: Problem with MMPBSA (Mon Dec 08 2008 - 08:28:22 PST)
Daniel Oehme
- Re: AMBER: Variable PBCAL values in MM-PBSA calculations (Sun Dec 07 2008 - 21:56:58 PST)
- Re: AMBER: Variable PBCAL values in MM-PBSA calculations (Wed Dec 03 2008 - 22:34:42 PST)
- AMBER: Variable PBCAL values in MM-PBSA calculations (Mon Dec 01 2008 - 15:45:23 PST)
David A. Case
- Re: AMBER: mdout file details (Wed Dec 31 2008 - 08:50:05 PST)
- Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Tue Dec 30 2008 - 13:31:56 PST)
- Re: AMBER: a question about ff03ua (Thu Dec 25 2008 - 13:01:56 PST)
- Re: AMBER: GB offset for proteins (Wed Dec 24 2008 - 11:11:21 PST)
- Re: AMBER: installation amber9 in fedora9 using bash shell (Wed Dec 24 2008 - 11:07:35 PST)
- Re: AMBER: xleap error (Wed Dec 24 2008 - 11:02:11 PST)
- Re: AMBER: AMBER10 AMBERTools antechamber (Tue Dec 23 2008 - 11:45:06 PST)
- Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Tue Dec 23 2008 - 05:26:15 PST)
- Re: AMBER: amber 9 compilation error with mvapich and intel compilers (Mon Dec 22 2008 - 05:35:28 PST)
- Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Sat Dec 20 2008 - 15:48:23 PST)
- Re: AMBER: amber 9 compilation error with mvapich and intel compilers (Sat Dec 20 2008 - 14:42:28 PST)
- Re: AMBER: Solvatebox problem (Fri Dec 19 2008 - 05:19:18 PST)
- Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 10:49:56 PST)
- Re: AMBER: solvent box again (Tue Dec 16 2008 - 12:02:05 PST)
- Re: AMBER: distance restraint in minimization (Tue Dec 16 2008 - 11:57:44 PST)
- Re: AMBER: relative weight of RDC constraints (Mon Dec 15 2008 - 08:44:19 PST)
- Re: AMBER: Initial velocities based on date and time are NOT changing ? (Mon Dec 15 2008 - 05:38:03 PST)
- Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Mon Dec 15 2008 - 04:54:33 PST)
- Re: AMBER: pressure component (Mon Dec 15 2008 - 04:43:44 PST)
- Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC (Sun Dec 14 2008 - 06:20:36 PST)
- Re: AMBER: ld: cannot find -lgcc_s (Fri Dec 12 2008 - 06:26:00 PST)
- Re: AMBER: reg.building ions (Fri Dec 12 2008 - 04:42:28 PST)
- Re: AMBER: reg.building ions (Fri Dec 12 2008 - 04:04:58 PST)
- Re: AMBER: tutorial A1, file missing readit.f (Thu Dec 11 2008 - 05:19:38 PST)
- Re: AMBER: how to add new solvent type in Amber (Wed Dec 10 2008 - 15:18:56 PST)
- Re: AMBER: reg-antichamber run (Wed Dec 10 2008 - 15:14:31 PST)
- Re: AMBER: parallel installation (Wed Dec 10 2008 - 05:09:00 PST)
- Re: AMBER: Constant pH dynamics (Tue Dec 09 2008 - 07:27:51 PST)
- Re: AMBER: interaction energies (Mon Dec 08 2008 - 08:59:28 PST)
- Re: AMBER: makeDIST_RST computation of r3 value with IAT < 0 (Fri Dec 05 2008 - 08:45:20 PST)
- Re: AMBER: using packmol file in Amber (Fri Dec 05 2008 - 07:58:51 PST)
- Re: AMBER: N(CN2)- ion (Fri Dec 05 2008 - 04:23:05 PST)
- Re: AMBER: using packmol file in Amber (Thu Dec 04 2008 - 08:32:49 PST)
- Re: AMBER: unable to open pdb file (Thu Dec 04 2008 - 03:41:32 PST)
- Re: AMBER: How do you evaluate forces on a fixed atom? (Tue Dec 02 2008 - 06:39:37 PST)
- Re: AMBER: using packmol file in Amber (Tue Dec 02 2008 - 06:19:20 PST)
- Re: AMBER: using packmol file in Amber (Tue Dec 02 2008 - 04:14:47 PST)
- Re: AMBER: makeDIST_RST error -- no map function for HH TYR (Mon Dec 01 2008 - 13:22:46 PST)
- Re: AMBER: Running Amber8 - Sander (Mon Dec 01 2008 - 07:37:32 PST)
- Re: AMBER: Is there an easy way to calculate the electric field at the center of a group of atoms (Mon Dec 01 2008 - 07:34:47 PST)
- Re: AMBER: N(CN2)- ion (Mon Dec 01 2008 - 06:47:14 PST)
- Re: AMBER: reg.dnasaveparm&tcrd (Mon Dec 01 2008 - 06:29:41 PST)
David Watson
- Re: AMBER: mpirun Permission denied. (Tue Dec 30 2008 - 21:04:40 PST)
- Re: AMBER: Playstation 3 Benchmarks (Mon Dec 22 2008 - 17:17:57 PST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 (Fri Dec 05 2008 - 14:30:32 PST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 (Fri Dec 05 2008 - 13:53:15 PST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 (Fri Dec 05 2008 - 12:32:45 PST)
David Witte
- AMBER: relative weight of RDC constraints (Mon Dec 15 2008 - 08:21:34 PST)
Dirar Homouz
- RE: AMBER: restraintmask - reference file is not working (Thu Dec 18 2008 - 15:46:23 PST)
- RE: AMBER: restraintmask - reference file is not working (Wed Dec 17 2008 - 11:40:48 PST)
- RE: AMBER: restraintmask - reference file is not working (Wed Dec 17 2008 - 01:41:00 PST)
- RE: AMBER: restraintmask - reference file is not working (Tue Dec 16 2008 - 16:51:08 PST)
- RE: AMBER: restraintmask - reference file is not working (Tue Dec 16 2008 - 16:45:44 PST)
- AMBER: restraintmask - reference file is not working (Tue Dec 16 2008 - 16:05:24 PST)
- AMBER: Pulling using restraintmask (Thu Dec 11 2008 - 12:30:00 PST)
drugdesign
- AMBER: mpirun Permission denied. (Wed Dec 24 2008 - 22:49:31 PST)
ecustipp
- AMBER: vertex atom mismatch (Fri Dec 26 2008 - 02:09:45 PST)
- Re:Re: AMBER: about mmpbsa out data (Wed Dec 24 2008 - 01:11:50 PST)
- AMBER: about mmpbsa out data (Tue Dec 23 2008 - 18:21:22 PST)
ecustipp.163.com
- Re: AMBER: (no subject) (Sun Dec 28 2008 - 23:58:20 PST)
Francesco Pietra
- Re: AMBER: RESP GAUSSIAN AMBER (Fri Dec 12 2008 - 03:13:13 PST)
FyD
- Re: AMBER: FAD RESP charges and parameters (Tue Dec 30 2008 - 06:19:15 PST)
- Re: AMBER: FAD RESP charges and parameters (Tue Dec 30 2008 - 00:45:01 PST)
- RE: AMBER: RESP GAUSSIAN AMBER (Wed Dec 17 2008 - 01:12:38 PST)
- Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III (Tue Dec 16 2008 - 04:17:15 PST)
- Re: AMBER: RESP GAUSSIAN AMBER (Mon Dec 15 2008 - 14:05:46 PST)
- Re: AMBER: RESP GAUSSIAN AMBER (Mon Dec 15 2008 - 12:41:24 PST)
- Re: AMBER: building new ions (Mon Dec 15 2008 - 06:09:04 PST)
- RE: AMBER: RESP GAUSSIAN AMBER (Sat Dec 13 2008 - 00:02:23 PST)
- RE: AMBER: RESP GAUSSIAN AMBER (Fri Dec 12 2008 - 23:23:10 PST)
- Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems (Fri Dec 12 2008 - 10:24:25 PST)
- Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems (Fri Dec 12 2008 - 09:14:05 PST)
- Re: AMBER: RESP GAUSSIAN AMBER (Fri Dec 12 2008 - 07:16:01 PST)
- RE: AMBER: RESP GAUSSIAN AMBER (Fri Dec 12 2008 - 06:25:06 PST)
- Re: AMBER: RESP GAUSSIAN AMBER (Thu Dec 11 2008 - 03:42:20 PST)
- Re: AMBER: reg-antichamber run (Thu Dec 11 2008 - 01:57:26 PST)
Gustavo Seabra
- Re: AMBER: comparison of MD trajectories recorded with pmemd and sander (Thu Dec 18 2008 - 06:58:13 PST)
- Re: AMBER: using packmol file in Amber (Mon Dec 15 2008 - 08:39:53 PST)
- Re: AMBER: Radial Distribution Function (Sun Dec 14 2008 - 23:41:02 PST)
- Re: AMBER: Radial Distribution Function (Wed Dec 10 2008 - 05:49:42 PST)
- Re: AMBER: Radial Distribution Function (Tue Dec 09 2008 - 07:38:54 PST)
- Re: AMBER: subroutine Work : Jarynski work theorem (Wed Dec 03 2008 - 05:59:06 PST)
- Re: AMBER: QM/MM and unpaired spin (Wed Dec 03 2008 - 05:53:00 PST)
- Re: AMBER: QM/MM and unpaired spin (Tue Dec 02 2008 - 19:11:25 PST)
Hannes Kopitz
- Re: AMBER: ptraj: how to select all non-hydrogen atoms (Wed Dec 03 2008 - 12:27:33 PST)
Hazard, E. Starr
- AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 (Fri Dec 05 2008 - 12:12:54 PST)
iccy liu
- RE: AMBER: solvent box again (Thu Dec 18 2008 - 11:41:41 PST)
- AMBER: solvent box again (Tue Dec 16 2008 - 10:32:32 PST)
- AMBER: how to add new solvent type in Amber (Mon Dec 08 2008 - 16:23:11 PST)
Ilyas Yildirim
- Re: AMBER: distance restraint between non-bonded molecules] (Sun Dec 21 2008 - 19:08:38 PST)
- Re: AMBER: distance restraint between non-bonded molecules] (Fri Dec 19 2008 - 15:06:35 PST)
- Re: AMBER: distance restraint between non-bonded molecules (Fri Dec 19 2008 - 07:22:32 PST)
- Re: AMBER: distance restraint between non-bonded molecules (Thu Dec 18 2008 - 13:29:26 PST)
- Re: AMBER: distance restraint between non-bonded molecules (Thu Dec 18 2008 - 11:29:30 PST)
- RE: AMBER: from dihe parameters to torsional energy (Wed Dec 17 2008 - 09:10:13 PST)
In Hee Park
- AMBER: idecomp=2 & RRES/LRES group specification (Fri Dec 19 2008 - 17:19:43 PST)
Jackie. J. Shen
- Re: AMBER: mpirun Permission denied. (Tue Dec 30 2008 - 18:32:17 PST)
- Re: AMBER: SMD-related questions (Tue Dec 30 2008 - 18:27:16 PST)
jani sahil
- Re: AMBER: regad-tutorial-dna-polyAT (Sun Dec 07 2008 - 21:13:30 PST)
Jeffrey
- AMBER: definition of dihedral in amber (Thu Dec 25 2008 - 07:38:38 PST)
- AMBER: How to build a cubic box of a newly synthesized compound? (Tue Dec 23 2008 - 22:34:13 PST)
- Re: RE: AMBER: from dihe parameters to torsional energy (Wed Dec 17 2008 - 18:18:29 PST)
- AMBER: from dihe parameters to torsional energy (Wed Dec 17 2008 - 01:15:17 PST)
- Re: Re: AMBER: Calculating the dielectrostatic constant from simulation? (Mon Dec 15 2008 - 17:34:54 PST)
- AMBER: Calculating the dielectrostatic constant from simulation? (Sun Dec 14 2008 - 23:07:25 PST)
Jifeng Wang
- Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 10:16:08 PST)
- Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems (Fri Dec 12 2008 - 08:50:56 PST)
jitrayut jitonnom
- AMBER: MM-PBSA : bad atom type: ZN (Mon Dec 08 2008 - 08:51:12 PST)
john smith
- Re: AMBER: forrtl severe(174) error with minimization and md (Mon Dec 15 2008 - 00:46:56 PST)
- AMBER: forrtl severe(174) error with minimization and md (Tue Dec 09 2008 - 22:20:57 PST)
Larry Layne
- AMBER: alascan error (Wed Dec 17 2008 - 12:19:22 PST)
- AMBER: alascan MUTANT_KEEP error (Tue Dec 16 2008 - 11:07:51 PST)
Lili Peng
- Re: AMBER: AMBER minimization problems (Sat Dec 20 2008 - 15:53:54 PST)
- Re: AMBER: AMBER minimization problems (Wed Dec 17 2008 - 08:35:58 PST)
- AMBER: AMBER minimization problems (Tue Dec 16 2008 - 23:14:00 PST)
llduan.itcc.nju.edu.cn
- AMBER: sgi4700 the time of MD simulation is 30 minute for 1ps about 2500 atom using 1cpu (Sat Dec 13 2008 - 06:36:45 PST)
luzhenw1.msu.edu
- Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 10:17:28 PST)
- Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 07:10:49 PST)
M. L. Dodson
- Re: AMBER: SMD-related questions (Mon Dec 29 2008 - 10:25:19 PST)
- Re: AMBER: How to build a cubic box of a newly synthesized compound? (Wed Dec 24 2008 - 09:45:23 PST)
- Re: AMBER: AMBER10 AMBERTools antechamber (Tue Dec 23 2008 - 12:00:13 PST)
- Re: AMBER: AMBER10 AMBERTools antechamber (Tue Dec 23 2008 - 08:45:46 PST)
- Re: AMBER: RESP GAUSSIAN AMBER (Mon Dec 15 2008 - 13:36:08 PST)
- Re: AMBER: RESP GAUSSIAN AMBER (Mon Dec 15 2008 - 09:52:48 PST)
Marina Grabar
- AMBER: interaction energies (Mon Dec 08 2008 - 03:29:36 PST)
Markus Kaukonen
- Re: AMBER: Initial velocities based on date and time are NOT changing ? (Tue Dec 16 2008 - 01:41:40 PST)
- AMBER: Initial velocities based on date and time are NOT changing ? (Mon Dec 15 2008 - 05:14:38 PST)
- AMBER: QM/MM and unpaired spin (Sun Nov 30 2008 - 23:30:02 PST)
Maryam Hamzehee
- Re: AMBER: problem with toturial A3 (MM-PBSA) (Sun Dec 14 2008 - 03:25:00 PST)
- AMBER: problem with toturial A3 (MM-PBSA) (Sat Dec 13 2008 - 07:22:58 PST)
Matthew Tessier
- RE: AMBER: Running md using glycam in AMBER (Thu Dec 11 2008 - 12:52:28 PST)
Mingfeng Yang
- AMBER: ptraj: how to select all non-hydrogen atoms (Wed Dec 03 2008 - 11:37:00 PST)
mirzo.jinr.ru
- Re: AMBER: prep files ATP-MG++ and for phosphorylated threonine (Tue Dec 09 2008 - 02:23:08 PST)
- AMBER: prep files ATP-MG++ and for phosphorylated threonine (Tue Dec 09 2008 - 00:01:42 PST)
moitrayee.mbu.iisc.ernet.in
- AMBER: ld: cannot find -lgcc_s (Fri Dec 12 2008 - 05:52:08 PST)
musa özboyacı
- AMBER: Switching function in NAMD (Tue Dec 23 2008 - 11:52:37 PST)
- AMBER: Solvatebox problem (Fri Dec 19 2008 - 02:24:56 PST)
N.R. Jena
- Re: AMBER: reg unstability of structure in md (Thu Dec 04 2008 - 22:48:50 PST)
- Re: AMBER: MM/GBSA Error during deccomposition (Thu Dec 04 2008 - 20:13:44 PST)
- Re: AMBER: MM/GBSA Error during deccomposition (Thu Dec 04 2008 - 05:08:45 PST)
- Re: AMBER: MM/GBSA Error during deccomposition (Thu Dec 04 2008 - 03:01:36 PST)
- AMBER: MM/GBSA Error during deccomposition (Wed Dec 03 2008 - 04:01:04 PST)
Neha Gandhi
- AMBER: Running md using glycam in AMBER (Wed Dec 10 2008 - 23:15:54 PST)
oguz gurbulak
- AMBER: a question about ff03ua (Thu Dec 25 2008 - 06:06:33 PST)
- Re: AMBER: using packmol file in Amber (Mon Dec 15 2008 - 07:57:08 PST)
- Re: AMBER: using packmol file in Amber (Fri Dec 05 2008 - 07:49:39 PST)
- Re: AMBER: using packmol file in Amber (Thu Dec 04 2008 - 07:36:03 PST)
- Re: AMBER: using packmol file in Amber (Tue Dec 02 2008 - 06:02:59 PST)
- Re: AMBER: using packmol file in Amber (Tue Dec 02 2008 - 03:06:10 PST)
Piotr Cieplak
- RE: AMBER: RESP GAUSSIAN AMBER (Fri Dec 12 2008 - 12:12:20 PST)
prabhakar g
- Re: AMBER: Radial Distribution Function (Fri Dec 12 2008 - 18:31:48 PST)
- Re: AMBER: Radial Distribution Function (Tue Dec 09 2008 - 19:33:27 PST)
- AMBER: Radial Distribution Function (Mon Dec 08 2008 - 18:37:52 PST)
Prem Prakash Pathak
- AMBER: unsubscribe amber (Tue Dec 16 2008 - 19:09:54 PST)
Rajendra P. OJHA
- AMBER: (no subject) (Fri Dec 26 2008 - 04:35:12 PST)
Ray Luo
- RE: AMBER: Problem with MMPBSA (Mon Dec 08 2008 - 11:47:15 PST)
- RE: AMBER: Variable PBCAL values in MM-PBSA calculations (Thu Dec 04 2008 - 11:06:45 PST)
- RE: AMBER: Variable PBCAL values in MM-PBSA calculations (Mon Dec 01 2008 - 17:55:37 PST)
Robert Duke
- Re: AMBER: amber 9 compilation error with mvapich and intelcompilers (Mon Dec 22 2008 - 06:36:33 PST)
- Re: AMBER: AMBER minimization problems (Sat Dec 20 2008 - 16:10:03 PST)
- Re: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 09:02:25 PST)
- Fw: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 09:20:40 PST)
- Re: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 09:18:46 PST)
- Re: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 08:42:07 PST)
- Re: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI (Tue Dec 16 2008 - 05:55:47 PST)
- Fw: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI (Tue Dec 16 2008 - 06:56:13 PST)
- Re: AMBER: AMBER 10 PMEMD / SGI_MIPS (Mon Dec 15 2008 - 07:26:12 PST)
- Re: AMBER: AMBER 10 PMEMD / SGI_MIPS (Mon Dec 15 2008 - 05:45:34 PST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 (Fri Dec 05 2008 - 14:46:57 PST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 (Fri Dec 05 2008 - 13:15:55 PST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 (Fri Dec 05 2008 - 12:32:04 PST)
Ross Walker
- RE: AMBER: mwcovar limit? (Wed Dec 31 2008 - 20:44:33 PST)
- RE: AMBER: AMBER10 AMBERTools antechamber (Tue Dec 23 2008 - 09:09:54 PST)
- RE: AMBER: Playstation 3 Benchmarks (Mon Dec 22 2008 - 17:20:38 PST)
- RE: AMBER: amber 9 compilation error with mvapich and intel compilers (Mon Dec 22 2008 - 09:46:58 PST)
- RE: AMBER: (Mon Dec 22 2008 - 08:41:23 PST)
- RE: AMBER: AMBER minimization problems (Thu Dec 18 2008 - 09:46:45 PST)
- RE: AMBER: from dihe parameters to torsional energy (Wed Dec 17 2008 - 09:28:21 PST)
- RE: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 09:01:37 PST)
- RE: AMBER: from dihe parameters to torsional energy (Wed Dec 17 2008 - 08:36:14 PST)
- RE: AMBER: AMBER minimization problems (Wed Dec 17 2008 - 08:18:06 PST)
- RE: AMBER: solvent box again (Tue Dec 16 2008 - 10:57:01 PST)
- RE: AMBER: AMBER 10 PMEMD / SGI_MIPS (Tue Dec 16 2008 - 08:16:11 PST)
- RE: AMBER: RESP GAUSSIAN AMBER (Mon Dec 15 2008 - 09:36:27 PST)
- RE: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI (Mon Dec 15 2008 - 07:18:04 PST)
- RE: AMBER: RESP GAUSSIAN AMBER (Fri Dec 12 2008 - 11:04:49 PST)
- RE: AMBER: ff99 (PK/IDIVF) (Fri Dec 12 2008 - 09:06:22 PST)
- RE: AMBER: RESP GAUSSIAN AMBER (Thu Dec 11 2008 - 20:00:27 PST)
- RE: AMBER: forrtl severe(174) error with minimization and md (Wed Dec 10 2008 - 07:57:42 PST)
- RE: AMBER: (no subject) (Tue Dec 09 2008 - 07:07:18 PST)
- RE: AMBER: reg-adding ions (Tue Dec 09 2008 - 07:05:04 PST)
- AMBER: RE: bugfix 11 & 12 (Mon Dec 08 2008 - 13:12:42 PST)
- RE: AMBER: reg-adding ions (Mon Dec 08 2008 - 08:33:18 PST)
- RE: AMBER: QM/MM and unpaired spin (Tue Dec 02 2008 - 19:42:37 PST)
- RE: AMBER: reg.dnasaveparm&tcrd (Mon Dec 01 2008 - 08:44:57 PST)
- RE: AMBER: QM/MM and unpaired spin (Mon Dec 01 2008 - 08:40:20 PST)
Ryan Pavlovicz
- AMBER: makeDIST_RST computation of r3 value with IAT < 0 (Wed Dec 03 2008 - 15:13:32 PST)
- AMBER: makeDIST_RST error -- no map function for HH TYR (Mon Dec 01 2008 - 11:30:01 PST)
Sally Pias
- AMBER: periodic boundary (Wed Dec 31 2008 - 00:37:25 PST)
- AMBER: GB offset for proteins (Sun Dec 07 2008 - 21:14:58 PST)
Sasha Buzko
- AMBER: Simulating peptide linkers with AMBER (Tue Dec 02 2008 - 12:03:42 PST)
saurabh agrawal
- Re: AMBER: ff99 (PK/IDIVF) (Tue Dec 16 2008 - 03:47:09 PST)
- RE: AMBER: ff99 (PK/IDIVF) (Sun Dec 14 2008 - 10:29:39 PST)
- AMBER: ff99 (PK/IDIVF) (Fri Dec 12 2008 - 05:26:58 PST)
Scott Brozell
- Re: AMBER: installation amber9 in fedora9 (Mon Dec 22 2008 - 21:41:22 PST)
- Re: AMBER: xleap (measureGeom) (Mon Dec 22 2008 - 14:10:46 PST)
- RE: AMBER: (no subject) (Tue Dec 09 2008 - 07:17:06 PST)
Sergey Samsonov
- Re: AMBER: seeking help regrading Zinc protein GBSA minimization (Mon Dec 01 2008 - 00:14:36 PST)
SilasConnor.gmx.at
- AMBER: RESP GAUSSIAN AMBER (Mon Dec 08 2008 - 10:31:24 PST)
sobereva
- Re: AMBER: installation amber9 in fedora9 (Tue Dec 23 2008 - 01:52:00 PST)
Starr Hazard
- AMBER: AMBER10 AMBERTools antechamber (Tue Dec 23 2008 - 08:36:05 PST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 (Fri Dec 05 2008 - 14:11:58 PST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 (Fri Dec 05 2008 - 13:10:11 PST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 (Fri Dec 05 2008 - 12:53:14 PST)
steinbrt.rci.rutgers.edu
- Re: AMBER: about mmpbsa out data (Tue Dec 23 2008 - 20:53:02 PST)
- Re: AMBER: sgi4700 the time of MD simulation is 30 minute for 1ps about 2500 atom using 1cpu (Sat Dec 13 2008 - 10:58:18 PST)
sychen
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 (Fri Dec 05 2008 - 19:46:20 PST)
Taufik Al-Sarraj
- AMBER: Re: (Mon Dec 22 2008 - 10:08:17 PST)
- AMBER: Materials and methods (Mon Dec 22 2008 - 10:05:22 PST)
- AMBER: xleap (measureGeom) (Sat Dec 20 2008 - 13:02:56 PST)
- Re: AMBER: distance restraint between non-bonded molecules] (Sat Dec 20 2008 - 10:44:43 PST)
- Re: AMBER: distance restraint between non-bonded molecules (Fri Dec 19 2008 - 07:14:51 PST)
- Re: AMBER: distance restraint between non-bonded molecules (Thu Dec 18 2008 - 12:41:05 PST)
- Re: AMBER: distance restraint between non-bonded molecules (Thu Dec 18 2008 - 08:49:51 PST)
- AMBER: distance restraint between non-bonded molecules (Wed Dec 17 2008 - 16:13:36 PST)
- Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 12:16:18 PST)
- Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 11:34:22 PST)
- Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 10:52:01 PST)
- Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 10:15:24 PST)
- Re: AMBER: distance restraint in minimization (Wed Dec 17 2008 - 09:44:55 PST)
- AMBER: distance restraint in minimization (Tue Dec 16 2008 - 14:44:35 PST)
- Re: AMBER: distance restraint in minimization (Tue Dec 16 2008 - 13:16:43 PST)
- AMBER: distance restraint in minimization (Tue Dec 16 2008 - 10:46:22 PST)
- AMBER: unable to open pdb file (Wed Dec 03 2008 - 18:44:09 PST)
Thomas Cheatham III
- Re: AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 09:16:47 PST)
unknown charset
- AMBER: comparison of MD trajectories recorded with pmemd and sander (Wed Dec 17 2008 - 06:04:26 PST)
- RE: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI (Tue Dec 16 2008 - 04:57:05 PST)
- AMBER: launching a job works with sander.MPI and fail with pmemd.MPI (Mon Dec 15 2008 - 06:41:55 PST)
Vijay Manickam Achari
- AMBER: xleap error (Wed Dec 24 2008 - 01:58:17 PST)
- AMBER: installation amber9 in fedora9 using bash shell (Tue Dec 23 2008 - 20:05:28 PST)
- AMBER: installation amber9 in fedora9 (Mon Dec 22 2008 - 20:44:12 PST)
waleed zalloum
- AMBER: (no subject) (Tue Dec 09 2008 - 04:22:39 PST)
Waqas Nasir
- AMBER: Distorted ring... (Thu Dec 11 2008 - 03:48:45 PST)
wl2290.columbia.edu
- Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Tue Dec 30 2008 - 14:15:59 PST)
- Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Tue Dec 30 2008 - 09:54:58 PST)
- Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Tue Dec 23 2008 - 07:52:39 PST)
- Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Mon Dec 22 2008 - 15:26:10 PST)
- AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) (Fri Dec 19 2008 - 10:16:39 PST)
Xioling Chuang
- AMBER: DNA-Gold parameters (Wed Dec 03 2008 - 03:37:55 PST)
Yunierkis Perez Castillo
- AMBER: side chain expression (Thu Dec 04 2008 - 08:43:14 PST)

Amber Archive Dec 2008 by author