Amber Archive Apr 2007 by author
382 messages
:
Starting
Wed Apr 04 2007 - 06:07:19 PDT,
Ending
Wed May 02 2007 - 06:07:23 PDT
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A Box
Re: AMBER: how to modify map.DG-AMBER file?
(Tue Apr 10 2007 - 16:56:21 PDT)
alfredoq.fcq.unc.edu.ar
AMBER: Problem using Ptraj
(Mon Apr 23 2007 - 08:41:56 PDT)
Andrea Bortolato
Re: AMBER: is possible to compile pmemd using scali MPI?
(Mon Apr 23 2007 - 05:31:53 PDT)
Andreas Svrcek-Seiler
Re: AMBER: Problems installing Amber9
(Fri Apr 27 2007 - 05:52:05 PDT)
Andy Purkiss-Trew
Re: AMBER: .prmtop entries
(Mon Apr 23 2007 - 04:13:18 PDT)
Anju Sharma
AMBER: Needed help regardng Simulated Annealing
(Wed Apr 11 2007 - 22:07:14 PDT)
Re: AMBER: Prblm rgrdng Simulated Annealing
(Wed Apr 11 2007 - 04:46:08 PDT)
Re: AMBER: Prblm rgrdng Simulated Annealing
(Wed Apr 11 2007 - 04:33:03 PDT)
AMBER: Prblm rgrdng Simulated Annealing
(Wed Apr 11 2007 - 03:06:08 PDT)
Re: AMBER: Problem while using antechamber
(Tue Apr 10 2007 - 02:18:07 PDT)
AMBER: Problem while using antechamber
(Mon Apr 09 2007 - 23:15:47 PDT)
AMBER: Regarding Simulated Annealing
(Tue Apr 03 2007 - 05:27:18 PDT)
anna.schrey.gmx.de
Re: AMBER: topology for postprocessed files?
(Wed Apr 18 2007 - 10:40:51 PDT)
Re: AMBER: topology for postprocessed files?
(Thu Apr 12 2007 - 03:42:41 PDT)
AMBER: topology for postprocessed files?
(Thu Apr 12 2007 - 02:57:28 PDT)
AMBER: supplement ptraj:problems with time correlation calculation (comp. with NMR experiments)
(Sun Apr 08 2007 - 07:15:22 PDT)
AMBER: ptraj:problems with time correlation calculation (comp. with NMR experiments)
(Sun Apr 08 2007 - 05:21:38 PDT)
Antonio Morreale
AMBER: protein-rna interaction & mmpbsa
(Thu Apr 26 2007 - 01:28:19 PDT)
Arvind Marathe
Re: AMBER: AMBER9 installation error on dual core AMD Opteron(tm) processor 275
(Fri Apr 13 2007 - 08:59:35 PDT)
AMBER: AMBER9 installation error on dual core AMD Opteron(tm) processor 275
(Fri Apr 13 2007 - 03:23:38 PDT)
Atila Iamarino
Re: AMBER: working with Antechamber
(Wed Apr 11 2007 - 11:59:03 PDT)
AMBER: working with Antechamber
(Wed Apr 11 2007 - 10:45:20 PDT)
Austin B. Yongye
Re: AMBER: using glycam04 parameters
(Wed Apr 18 2007 - 09:03:35 PDT)
Re: AMBER: using glycam04 parameters
(Wed Apr 18 2007 - 06:24:38 PDT)
AYTUG TUNCEL
Re: Re: AMBER: parse radii
(Mon Apr 09 2007 - 01:02:59 PDT)
AMBER: parse radii
(Wed Apr 04 2007 - 02:10:10 PDT)
Beale, John
AMBER: PDB files
(Mon Apr 30 2007 - 09:16:59 PDT)
AMBER: Antechamber
(Thu Apr 19 2007 - 06:51:03 PDT)
AMBER: Antechamber Warning
(Wed Apr 18 2007 - 12:39:31 PDT)
AMBER: PDBs
(Tue Apr 17 2007 - 05:22:42 PDT)
AMBER: Charges in antechamber
(Thu Apr 05 2007 - 08:46:34 PDT)
AMBER: Xleap errors
(Mon Apr 02 2007 - 10:20:43 PDT)
Ben Sattelle
RE: AMBER: restraint value: written but none specified
(Fri Apr 20 2007 - 16:05:47 PDT)
Re: AMBER: restraint value: written but none specified
(Fri Apr 20 2007 - 15:08:55 PDT)
Re: AMBER: restraint value: written but none specified
(Fri Apr 20 2007 - 14:51:30 PDT)
AMBER: restraint value: written but none specified
(Fri Apr 20 2007 - 13:42:56 PDT)
Benjamin Juhl
Re: AMBER: amber9: running parallel error
(Thu Apr 12 2007 - 01:33:48 PDT)
Re: AMBER: Problem while using antechamber
(Tue Apr 10 2007 - 00:12:13 PDT)
Bill Ross
Re: AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38
(Fri Apr 27 2007 - 16:07:54 PDT)
Re: AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38
(Fri Apr 27 2007 - 13:41:20 PDT)
Re: AMBER: choice of alpha carbons vs side chains
(Wed Apr 04 2007 - 16:28:34 PDT)
Bo Baker
RE: AMBER: Energy minimization problem
(Thu Apr 05 2007 - 03:14:31 PDT)
RE: AMBER: Energy minimization problem
(Wed Apr 04 2007 - 17:02:42 PDT)
AMBER: Energy minimization problem
(Tue Apr 03 2007 - 18:24:05 PDT)
Carlos P. Sosa
Re: AMBER: Blue Gene, compile Amber9?
(Fri Apr 06 2007 - 11:55:28 PDT)
Carlos Simmerling
Re: AMBER:a question about RMSD
(Tue Apr 24 2007 - 06:06:40 PDT)
Re: AMBER: amber equation of ff99
(Tue Apr 24 2007 - 09:18:57 PDT)
Re: AMBER: problem regarding implicit simulation
(Tue Apr 24 2007 - 04:25:31 PDT)
Re: AMBER: problem regarding implicit simulation
(Mon Apr 23 2007 - 04:30:34 PDT)
Re: AMBER: Prblm rgrdng Simulated Annealing
(Wed Apr 11 2007 - 04:39:30 PDT)
Re: AMBER: Prblm rgrdng Simulated Annealing
(Wed Apr 11 2007 - 04:23:43 PDT)
Re: AMBER: sander (AMBER 9) and -y flag -- not working?
(Tue Apr 10 2007 - 12:10:41 PDT)
Re: AMBER: Constant volume simulations
(Tue Apr 10 2007 - 08:35:14 PDT)
Re: AMBER: RE: dihedral term charge dependence
(Mon Apr 02 2007 - 09:14:15 PDT)
Cenk Andac
Re: AMBER: Request for addition of a useful command in ptraj module of AMBER #2
(Mon Apr 23 2007 - 15:35:36 PDT)
AMBER: Request for addition of a useful command in ptraj module of AMBER #2
(Tue Apr 17 2007 - 10:24:37 PDT)
AMBER: Request for addition of a useful command in ptraj module of AMBER
(Tue Apr 17 2007 - 10:18:30 PDT)
Re: AMBER: Question about MMPBSA v9
(Wed Apr 11 2007 - 03:38:12 PDT)
AMBER: Question about MMPBSA v9
(Mon Apr 09 2007 - 03:54:39 PDT)
Chengwen Chen
AMBER: a problem of surface area calulated by MM/PBSA
(Mon Apr 30 2007 - 00:34:38 PDT)
Re: AMBER: amber equation of ff99
(Tue Apr 24 2007 - 19:19:15 PDT)
AMBER: amber equation of ff99
(Tue Apr 24 2007 - 09:13:54 PDT)
AMBER: about define improper torsion in .frcmod file
(Wed Apr 04 2007 - 02:02:57 PDT)
Chris Moth
Re: AMBER: restraint value: written but none specified
(Fri Apr 20 2007 - 14:16:52 PDT)
AMBER: ptraj and quasi harmonic analysis
(Thu Apr 19 2007 - 12:58:52 PDT)
Re: AMBER: signal SIGSEGV(11)
(Wed Apr 18 2007 - 13:22:58 PDT)
Re: AMBER: sander (AMBER 9) and -y flag -- not working?
(Tue Apr 10 2007 - 11:36:22 PDT)
AMBER: SANDER PMEMD ntpr ntwx discrepancy (?bug? report)
(Mon Apr 09 2007 - 10:32:35 PDT)
AMBER: SANDER PMEMD ntpr ntwx discrepancy (?bug? report)
(Fri Apr 06 2007 - 14:07:17 PDT)
AMBER: netcdf support needed (Amber 9, sander imin = 5, -y flag)
(Fri Apr 06 2007 - 11:50:29 PDT)
Christopher Gaughan
Re: AMBER: Constant volume simulations
(Tue Apr 10 2007 - 10:12:14 PDT)
Re: AMBER: Constant volume simulations
(Tue Apr 10 2007 - 08:50:39 PDT)
Re: AMBER: Constant volume simulations
(Tue Apr 10 2007 - 08:31:58 PDT)
AMBER: Constant volume simulations
(Mon Apr 09 2007 - 11:59:26 PDT)
AMBER: choice of alpha carbons vs side chains
(Wed Apr 04 2007 - 15:34:31 PDT)
crowfoot.unr.nevada.edu
AMBER: Multiple Bonds to one Atom
(Thu Apr 12 2007 - 13:41:36 PDT)
Daniel Oehme
AMBER: QM/MM NPT Simulation
(Thu Apr 19 2007 - 21:46:14 PDT)
David A. Case
Re: AMBER: PDB files
(Mon Apr 30 2007 - 13:00:33 PDT)
Re: AMBER: AMBER MINIMIZATION
(Mon Apr 30 2007 - 08:24:34 PDT)
Re: AMBER: a problem of surface area calulated by MM/PBSA
(Mon Apr 30 2007 - 08:20:43 PDT)
Re: AMBER: thermodynamic integration
(Sat Apr 28 2007 - 14:26:28 PDT)
Re: AMBER: Error in protonating
(Sat Apr 28 2007 - 14:26:08 PDT)
Re: AMBER: Error on compiling AMBER8
(Wed Apr 25 2007 - 11:33:11 PDT)
Re: AMBER: Error on compiling AMBER8
(Tue Apr 24 2007 - 20:31:44 PDT)
Re: AMBER: prep file new residue
(Tue Apr 24 2007 - 12:12:44 PDT)
Re: AMBER: Problems with AMBER8 on 32-bit FC6
(Mon Apr 23 2007 - 14:17:09 PDT)
Re: AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out"
(Sat Apr 21 2007 - 12:04:23 PDT)
Re: AMBER: restraint value: written but none specified
(Fri Apr 20 2007 - 14:15:05 PDT)
Re: AMBER: ptraj and quasi harmonic analysis
(Fri Apr 20 2007 - 09:49:26 PDT)
Re: AMBER: rigid epoxide substrate
(Fri Apr 20 2007 - 08:30:42 PDT)
Re: AMBER: ptraj and quasi harmonic analysis
(Fri Apr 20 2007 - 08:23:34 PDT)
Re: AMBER: AIX 5 test failures: -NaNQ
(Thu Apr 19 2007 - 18:13:46 PDT)
Re: AMBER: Blue Gene, compile Amber9?
(Thu Apr 19 2007 - 14:31:25 PDT)
Re: AMBER: regarding frcmod file
(Thu Apr 19 2007 - 09:14:03 PDT)
Re: AMBER: signal SIGSEGV(11)
(Wed Apr 18 2007 - 08:49:24 PDT)
Re: AMBER: using glycam04 parameters
(Wed Apr 18 2007 - 08:28:27 PDT)
Re: AMBER: frcmod file
(Wed Apr 18 2007 - 08:22:01 PDT)
Re: AMBER: using glycam04 parameters
(Tue Apr 17 2007 - 14:37:35 PDT)
Re: AMBER: Re: MM-PBSA amber script problem
(Tue Apr 17 2007 - 14:35:59 PDT)
Re: AMBER: nscm in simulation annealing
(Tue Apr 17 2007 - 09:18:02 PDT)
Re: AMBER: mdfil.f
(Mon Apr 16 2007 - 10:25:02 PDT)
Re: AMBER: Problem with PCSHIFT module
(Sun Apr 15 2007 - 21:24:01 PDT)
Re: AMBER: Amber 8 support of CHARMM ff?
(Sat Apr 14 2007 - 12:21:23 PDT)
Re: AMBER: polarization and water density
(Fri Apr 13 2007 - 12:53:42 PDT)
Re: AMBER: nscm in simulation annealing
(Fri Apr 13 2007 - 12:48:13 PDT)
Re: AMBER: Restraints and free energy
(Fri Apr 13 2007 - 10:22:49 PDT)
Re: AMBER: nscm in simulation annealing
(Fri Apr 13 2007 - 10:22:32 PDT)
Re: AMBER: nscm in simulation annealing
(Thu Apr 12 2007 - 17:05:01 PDT)
Re: AMBER: bad atom type errors in GB for halides?
(Thu Apr 12 2007 - 17:04:55 PDT)
Re: AMBER: nscm in simulation annealing
(Thu Apr 12 2007 - 09:41:03 PDT)
Re: AMBER: working with Antechamber
(Wed Apr 11 2007 - 12:56:00 PDT)
Re: AMBER: Problem with Sander restart file.
(Wed Apr 11 2007 - 11:11:40 PDT)
Re: AMBER: Question about MMPBSA v9
(Tue Apr 10 2007 - 19:20:58 PDT)
Re: AMBER: Problems during compilation and test.
(Tue Apr 10 2007 - 18:27:39 PDT)
Re: AMBER: Constant volume simulations
(Mon Apr 09 2007 - 13:24:09 PDT)
Re: AMBER: ptraj:problems with time correlation calculation (comp. with NMR experiments)
(Mon Apr 09 2007 - 10:27:59 PDT)
Re: AMBER: Fails to load libraries present in /leap/lib/
(Mon Apr 09 2007 - 10:25:41 PDT)
Re: AMBER: NTX=7 ?............lastist= ?...........lastrst= ?????
(Mon Apr 09 2007 - 10:21:21 PDT)
Re: AMBER: supplement ptraj:problems with time correlation calculation (comp. with NMR experiments)
(Mon Apr 09 2007 - 07:56:56 PDT)
Re: AMBER: PDB file format for AMBER
(Sat Apr 07 2007 - 08:56:18 PDT)
Re: AMBER: SANDER PMEMD ntpr ntwx discrepancy (?bug? report)
(Fri Apr 06 2007 - 15:37:46 PDT)
Re: AMBER: Energy minimization problem
(Wed Apr 04 2007 - 18:25:26 PDT)
Re: AMBER: about define improper torsion in .frcmod file
(Wed Apr 04 2007 - 08:25:11 PDT)
Re: AMBER: Energy minimization problem
(Tue Apr 03 2007 - 18:39:37 PDT)
Re: AMBER: nmode
(Tue Apr 03 2007 - 09:31:54 PDT)
Re: AMBER: nmode
(Tue Apr 03 2007 - 08:25:52 PDT)
Re: AMBER: phosphorylated residues
(Mon Apr 02 2007 - 15:13:37 PDT)
Re: AMBER: Xleap errors
(Mon Apr 02 2007 - 10:32:47 PDT)
Re: AMBER: Error at Equilibration....
(Mon Apr 02 2007 - 08:45:57 PDT)
David Cerutti
Re: AMBER: Explicit water opinion
(Fri Apr 13 2007 - 15:58:32 PDT)
AMBER: Extra points... virial computation
(Sat Apr 07 2007 - 23:48:11 PDT)
AMBER: Extra Points... How to Deal with Them
(Mon Apr 02 2007 - 23:39:23 PDT)
David LeBard
Re: AMBER: Error on compile amber8
(Mon Apr 23 2007 - 22:45:45 PDT)
AMBER: Problems with AMBER8 on 32-bit FC6
(Mon Apr 23 2007 - 11:51:02 PDT)
David Mobley
AMBER: bad atom type errors in GB for halides?
(Thu Apr 12 2007 - 10:19:51 PDT)
Re: AMBER: working with Antechamber
(Wed Apr 11 2007 - 11:34:55 PDT)
AMBER: temperature artifacts with andersen and GB?
(Wed Apr 11 2007 - 09:50:17 PDT)
Re: AMBER: sander (AMBER 9) and -y flag -- not working?
(Tue Apr 10 2007 - 12:31:56 PDT)
Re: AMBER: sander (AMBER 9) and -y flag -- not working?
(Tue Apr 10 2007 - 12:04:52 PDT)
Re: AMBER: sander (AMBER 9) and -y flag -- not working?
(Tue Apr 10 2007 - 11:52:29 PDT)
AMBER: sander (AMBER 9) and -y flag -- not working?
(Tue Apr 10 2007 - 11:22:39 PDT)
deepti nayar
AMBER: frcmod file
(Tue Apr 17 2007 - 23:31:52 PDT)
AMBER: vmd and amber
(Tue Apr 17 2007 - 04:58:51 PDT)
Re: AMBER: problem related to visualizing of structure
(Tue Apr 10 2007 - 02:42:58 PDT)
Re: AMBER: problem related to visualizing of structure
(Tue Apr 10 2007 - 02:18:38 PDT)
AMBER: problem related to visualizing of structure
(Mon Apr 09 2007 - 23:33:40 PDT)
AMBER: restraint command not taken
(Mon Apr 02 2007 - 02:54:44 PDT)
AMBER: restraint command not taken
(Mon Apr 02 2007 - 02:25:12 PDT)
AMBER: restraint command not taken
(Mon Apr 02 2007 - 03:21:51 PDT)
Dr M. Blomberg
AMBER: prep file new residue
(Mon Apr 23 2007 - 01:48:27 PDT)
AMBER: rigid epoxide substrate
(Fri Apr 20 2007 - 04:24:13 PDT)
Edoardo Saccenti
Re: AMBER: Problem with PCSHIFT module
(Thu Apr 12 2007 - 05:40:55 PDT)
Re: AMBER: Problem with PCSHIFT module
(Tue Apr 03 2007 - 01:08:38 PDT)
Esther Brugger
AMBER: principal mask dorotation
(Thu Apr 05 2007 - 14:46:51 PDT)
AMBER: principal axis calculation in Ptraj
(Tue Apr 03 2007 - 14:05:44 PDT)
Evan Kelly
Re: AMBER: ptraj hbond
(Sun Apr 08 2007 - 19:00:29 PDT)
AMBER: ptraj hbond
(Sun Apr 08 2007 - 17:37:04 PDT)
Florian Haberl
Re: AMBER: membrane simulation
(Mon Apr 16 2007 - 07:04:04 PDT)
FyD
Re: AMBER: Protonation/deprotonation of terminal residues
(Wed Apr 18 2007 - 11:26:47 PDT)
Re: AMBER: using glycam04 parameters
(Wed Apr 18 2007 - 03:57:02 PDT)
AMBER: Release of the R.E.D.-III tools
(Sun Apr 15 2007 - 03:10:25 PDT)
Giulio Rastelli
AMBER: Print individual free energies in MD trajectories using MM_PBSA
(Fri Apr 27 2007 - 09:05:39 PDT)
Gohlke.bioinformatik.uni-frankfurt.de
Re: Re: AMBER: parse radii
(Mon Apr 09 2007 - 02:35:06 PDT)
gsciaini.qi.fcen.uba.ar
Re: AMBER: AMBER MINIMIZATION
(Mon Apr 30 2007 - 14:08:47 PDT)
gurpreet singh
Re: AMBER: problem regarding implicit simulation
(Tue Apr 24 2007 - 04:18:57 PDT)
AMBER: problem regarding implicit simulation
(Sun Apr 22 2007 - 23:16:35 PDT)
Gustavo Seabra
Re: AMBER: Employing SCC-DFTB with a periodic boundary condtion
(Thu Apr 26 2007 - 06:18:32 PDT)
Re: AMBER: QM/MM simulation with SCC-DFTB
(Tue Apr 24 2007 - 03:48:11 PDT)
Re: AMBER: regarding frcmod file
(Thu Apr 19 2007 - 08:50:44 PDT)
Re: AMBER: problem with calculating RMSD
(Wed Apr 18 2007 - 07:50:21 PDT)
Re: AMBER: problem with calculating RMSD
(Tue Apr 17 2007 - 05:41:26 PDT)
Re: AMBER: vmd and amber
(Tue Apr 17 2007 - 05:33:48 PDT)
Hans Lee
Re: AMBER: ptraj and quasi harmonic analysis
(Fri Apr 20 2007 - 09:35:49 PDT)
Re: AMBER: ptraj and quasi harmonic analysis
(Thu Apr 19 2007 - 18:46:38 PDT)
Re: AMBER: ptraj and quasi harmonic analysis
(Wed Apr 18 2007 - 07:47:11 PDT)
AMBER: ptraj and quasi harmonic analysis
(Mon Apr 16 2007 - 14:19:34 PDT)
Harald Lanig
AMBER: Projecting trajectories onto normal modes
(Mon Apr 16 2007 - 07:50:38 PDT)
Hayden Eastwood
RE: AMBER: PDB files
(Mon Apr 30 2007 - 10:20:14 PDT)
RE: AMBER: PDB files
(Mon Apr 30 2007 - 10:12:01 PDT)
AMBER: Problem with calcpka.pl and constant pH
(Mon Apr 30 2007 - 06:04:11 PDT)
AMBER: Problem with calcpka.pl and constant pH
(Mon Apr 30 2007 - 04:35:23 PDT)
AMBER: Explicit water opinion
(Fri Apr 13 2007 - 11:39:19 PDT)
Henar Martínez García
AMBER: Problem with MM-PBSA statistics
(Mon Apr 30 2007 - 02:53:38 PDT)
HL Eastwood
AMBER: mobile proton algorithm
(Tue Apr 24 2007 - 12:25:10 PDT)
Holger Gohlke
Re: AMBER: parse radii
(Wed Apr 04 2007 - 02:24:17 PDT)
Hu, Shaowen (JSC-SK)[USRA]
RE: AMBER: nscm in simulation annealing
(Tue Apr 17 2007 - 09:59:43 PDT)
RE: AMBER: nscm in simulation annealing
(Tue Apr 17 2007 - 09:26:01 PDT)
RE: AMBER: nscm in simulation annealing
(Tue Apr 17 2007 - 08:25:05 PDT)
RE: AMBER: nscm in simulation annealing
(Fri Apr 13 2007 - 13:13:07 PDT)
RE: AMBER: nscm in simulation annealing
(Fri Apr 13 2007 - 11:36:59 PDT)
RE: AMBER: nscm in simulation annealing
(Fri Apr 13 2007 - 08:32:26 PDT)
RE: AMBER: nscm in simulation annealing
(Thu Apr 12 2007 - 10:53:18 PDT)
AMBER: nscm in simulation annealing
(Thu Apr 12 2007 - 07:38:09 PDT)
AMBER: dihedral angles restraint for DNA
(Tue Apr 10 2007 - 10:51:13 PDT)
Ilyas Yildirim
Re: AMBER: bad atom type errors in GB for halides?
(Thu Apr 12 2007 - 12:57:13 PDT)
j j
Re: AMBER: Problem using Ptraj
(Mon Apr 23 2007 - 09:47:50 PDT)
Re: AMBER: mol2 format
(Mon Apr 23 2007 - 02:04:53 PDT)
Re: AMBER: NTX=7 ?............lastist= ?...........lastrst= ?????
(Mon Apr 09 2007 - 07:18:58 PDT)
janavi raghavan
AMBER: sander bomb
(Tue Apr 03 2007 - 07:28:39 PDT)
Jardas sucuriba
RE: AMBER: NAD parameters
(Wed Apr 25 2007 - 15:46:17 PDT)
AMBER: NAD parameters
(Tue Apr 24 2007 - 11:02:56 PDT)
AMBER: mol2 format
(Sun Apr 22 2007 - 15:57:12 PDT)
Jason DeChancie
AMBER: QM/MM Umbrella sampling
(Fri Apr 27 2007 - 13:53:08 PDT)
Jerome.GOLEBIOWSKI.unice.fr
Re: AMBER: QM/MM Umbrella sampling
(Sat Apr 28 2007 - 00:55:49 PDT)
Jesper Soerensen
AMBER: Protonation/deprotonation of terminal residues
(Wed Apr 18 2007 - 05:56:26 PDT)
Jingyuan Luke
AMBER: Sander Bomb in subroutine nonbond_list
(Mon Apr 09 2007 - 19:34:51 PDT)
Jiri Sponer
Re: AMBER: CHARMM vs. AMBER ff literature
(Thu Apr 12 2007 - 05:58:32 PDT)
Jiten
AMBER: Re: amber mm-pbsa problem
(Mon Apr 16 2007 - 18:39:26 PDT)
Re: AMBER: Amber:PBSA&Extract_coords problem (Needed help)
(Sat Apr 14 2007 - 06:51:58 PDT)
jitrayut jitonnom
AMBER: Binding free energy errors: Grid setting fail
(Sun Apr 29 2007 - 06:48:17 PDT)
AMBER: MM-PBSA: Can't finish the binding energy process
(Mon Apr 23 2007 - 05:34:48 PDT)
AMBER: MM-PBSA: decompose energy error
(Mon Apr 23 2007 - 04:31:43 PDT)
John E. Kerrigan
Re: AMBER: PDBs
(Tue Apr 17 2007 - 05:40:54 PDT)
Jojart Balazs
AMBER: membrane simulation
(Sun Apr 15 2007 - 11:06:31 PDT)
Junmei Wang
RE: AMBER: Antechamber
(Thu Apr 19 2007 - 06:58:14 PDT)
Kateryna Miroshnychenko
AMBER: RE: dihedral term charge dependence
(Tue Apr 03 2007 - 06:59:08 PDT)
Khatcharin Siriwong
Re: AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out"
(Sat Apr 21 2007 - 20:57:18 PDT)
AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out"
(Sat Apr 21 2007 - 00:42:14 PDT)
Re: AMBER: amber9: running parallel error
(Wed Apr 18 2007 - 00:03:13 PDT)
RE: AMBER: amber9: running parallel error
(Wed Apr 18 2007 - 00:00:29 PDT)
RE: AMBER: amber9: running parallel error
(Wed Apr 11 2007 - 20:40:27 PDT)
AMBER: amber9: running parallel error
(Wed Apr 11 2007 - 01:08:16 PDT)
Kijeong Kwac
AMBER: RE: RE: AMBER: QMMM with printcharges
(Thu Apr 19 2007 - 08:42:38 PDT)
AMBER: QMMM with printcharges
(Fri Apr 13 2007 - 17:37:45 PDT)
kkirschn.hamilton.edu
Re: AMBER: using glycam04 parameters
(Wed Apr 25 2007 - 13:02:49 PDT)
Re: AMBER: using glycam04 parameters
(Thu Apr 19 2007 - 10:53:37 PDT)
Kristina Furse
Re: AMBER: Attaching capping groups
(Wed Apr 11 2007 - 19:30:30 PDT)
Liang, Lei
Re: AMBER: Problems during compilation and test.
(Mon Apr 09 2007 - 10:21:39 PDT)
AMBER: Problems during compilation and test.
(Thu Apr 05 2007 - 13:43:23 PDT)
M. L. Dodson
Re: AMBER: Projecting trajectories onto normal modes
(Mon Apr 16 2007 - 08:41:50 PDT)
Marie Brut
Re: AMBER: nmode
(Tue Apr 03 2007 - 08:42:17 PDT)
AMBER: nmode
(Tue Apr 03 2007 - 03:17:39 PDT)
Mark Williamson
Re: AMBER: AMBER9 installation error on dual core AMD Opteron(tm) processor 275
(Fri Apr 13 2007 - 05:51:54 PDT)
Martin Stennett
Re: AMBER: Problem with Sander restart file.
(Wed Apr 11 2007 - 04:45:03 PDT)
AMBER: Problem with Sander restart file.
(Wed Apr 11 2007 - 03:56:37 PDT)
Melinda Layten
Re: AMBER: Request for addition of a useful command in ptraj module of AMBER #2
(Mon Apr 23 2007 - 14:52:26 PDT)
Mike Hanby
RE: AMBER: Blue Gene, compile Amber9?
(Fri Apr 20 2007 - 12:33:39 PDT)
RE: AMBER: Blue Gene, compile Amber9?
(Thu Apr 19 2007 - 07:34:46 PDT)
RE: AMBER: Blue Gene, compile Amber9?
(Tue Apr 10 2007 - 08:13:11 PDT)
RE: AMBER: Blue Gene, compile Amber9?
(Tue Apr 10 2007 - 07:04:13 PDT)
AMBER: Blue Gene, compile Amber9?
(Fri Apr 06 2007 - 10:22:57 PDT)
Myunggi Yi
Re: AMBER: Work with constand pH
(Fri Apr 27 2007 - 18:42:32 PDT)
Re: AMBER: Work with constand pH
(Wed Apr 25 2007 - 06:49:59 PDT)
Re: AMBER: ptraj and quasi harmonic analysis
(Wed Apr 18 2007 - 09:46:22 PDT)
nag raj
Re: AMBER: membrane simulation
(Thu Apr 19 2007 - 05:51:56 PDT)
Re: AMBER: membrane simulation
(Wed Apr 18 2007 - 19:53:27 PDT)
Re: AMBER: membrane simulation
(Sun Apr 15 2007 - 22:29:32 PDT)
Navnit Kumar Mishra
Re: AMBER: MM-PBSA: Can't finish the binding energy process
(Mon Apr 23 2007 - 07:04:12 PDT)
Re: AMBER: Problem with Sander restart file.
(Wed Apr 11 2007 - 04:19:20 PDT)
Neelanjana Sengupta
AMBER: Error in protonating
(Fri Apr 27 2007 - 04:31:52 PDT)
AMBER: .prmtop entries
(Sun Apr 22 2007 - 22:53:46 PDT)
Re: AMBER: Attaching capping groups
(Thu Apr 12 2007 - 19:54:30 PDT)
AMBER: Attaching capping groups
(Wed Apr 11 2007 - 18:28:33 PDT)
AMBER: Fails to load libraries present in /leap/lib/
(Mon Apr 09 2007 - 02:33:29 PDT)
AMBER: PDB file format for AMBER
(Fri Apr 06 2007 - 19:41:43 PDT)
Nicolas Lux Fawzi
AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? 2nd try
(Tue Apr 17 2007 - 14:50:07 PDT)
AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters?
(Tue Apr 17 2007 - 12:00:18 PDT)
odde
AMBER: Re: MM-PBSA amber script problem
(Tue Apr 17 2007 - 11:45:06 PDT)
Re: AMBER: Re: amber mm-pbsa problem
(Tue Apr 17 2007 - 06:57:37 PDT)
AMBER: MM-PBSA_binding energy script error
(Mon Apr 16 2007 - 16:33:14 PDT)
AMBER: Amber:PBSA&Extract_coords problem (Needed help)
(Fri Apr 13 2007 - 12:06:42 PDT)
Pankaj R. Daga
Re: AMBER: signal SIGSEGV(11)
(Tue Apr 24 2007 - 07:55:14 PDT)
Re: AMBER: signal SIGSEGV(11)
(Wed Apr 18 2007 - 12:16:48 PDT)
AMBER: signal SIGSEGV(11)
(Wed Apr 18 2007 - 08:25:55 PDT)
Patrick McCarren
Re: AMBER: AIX 5 test failures: -NaNQ
(Wed Apr 25 2007 - 16:44:15 PDT)
Re: AMBER: AIX 5 test failures: -NaNQ
(Mon Apr 23 2007 - 14:51:46 PDT)
Re: AMBER: AIX 5 test failures: -NaNQ
(Fri Apr 20 2007 - 16:01:53 PDT)
Re: AMBER: process and plot matrix data
(Fri Apr 20 2007 - 03:02:15 PDT)
AMBER: AIX 5 test failures: -NaNQ
(Thu Apr 19 2007 - 16:30:35 PDT)
Peljidiyn Genden
AMBER: mdfil.f
(Sat Apr 14 2007 - 00:43:27 PDT)
Pradipta Bandyopadhyay
AMBER: ff02 + POL3 - polar interactions !!
(Wed Apr 18 2007 - 09:04:22 PDT)
Re: AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? 2nd try
(Tue Apr 17 2007 - 21:33:52 PDT)
rdauria.uci.edu
AMBER: pressure tensor in a slab configuration
(Mon Apr 30 2007 - 19:16:08 PDT)
Rita Cassia
AMBER: Sander....
(Tue Apr 03 2007 - 01:23:06 PDT)
Robert Duke
Re: AMBER: mdfil.f
(Mon Apr 16 2007 - 10:02:28 PDT)
Re: AMBER: Blue Gene, compile Amber9?
(Tue Apr 10 2007 - 08:42:11 PDT)
Ross Walker
RE: AMBER: QM/MM Umbrella sampling
(Fri Apr 27 2007 - 15:01:46 PDT)
RE: AMBER: Problems installing Amber9
(Fri Apr 27 2007 - 08:56:41 PDT)
RE: AMBER: Error in protonating
(Fri Apr 27 2007 - 08:46:50 PDT)
RE: AMBER: signal SIGSEGV(11)
(Tue Apr 24 2007 - 12:43:49 PDT)
RE: AMBER: NAD parameters
(Tue Apr 24 2007 - 12:32:27 PDT)
RE: AMBER: AIX 5 test failures: -NaNQ
(Mon Apr 23 2007 - 15:47:20 PDT)
RE: AMBER: Ewald BOMB....... what is this..
(Sat Apr 21 2007 - 10:08:15 PDT)
RE: AMBER: restraint value: written but none specified
(Fri Apr 20 2007 - 15:37:01 PDT)
RE: AMBER: QM/MM NPT Simulation
(Fri Apr 20 2007 - 08:22:25 PDT)
RE: AMBER: AIX 5 test failures: -NaNQ
(Thu Apr 19 2007 - 18:20:46 PDT)
RE: AMBER: Problems with Machine file for sander.MPI
(Thu Apr 19 2007 - 14:02:24 PDT)
RE: AMBER: using glycam04 parameters
(Thu Apr 19 2007 - 12:00:01 PDT)
RE: AMBER: RE: RE: AMBER: QMMM with printcharges
(Thu Apr 19 2007 - 09:42:15 PDT)
RE: AMBER: signal SIGSEGV(11)
(Wed Apr 18 2007 - 09:09:10 PDT)
RE: AMBER: problem with calculating RMSD
(Wed Apr 18 2007 - 09:03:37 PDT)
RE: AMBER: frcmod file
(Wed Apr 18 2007 - 08:51:20 PDT)
RE: AMBER: printcharges option when using QM/MM simulation
(Wed Apr 18 2007 - 08:31:17 PDT)
RE: AMBER: QMMM with printcharges
(Tue Apr 17 2007 - 14:37:27 PDT)
RE: AMBER: nscm in simulation annealing
(Tue Apr 17 2007 - 09:25:35 PDT)
RE: AMBER: mdfil.f
(Mon Apr 16 2007 - 09:43:01 PDT)
RE: AMBER: Attaching capping groups
(Sun Apr 15 2007 - 20:49:26 PDT)
RE: AMBER: Attaching capping groups
(Wed Apr 11 2007 - 20:49:36 PDT)
RE: AMBER: amber9: running parallel error
(Wed Apr 11 2007 - 06:43:19 PDT)
RE: AMBER: NTX=7 ?............lastist= ?...........lastrst= ?????
(Tue Apr 10 2007 - 15:53:19 PDT)
RE: AMBER: Fails to load libraries present in /leap/lib/
(Tue Apr 10 2007 - 15:53:07 PDT)
RE: AMBER: Blue Gene, compile Amber9?
(Fri Apr 06 2007 - 14:23:33 PDT)
AMBER: FW: parameter
(Wed Apr 04 2007 - 08:18:07 PDT)
RE: AMBER: Regarding Simulated Annealing
(Tue Apr 03 2007 - 08:43:55 PDT)
RE: AMBER: sander bomb
(Tue Apr 03 2007 - 08:35:40 PDT)
RE: AMBER: Sander....
(Tue Apr 03 2007 - 08:28:51 PDT)
Ruchi Sachdeva
AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38
(Tue Apr 24 2007 - 20:54:14 PDT)
AMBER: A test email
(Thu Apr 19 2007 - 23:54:55 PDT)
Sandeep Kaushik
AMBER: H-bond analysis............acceptorH absent..!!!
(Sun Apr 15 2007 - 23:32:28 PDT)
Re: AMBER: NTX=7 ?............lastist= ?...........lastrst= ?????
(Wed Apr 11 2007 - 23:11:40 PDT)
AMBER: NTX=7 ?............lastist= ?...........lastrst= ?????
(Mon Apr 09 2007 - 03:35:54 PDT)
AMBER: Problem with sander.MPI
(Mon Apr 02 2007 - 06:06:21 PDT)
AMBER: Error at Equilibration....
(Mon Apr 02 2007 - 00:14:17 PDT)
Sangwai, Ashishvikas
AMBER: Cut off for cavities
(Mon Apr 02 2007 - 11:47:30 PDT)
Santanu Roy
AMBER: regarding frcmod file
(Thu Apr 19 2007 - 08:28:01 PDT)
Sara Alexandra Moura
Re: AMBER: using glycam04 parameters
(Thu Apr 19 2007 - 11:35:16 PDT)
Re: AMBER: using glycam04 parameters
(Thu Apr 19 2007 - 09:27:38 PDT)
Re: AMBER: using glycam04 parameters
(Wed Apr 18 2007 - 08:10:35 PDT)
Re: AMBER: using glycam04 parameters
(Wed Apr 18 2007 - 07:59:10 PDT)
AMBER: using glycam04 parameters
(Tue Apr 17 2007 - 12:17:44 PDT)
Scott Brozell
Re: AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38
(Fri Apr 27 2007 - 13:25:23 PDT)
Re: AMBER: AIX 5 test failures: -NaNQ
(Mon Apr 23 2007 - 10:10:23 PDT)
Re: AMBER: AIX 5 test failures: -NaNQ
(Thu Apr 19 2007 - 17:13:54 PDT)
Re: AMBER: MD at constan pH
(Fri Apr 06 2007 - 09:41:39 PDT)
Re: AMBER: Problems during compilation and test.
(Thu Apr 05 2007 - 19:11:30 PDT)
Re: AMBER: amber 9 installation: broken pipe
(Thu Apr 05 2007 - 18:46:09 PDT)
Re: AMBER: Charges in antechamber
(Thu Apr 05 2007 - 13:43:59 PDT)
Sean Rathlef
Re: AMBER: enzyme kinetics in silico
(Tue Apr 03 2007 - 14:08:10 PDT)
Sergey Samsonov
Re: AMBER: MM-PBSA: decompose energy error
(Mon Apr 23 2007 - 04:56:30 PDT)
Servaas Michielssens
AMBER: thermodynamic integration
(Sat Apr 28 2007 - 10:48:10 PDT)
Seth Lilavivat
AMBER: Amber 8 support of CHARMM ff?
(Sat Apr 14 2007 - 11:36:35 PDT)
AMBER: CHARMM vs. AMBER ff literature
(Wed Apr 11 2007 - 08:21:07 PDT)
Sophie Barbe
Re: AMBER: AMBER MINIMIZATION
(Mon Apr 30 2007 - 09:23:41 PDT)
AMBER: AMBER MINIMIZATION
(Mon Apr 30 2007 - 06:55:53 PDT)
AMBER: Restraints and free energy
(Fri Apr 13 2007 - 09:05:06 PDT)
Srinivas Odde
AMBER: Extracting Coords&MMPBSA&ambpdb
(Tue Apr 24 2007 - 08:51:48 PDT)
Stern, Julie
AMBER: amber 9 installation: broken pipe
(Thu Apr 05 2007 - 16:54:16 PDT)
Tamara Rogers
AMBER: ptraj bug?
(Wed Apr 18 2007 - 15:09:39 PDT)
Terry Lang
Re: AMBER: Problems with Machine file for sander.MPI
(Tue Apr 24 2007 - 16:55:11 PDT)
AMBER: Problems with Machine file for sander.MPI
(Thu Apr 19 2007 - 13:15:45 PDT)
Thomas Cheatham
Re: AMBER: CHARMM vs. AMBER ff literature
(Wed Apr 11 2007 - 14:21:14 PDT)
Thomas Cheatham III
Re: AMBER: Problem using Ptraj
(Mon Apr 23 2007 - 10:02:17 PDT)
Re: AMBER: ptraj and quasi harmonic analysis
(Thu Apr 19 2007 - 13:26:35 PDT)
Thérèse Malliavin
AMBER: polarization and water density
(Fri Apr 13 2007 - 02:36:44 PDT)
tonglei
AMBER: How can I modify the frcmod file of ligand with a nonstandard guanidine
(Thu Apr 12 2007 - 00:13:34 PDT)
tri nam Vo
Re: AMBER: Work with constand pH
(Thu Apr 26 2007 - 20:37:53 PDT)
Re: AMBER: Error on compiling AMBER8
(Wed Apr 25 2007 - 09:35:31 PDT)
AMBER: Work with constand pH
(Wed Apr 25 2007 - 01:13:05 PDT)
AMBER: Error on compiling AMBER8
(Tue Apr 24 2007 - 19:03:16 PDT)
Re: AMBER: Error on compile amber8
(Mon Apr 23 2007 - 23:47:27 PDT)
AMBER: Error on compile amber8
(Mon Apr 23 2007 - 22:04:34 PDT)
Re: AMBER: problem with calculating RMSD
(Wed Apr 18 2007 - 01:22:45 PDT)
AMBER: problem with calculating RMSD
(Tue Apr 17 2007 - 00:01:35 PDT)
Re: AMBER: pH effect on protein folding
(Fri Apr 06 2007 - 23:27:40 PDT)
Re: AMBER: MD at constan pH
(Fri Apr 06 2007 - 21:05:20 PDT)
Re: AMBER: MD at constan pH
(Fri Apr 06 2007 - 20:53:52 PDT)
AMBER: MD at constan pH
(Fri Apr 06 2007 - 07:10:18 PDT)
Vijay Manickam Achari
AMBER: Ewald BOMB....... what is this..
(Wed Apr 18 2007 - 20:13:38 PDT)
AMBER: Sander BOMB.. simulation terminates by itself...
(Wed Apr 18 2007 - 18:24:28 PDT)
vijayaraj.clri.info
AMBER: ptraj secstruct core dumped error
(Tue Apr 17 2007 - 06:45:04 PDT)
Vlad Cojocaru
Re: AMBER: Request for addition of a useful command in ptraj module of AMBER #2
(Tue Apr 24 2007 - 01:30:40 PDT)
Re: AMBER: process and plot matrix data
(Fri Apr 20 2007 - 06:18:46 PDT)
AMBER: process and plot matrix data
(Fri Apr 20 2007 - 02:28:12 PDT)
Re: AMBER: membrane simulation
(Thu Apr 19 2007 - 02:07:52 PDT)
Re: AMBER: topology for postprocessed files?
(Thu Apr 12 2007 - 03:07:08 PDT)
Re: AMBER: Constant volume simulations
(Tue Apr 10 2007 - 09:02:42 PDT)
Re: AMBER: Constant volume simulations
(Tue Apr 10 2007 - 08:39:45 PDT)
Re: AMBER: problem related to visualizing of structure
(Tue Apr 10 2007 - 02:32:01 PDT)
Re: AMBER: problem related to visualizing of structure
(Tue Apr 10 2007 - 01:25:06 PDT)
AMBER: I'm sorry ... please ignore the junk !!
(Mon Apr 09 2007 - 03:50:54 PDT)
AMBER: Vlad has Tagged you! :)
(Mon Apr 09 2007 - 03:06:37 PDT)
Re: AMBER: restraint command not taken
(Mon Apr 02 2007 - 09:57:37 PDT)
Re: AMBER: restraint command not taken
(Mon Apr 02 2007 - 09:16:16 PDT)
Williamson, Mark
AMBER: RE: dihedral term charge dependence
(Mon Apr 02 2007 - 09:07:29 PDT)
Xu, Yong
RE: AMBER: enzyme kinetics in silico
(Tue Apr 03 2007 - 12:26:45 PDT)
yxamber
undefinedRe: AMBER: phosphorylated residues
(Tue Apr 03 2007 - 06:12:35 PDT)
AMBER: phosphorylated residues
(Sun Apr 01 2007 - 22:13:17 PDT)
Ângela dos Reis
Re: AMBER: Problems installing Amber9
(Fri Apr 27 2007 - 10:34:38 PDT)
AMBER: Problems installing Amber9
(Fri Apr 27 2007 - 04:14:05 PDT)
한재범
AMBER: Employing SCC-DFTB with a periodic boundary condtion
(Wed Apr 25 2007 - 23:48:58 PDT)
AMBER: QM/MM simulation with SCC-DFTB
(Tue Apr 24 2007 - 01:19:25 PDT)
AMBER: printcharges option when using QM/MM simulation
(Tue Apr 17 2007 - 23:41:33 PDT)
Last message date
:
Wed May 02 2007 - 06:07:23 PDT
Archived on
: Fri Apr 26 2024 - 05:53:37 PDT
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