Amber Archive May 2008 by author
634 messages
:
Starting
Sun May 04 2008 - 06:07:16 PDT,
Ending
Sun Jun 01 2008 - 06:08:25 PDT
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Adrian Roitberg
Re: AMBER: how to overcome theunusual bonds formation
(Thu May 29 2008 - 05:07:14 PDT)
Re: AMBER: B-factor calculation from data with different write frequencies
(Wed May 28 2008 - 11:58:53 PDT)
Re: AMBER: B-factor calculation from data with different write frequencies
(Wed May 28 2008 - 10:54:09 PDT)
Re: AMBER: Which is best temperature controlling method
(Wed May 28 2008 - 10:43:09 PDT)
Re: AMBER: restarting molecular dynamics
(Wed May 28 2008 - 08:48:45 PDT)
Re: AMBER: restarting molecular dynamics
(Wed May 28 2008 - 06:34:17 PDT)
Re: AMBER: mass weighted rms fit
(Sun May 25 2008 - 09:26:11 PDT)
Re: AMBER: analysis REMD
(Tue May 20 2008 - 12:17:39 PDT)
Re: AMBER: massively parallel computation
(Tue May 20 2008 - 07:11:46 PDT)
Re: AMBER: steered MD initial state
(Tue May 06 2008 - 10:16:52 PDT)
Re: AMBER: Jarzinsky relationship
(Mon May 05 2008 - 08:13:51 PDT)
Re: AMBER: Jarzinsky relationship
(Mon May 05 2008 - 07:46:53 PDT)
Alan
AMBER: gasteiger is not working with ambertools 1.0
(Mon May 19 2008 - 07:51:05 PDT)
AMBER: ambertools: static linking of user binaries is not supported on Mac OS X
(Mon May 19 2008 - 02:39:32 PDT)
Alejandro Valbuena
AMBER: install amber tools
(Wed May 28 2008 - 03:14:35 PDT)
Alessandro Nascimento
Re: AMBER: nab
(Mon May 12 2008 - 17:59:27 PDT)
Re: AMBER: MM_PBSA output file
(Fri May 09 2008 - 09:22:35 PDT)
amor san juan
Re: AMBER: ligand unit charge is not zero
(Thu May 29 2008 - 05:32:57 PDT)
AMBER: ligand unit charge is not zero
(Thu May 29 2008 - 01:44:58 PDT)
Anamika Awasthi
AMBER: is in vacuo simulation neccessary?
(Sun May 25 2008 - 22:18:58 PDT)
Re: AMBER: regarding segfault during energy minimization
(Wed Apr 30 2008 - 22:57:35 PDT)
Andreas Svrcek-Seiler
Re: AMBER: self-diffusion coefficient and Berendsen
(Fri May 23 2008 - 02:22:57 PDT)
Re: AMBER: nab
(Tue May 13 2008 - 02:39:19 PDT)
Andrew Emerson
AMBER: Re: amber 9 compilation problem on IBM SP5
(Mon May 05 2008 - 00:57:53 PDT)
Anselm Horn
AMBER: Weighting factors in RESP charge fitting
(Fri May 16 2008 - 05:32:22 PDT)
Arturas Ziemys
Re: AMBER: parallel test / libmpi_f90.so.0
(Wed May 28 2008 - 08:24:14 PDT)
AMBER: parallel test / libmpi_f90.so.0
(Wed May 28 2008 - 08:10:36 PDT)
Atro Tossavainen
Re: AMBER: Installing PMEMD with Amber10
(Sat May 31 2008 - 04:23:31 PDT)
Re: AMBER: Installing PMEMD with Amber10
(Thu May 29 2008 - 23:42:02 PDT)
Re: AMBER: compilation problem with AMBER10
(Wed May 28 2008 - 01:04:09 PDT)
Re: AMBER: massively parallel computation
(Wed May 21 2008 - 10:49:03 PDT)
Re: AMBER: massively parallel computation
(Wed May 21 2008 - 00:17:10 PDT)
Austin B. Yongye
Re: AMBER: about glycam06
(Sat May 03 2008 - 18:59:47 PDT)
Benjamin Juhl
AMBER: protonate in Amber10
(Wed May 28 2008 - 07:55:06 PDT)
Re: AMBER: reset time and comments
(Thu May 08 2008 - 02:12:11 PDT)
Bertrand P. S. Russell
Re: AMBER: Installation problem of AMBER on cluster
(Mon May 05 2008 - 05:40:56 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Mon May 05 2008 - 00:09:20 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Mon May 05 2008 - 00:03:39 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Sun May 04 2008 - 18:50:13 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Fri May 02 2008 - 03:11:15 PDT)
bhargav patel
AMBER: compilation problem with AMBER10
(Tue May 27 2008 - 22:56:15 PDT)
Bill Ross
Re: AMBER: B-factor calculation from data with different write frequencies
(Wed May 28 2008 - 11:18:06 PDT)
Re: AMBER: B-factor calculation from data with different write frequencies
(Wed May 28 2008 - 11:11:30 PDT)
Re: AMBER: B-factor calculation from data with different write frequencies
(Wed May 28 2008 - 10:47:28 PDT)
Re: AMBER: B-factor calculation from data with different write frequencies
(Tue May 27 2008 - 09:44:23 PDT)
Re: AMBER: potassium ion
(Thu May 22 2008 - 11:27:21 PDT)
Re: AMBER: to unsubscribe email
(Mon May 12 2008 - 10:46:24 PDT)
Re: AMBER: Improper dihedral parameters
(Tue May 06 2008 - 12:23:55 PDT)
Re: AMBER: about glycam06
(Sun May 04 2008 - 15:46:05 PDT)
Campbell, Patrick
AMBER: VMD Movie 3
(Fri May 30 2008 - 07:56:41 PDT)
AMBER: VMD Movie 4
(Thu May 29 2008 - 12:37:43 PDT)
AMBER: VMD Movie 3
(Thu May 29 2008 - 11:12:20 PDT)
AMBER: VMD Movie 2
(Thu May 29 2008 - 10:39:20 PDT)
AMBER: VMD Movie
(Wed May 28 2008 - 16:33:39 PDT)
Carlos Simmerling
Re: AMBER: VMD Movie 2
(Thu May 29 2008 - 10:48:10 PDT)
Re: AMBER: VMD Movie
(Wed May 28 2008 - 17:10:03 PDT)
Re: AMBER: using amber ports in Gromacs
(Sun May 25 2008 - 12:32:05 PDT)
Re: AMBER: about hydrogen bond in amber force field
(Thu May 22 2008 - 00:08:08 PDT)
Re: AMBER: analysis REMD
(Wed May 21 2008 - 10:18:06 PDT)
Re: AMBER: analysis REMD
(Tue May 20 2008 - 05:11:29 PDT)
Re: AMBER: Hybrid REMD amber10
(Mon May 19 2008 - 23:55:06 PDT)
Re: AMBER: analysis REMD
(Mon May 19 2008 - 23:51:22 PDT)
Re: AMBER: GBSA SA calculation
(Tue May 13 2008 - 10:46:30 PDT)
Re: AMBER: initial velocities of MD
(Tue May 13 2008 - 09:59:26 PDT)
Re: AMBER: GBSA SA calculation
(Wed May 07 2008 - 15:05:26 PDT)
Re: AMBER: GBSA SA calculation
(Wed May 07 2008 - 12:05:44 PDT)
Carra, Claudio (JSC-SK)[USRA]
AMBER: DFTB parameters for O-P
(Tue May 06 2008 - 13:01:55 PDT)
AMBER: test.parallel.QMMM problem
(Fri May 02 2008 - 06:37:28 PDT)
Catein Catherine
AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222-
(Tue May 13 2008 - 03:17:29 PDT)
Cenk \(Jenk\) Andac
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Thu May 29 2008 - 17:24:38 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Sat May 24 2008 - 05:26:37 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Sat May 24 2008 - 05:02:34 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Fri May 23 2008 - 09:35:36 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Fri May 23 2008 - 07:57:48 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Thu May 22 2008 - 15:29:55 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Thu May 22 2008 - 15:28:34 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Thu May 22 2008 - 15:24:33 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Wed May 21 2008 - 06:33:35 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Mon May 19 2008 - 14:18:11 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Mon May 19 2008 - 13:40:37 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Mon May 19 2008 - 09:48:21 PDT)
RE: AMBER: Amber10 testing problem
(Wed May 14 2008 - 02:13:13 PDT)
AMBER: Amber10 testing problem
(Tue May 13 2008 - 12:46:02 PDT)
Re: AMBER: rms
(Mon May 12 2008 - 06:51:56 PDT)
AMBER: parmbsc0 parameters for RNA.DNA systems
(Sat May 10 2008 - 06:47:50 PDT)
cgji
AMBER: About Hydrophobic Interactions.
(Mon May 12 2008 - 09:14:00 PDT)
chen bents
AMBER: Calculate the RESP charge Fe3+ of heme (p450)
(Thu May 22 2008 - 19:16:12 PDT)
Chih-Ying Lin
AMBER: Force field in water and in vacuum ??
(Thu May 22 2008 - 08:46:15 PDT)
AMBER: Adjust Force Field parameters
(Thu May 08 2008 - 16:46:21 PDT)
AMBER: Azobenzene: AMBER+Gromos Force Field parameters
(Wed May 07 2008 - 14:43:17 PDT)
AMBER: Improper dihedral parameters
(Tue May 06 2008 - 12:00:36 PDT)
Re: AMBER: NON-BONDED parameters
(Mon May 05 2008 - 15:10:05 PDT)
AMBER: NON-BONDED parameters
(Mon May 05 2008 - 10:32:23 PDT)
Re: RE: RE: AMBER: point charges
(Sat May 03 2008 - 14:47:23 PDT)
Re: RE: AMBER: point charges
(Fri May 02 2008 - 15:42:18 PDT)
AMBER: point charges
(Fri May 02 2008 - 13:53:50 PDT)
Chris Moth
Re: AMBER: how to calculate delta G from IC50
(Tue May 20 2008 - 05:30:29 PDT)
Cristina Sisu
Re: AMBER: MMPBSA error
(Sat May 31 2008 - 07:53:32 PDT)
AMBER: MMPBSA error
(Sat May 31 2008 - 07:00:08 PDT)
Re: AMBER: Sander instead of PMEMD
(Fri May 30 2008 - 08:22:10 PDT)
Re: AMBER: Sander instead of PMEMD
(Fri May 30 2008 - 07:32:27 PDT)
AMBER: Sander instead of PMEMD
(Fri May 30 2008 - 06:47:13 PDT)
AMBER: using amber ports in Gromacs
(Sun May 25 2008 - 11:28:26 PDT)
AMBER: using amber ports in gromacs
(Sun May 25 2008 - 11:22:58 PDT)
Re: AMBER: from Gromax to AMBER
(Tue May 13 2008 - 06:49:12 PDT)
AMBER: from Gromax to AMBER
(Tue May 13 2008 - 03:00:24 PDT)
Da-Wei Li
Re: AMBER: Improper dihedral parameters
(Tue May 06 2008 - 12:30:29 PDT)
Darek Czapiewski
AMBER: peptide at the box center during NVT-MD
(Mon May 26 2008 - 03:01:45 PDT)
David A. Case
Re: AMBER: igb and ibelly
(Fri May 30 2008 - 13:20:52 PDT)
Re: AMBER: nab
(Fri May 30 2008 - 07:55:10 PDT)
Re: AMBER: protonate in Amber10
(Thu May 29 2008 - 14:10:34 PDT)
Re: AMBER: Segmentation faults trying to run sander mpi
(Thu May 29 2008 - 08:20:08 PDT)
Re: AMBER: Which is best temperature controlling method
(Thu May 29 2008 - 07:35:36 PDT)
Re: AMBER: Which is best temperature controlling method
(Wed May 28 2008 - 10:32:33 PDT)
Re: AMBER: mbondi radii for gaff atom types
(Wed May 28 2008 - 10:31:30 PDT)
Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error
(Wed May 28 2008 - 10:27:31 PDT)
Re: AMBER: Segmentation faults trying to run sander mpi
(Wed May 28 2008 - 10:00:34 PDT)
Re: AMBER: install amber tools
(Wed May 28 2008 - 09:56:30 PDT)
Re: AMBER: Parallel Self-guided Langevin simulation
(Wed May 28 2008 - 09:46:55 PDT)
Re: AMBER: Hydration free energies of charged ions using PME
(Wed May 28 2008 - 09:51:26 PDT)
Re: AMBER: bugfix (imin=5) in amber9
(Tue May 27 2008 - 22:16:40 PDT)
Re: AMBER: Which is best temperature controlling method
(Tue May 27 2008 - 21:59:23 PDT)
Re: AMBER: peptide at the box center during NVT-MD
(Mon May 26 2008 - 09:09:51 PDT)
Re: AMBER: Parallel Self-guided Langevin simulation
(Sun May 25 2008 - 23:06:03 PDT)
Re: AMBER: self-diffusion coefficient and Berendsen
(Sun May 25 2008 - 21:09:32 PDT)
Re: AMBER: how to extract energy
(Sat May 24 2008 - 13:21:22 PDT)
Re: AMBER: self-diffusion coefficient and Berendsen
(Sat May 24 2008 - 13:20:27 PDT)
Re: AMBER: Calculate the RESP charge Fe3+ of heme (p450)
(Thu May 22 2008 - 22:35:29 PDT)
Re: AMBER: COM RESTRAINT
(Thu May 22 2008 - 22:19:24 PDT)
Re: AMBER: Parallel Self-guided Langevin simulation
(Thu May 22 2008 - 03:16:23 PDT)
Re: AMBER: amber tools installation
(Wed May 21 2008 - 08:30:32 PDT)
Re: AMBER: xLeap compilation issues
(Tue May 20 2008 - 22:27:53 PDT)
Re: AMBER: building quadruplex with nab
(Tue May 20 2008 - 22:08:10 PDT)
Re: AMBER: anal
(Tue May 20 2008 - 01:25:13 PDT)
Re: AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222-
(Sun May 18 2008 - 13:09:00 PDT)
Re: AMBER: Amber 10 ambpdb bug?
(Sat May 17 2008 - 21:37:09 PDT)
AMBER: Versions of mopac
(Fri May 16 2008 - 19:04:10 PDT)
Re: AMBER: MKL libraries/Amber10
(Fri May 16 2008 - 13:27:40 PDT)
Re: AMBER: Problems installing Amber Tools for Amber 10
(Fri May 16 2008 - 13:24:08 PDT)
Re: Re: AMBER: Amber10:Compiling with gcc 2.4.1
(Fri May 16 2008 - 13:16:56 PDT)
Re: AMBER: PGI amber9 problems
(Fri May 16 2008 - 04:29:06 PDT)
Re: AMBER: Problems installing Amber Tools for Amber 10
(Thu May 15 2008 - 21:47:19 PDT)
Re: AMBER: Amber10:Compiling with gcc 2.4.1
(Thu May 15 2008 - 20:42:31 PDT)
Re: AMBER: periodic boundary condition
(Wed May 14 2008 - 06:50:40 PDT)
Re: AMBER: Ewald PARAMETER RANGE WRONG
(Mon May 12 2008 - 09:00:44 PDT)
Re: AMBER: parmbsc0 parameters for RNA.DNA systems
(Sat May 10 2008 - 08:27:36 PDT)
Re: AMBER: cannot read big .pdb files
(Sat May 10 2008 - 08:24:41 PDT)
Re: AMBER: velocity autocorrelation function for SPC felxible water model
(Thu May 08 2008 - 15:54:57 PDT)
Re: AMBER: nmode "Atom out of bounds" for min of multiple ligands
(Thu May 08 2008 - 13:49:31 PDT)
Re: AMBER: AmberTools on OS X fails tests
(Thu May 08 2008 - 12:30:53 PDT)
Re: AMBER: xleap (draw using edit)
(Thu May 08 2008 - 11:02:58 PDT)
Re: AMBER: velocity autocorrelation function for SPC felxible water model
(Thu May 08 2008 - 11:00:28 PDT)
Re: AMBER: mm_pbsa problem: bad atom type: IP
(Thu May 08 2008 - 10:27:22 PDT)
Re: AMBER: Discontinuous Constant pH Restarts
(Thu May 08 2008 - 10:21:57 PDT)
Re: AMBER: Ewald error estimate
(Thu May 08 2008 - 10:16:43 PDT)
Re: AMBER: How to transfer unformatted coordinates into formatted ones
(Thu May 08 2008 - 10:13:59 PDT)
Re: AMBER: Hydroxyprolines!!!
(Wed May 07 2008 - 18:26:16 PDT)
Re: AMBER: How to transfer unformatted coordinates into formatted ones
(Wed May 07 2008 - 18:14:04 PDT)
Re: AMBER: Discontinuous Constant pH Restarts
(Wed May 07 2008 - 14:34:23 PDT)
Re: AMBER: GBSA SA calculation
(Wed May 07 2008 - 14:17:07 PDT)
Re: AMBER: uninstall of AMBER
(Wed May 07 2008 - 09:07:25 PDT)
Re: AMBER: Ewald error estimate
(Wed May 07 2008 - 08:57:03 PDT)
Re: AMBER: single stranded DNA
(Tue May 06 2008 - 15:41:29 PDT)
Re: AMBER: mm_pbsa.pl not reading parameters for nmode
(Tue May 06 2008 - 11:13:54 PDT)
Re: AMBER: Minimization in Octahedric Box
(Tue May 06 2008 - 10:28:20 PDT)
Re: AMBER: NON-BONDED parameters
(Mon May 05 2008 - 16:54:32 PDT)
Re: AMBER: About reading in heme and CO molecule together with myoglobin
(Mon May 05 2008 - 16:51:44 PDT)
Re: AMBER: Units, units units
(Mon May 05 2008 - 16:02:57 PDT)
Re: AMBER: misplacement of TER by leap
(Mon May 05 2008 - 11:55:29 PDT)
Re: AMBER: unable to compile AmberTools 1.0
(Mon May 05 2008 - 11:14:44 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Sun May 04 2008 - 18:32:02 PDT)
Re: AMBER: Help with NMODE
(Sun May 04 2008 - 18:26:07 PDT)
Re: AMBER: Amber10 Installation error - incorrect file suffix
(Sun May 04 2008 - 18:20:55 PDT)
Re: AMBER: GAFF Schema
(Sun May 04 2008 - 18:21:59 PDT)
Re: RE: RE: AMBER: point charges
(Sat May 03 2008 - 17:36:08 PDT)
Re: AMBER: about glycam06
(Sat May 03 2008 - 17:32:10 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Sat May 03 2008 - 16:56:32 PDT)
Re: AMBER: about glycam06
(Sat May 03 2008 - 16:49:27 PDT)
Re: AMBER: Example .prepi file for nonstandard amino acids
(Fri May 02 2008 - 15:54:03 PDT)
Re: AMBER: Discontinuous Constant pH Restarts
(Fri May 02 2008 - 12:44:31 PDT)
Re: AMBER: Help with NMODE
(Fri May 02 2008 - 12:28:51 PDT)
Re: AMBER: Help with NMODE
(Fri May 02 2008 - 10:06:33 PDT)
Re: AMBER: cfortran.h error with xlf90 compiler
(Fri May 02 2008 - 10:10:54 PDT)
Re: AMBER: Help with NMODE
(Fri May 02 2008 - 09:23:34 PDT)
Re: AMBER: Amber10 installation error
(Fri May 02 2008 - 09:07:50 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Thu May 01 2008 - 11:55:17 PDT)
David Mobley
Re: AMBER: Jarzynski
(Fri May 30 2008 - 09:02:28 PDT)
Re: AMBER: Jarzinsky relationship
(Thu May 08 2008 - 14:29:29 PDT)
David Watson
Re: AMBER: cannot read big .pdb files
(Mon May 12 2008 - 16:32:49 PDT)
Dirar Homouz
RE: AMBER: Parallel Self-guided Langevin simulation
(Wed May 28 2008 - 22:18:34 PDT)
RE: AMBER: Parallel Self-guided Langevin simulation
(Tue May 27 2008 - 23:31:03 PDT)
RE: AMBER: Parallel Self-guided Langevin simulation
(Thu May 22 2008 - 08:58:27 PDT)
AMBER: Parallel Self-guided Langevin simulation
(Wed May 21 2008 - 15:23:27 PDT)
Dong Xu
AMBER: ptraj has trouble with x-plor psf file from VMD
(Thu May 29 2008 - 13:23:56 PDT)
Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Thu May 29 2008 - 12:19:53 PDT)
AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Wed May 28 2008 - 22:56:48 PDT)
Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Tue May 27 2008 - 11:20:09 PDT)
AMBER: mass weighted rms fit
(Sun May 25 2008 - 09:11:43 PDT)
AMBER: ptraj mask not working with psf file
(Fri May 23 2008 - 19:53:27 PDT)
Re: AMBER: AMBER entropy calculation
(Wed May 14 2008 - 17:37:27 PDT)
Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Mon May 12 2008 - 21:09:11 PDT)
AMBER: Ligand energy minimization
(Mon May 12 2008 - 15:07:31 PDT)
AMBER: Calculate number of ions
(Sat May 10 2008 - 11:32:01 PDT)
dpandit.brandeis.edu
RE: AMBER: NTC and NTF
(Thu May 29 2008 - 12:39:33 PDT)
AMBER: NTC and NTF
(Thu May 29 2008 - 12:18:14 PDT)
RE: AMBER: Restart MD Simulation
(Sat May 24 2008 - 06:40:40 PDT)
AMBER: Restart MD Simulation
(Fri May 23 2008 - 14:56:23 PDT)
E.M.
AMBER: divcon
(Tue May 13 2008 - 09:58:49 PDT)
Re: AMBER: distance
(Fri May 09 2008 - 07:43:12 PDT)
Re: AMBER: Jarzinsky relationship
(Thu May 08 2008 - 03:58:10 PDT)
AMBER: reset time and comments
(Wed May 07 2008 - 21:13:02 PDT)
AMBER: Units, units units
(Mon May 05 2008 - 15:18:37 PDT)
Re: AMBER: Jarzinsky relationship
(Mon May 05 2008 - 08:02:49 PDT)
AMBER: Torsion angle restrains and Jarzinsky
(Mon May 05 2008 - 00:06:56 PDT)
AMBER: Jarzinsky relationship
(Sun May 04 2008 - 19:39:51 PDT)
fatima.chami.durham.ac.uk
Re: AMBER: Jarzynski
(Sat May 31 2008 - 04:50:24 PDT)
AMBER: Jarzynski
(Fri May 30 2008 - 04:44:41 PDT)
AMBER: solvatebox
(Thu May 29 2008 - 04:46:42 PDT)
AMBER: PBC in 2D
(Fri May 23 2008 - 06:13:39 PDT)
AMBER: COM RESTRAINT
(Thu May 22 2008 - 05:17:09 PDT)
Re: AMBER: STEERED MD
(Sat May 17 2008 - 03:26:28 PDT)
AMBER: STEERED MD
(Fri May 16 2008 - 09:25:55 PDT)
finke.oakland.edu
Re: AMBER: Example .prepi file for nonstandard amino acids
(Fri May 02 2008 - 18:06:30 PDT)
AMBER: Example .prepi file for nonstandard amino acids
(Fri May 02 2008 - 15:00:45 PDT)
Florian Haberl
Re: AMBER: Sander instead of PMEMD
(Fri May 30 2008 - 08:31:18 PDT)
Re: AMBER: Sander instead of PMEMD
(Fri May 30 2008 - 08:06:42 PDT)
Re: AMBER: how to overcome theunusual bonds formation
(Thu May 29 2008 - 04:54:20 PDT)
Re: AMBER: trajectories into trajectory
(Sun May 25 2008 - 05:10:41 PDT)
Francesco Pietra
Re: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd'
(Sat May 31 2008 - 11:31:04 PDT)
Fw: RE: Fw: RE: AMBER: MKL libraries/Amber10
(Sat May 31 2008 - 07:22:35 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Fri May 30 2008 - 23:44:24 PDT)
Re: AMBER: Sander instead of PMEMD
(Fri May 30 2008 - 10:59:35 PDT)
Re: AMBER: Sander instead of PMEMD
(Fri May 30 2008 - 10:47:57 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Fri May 30 2008 - 02:40:41 PDT)
Re: AMBER: Sander instead of PMEMD
(Fri May 30 2008 - 08:17:15 PDT)
AMBER: Fw: rmsd vs frame
(Wed May 28 2008 - 16:19:11 PDT)
AMBER: rmsd vs frame
(Wed May 28 2008 - 15:56:24 PDT)
AMBER: Fw: Amber9 vs Amber10+MKL benchmark
(Sat May 24 2008 - 07:50:45 PDT)
AMBER: Fw: Amber9 vs Amber10+MKL benchmark
(Sat May 24 2008 - 06:51:53 PDT)
AMBER: Amber9 vs Amber10+MKL benchmark
(Sat May 24 2008 - 06:48:12 PDT)
RE: AMBER: how to extract energy
(Sat May 24 2008 - 00:24:13 PDT)
Re: AMBER: $AMBERHOME/dat/slko
(Thu May 22 2008 - 10:48:49 PDT)
RE: AMBER: $AMBERHOME/dat/slko
(Thu May 22 2008 - 08:44:10 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Thu May 22 2008 - 03:06:48 PDT)
Re: AMBER: $AMBERHOME/dat/slko
(Thu May 22 2008 - 02:14:55 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Wed May 21 2008 - 12:09:10 PDT)
AMBER: $AMBERHOME/dat/slko
(Wed May 21 2008 - 05:47:59 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Mon May 19 2008 - 14:17:25 PDT)
Re: Fw: RE: AMBER: MKL libraries/Amber10
(Mon May 19 2008 - 08:24:43 PDT)
Fw: RE: AMBER: MKL libraries/Amber10
(Sun May 18 2008 - 10:33:54 PDT)
Fw: RE: AMBER: MKL libraries/Amber10
(Sat May 17 2008 - 14:14:18 PDT)
Fw: RE: AMBER: MKL libraries/Amber10
(Sat May 17 2008 - 10:33:10 PDT)
RE: AMBER: MKL libraries/Amber10
(Sat May 17 2008 - 10:12:06 PDT)
RE: AMBER: MKL libraries/Amber10
(Fri May 16 2008 - 09:31:17 PDT)
AMBER: MKL libraries/Amber10
(Thu May 15 2008 - 11:01:34 PDT)
AMBER: Solvent mixture box
(Sun May 11 2008 - 10:04:52 PDT)
frustrated modeller
AMBER: bye
(Mon May 19 2008 - 11:29:40 PDT)
Furia Gargano
AMBER: rmsd per residue
(Tue May 06 2008 - 07:28:59 PDT)
FyD
Re: AMBER: Iron-Sulfur Cluster
(Sat May 31 2008 - 05:35:31 PDT)
Re: AMBER: RESP charges of an unusual substrate
(Sun May 18 2008 - 23:46:40 PDT)
Re: AMBER: neutral C-terminus and N-terminus parameters for amber
(Sat May 10 2008 - 00:52:10 PDT)
Re: AMBER: Deriving Force Field Parameters
(Mon May 05 2008 - 07:14:22 PDT)
Re: AMBER: Cysteine sulphonic acid parameters
(Thu May 01 2008 - 05:03:19 PDT)
Geoff Wood
Re: AMBER: Hybrid REMD amber10
(Tue May 20 2008 - 07:24:11 PDT)
AMBER: Hybrid REMD amber10
(Mon May 19 2008 - 05:41:54 PDT)
Germain Vallverdu
Re: AMBER: Which is best temperature controlling method
(Wed May 28 2008 - 13:24:55 PDT)
Re: AMBER: restarting molecular dynamics
(Wed May 28 2008 - 07:25:23 PDT)
AMBER: restarting molecular dynamics
(Wed May 28 2008 - 06:18:16 PDT)
German Erlenkamp
AMBER: Umbrella Sampling for proteins
(Mon May 26 2008 - 02:23:56 PDT)
guardiani.fi.infn.it
AMBER: Minimization in Octahedric Box
(Tue May 06 2008 - 04:31:50 PDT)
Guillermo Mulliert Carlín
Re: AMBER: Mn2+ parameters in AMBER
(Thu May 22 2008 - 23:26:51 PDT)
Gustavo Seabra
Re: AMBER: $AMBERHOME/dat/slko
(Thu May 22 2008 - 11:41:41 PDT)
Re: AMBER: $AMBERHOME/dat/slko
(Thu May 22 2008 - 10:00:36 PDT)
Re: AMBER: $AMBERHOME/dat/slko
(Wed May 21 2008 - 07:29:35 PDT)
Re: Fw: RE: AMBER: MKL libraries/Amber10
(Mon May 19 2008 - 07:18:07 PDT)
Re: AMBER: MKL libraries/Amber10
(Thu May 15 2008 - 16:02:42 PDT)
Re: AMBER: Amber10:Compiling with gcc 2.4.1
(Thu May 15 2008 - 15:58:05 PDT)
Re: AMBER: divcon
(Tue May 13 2008 - 10:43:35 PDT)
Re: AMBER: help to install AMBER9
(Mon May 12 2008 - 07:56:41 PDT)
Re: AMBER: help to install AMBER9
(Fri May 09 2008 - 08:01:04 PDT)
Re: AMBER: QM/MM
(Fri May 09 2008 - 07:18:21 PDT)
Re: AMBER: DFTB parameters for O-P
(Wed May 07 2008 - 12:19:50 PDT)
Re: AMBER: steered MD initial state
(Tue May 06 2008 - 09:37:54 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Fri May 02 2008 - 14:16:22 PDT)
Hakkim Boy
AMBER: trajectories into trajectory
(Sun May 25 2008 - 04:30:22 PDT)
Hans Martin Senn
Re: AMBER: ambertools: static linking of user binaries is not supported on Mac OS X
(Mon May 19 2008 - 03:35:24 PDT)
AMBER: AmberTools on OS X fails tests
(Thu May 08 2008 - 11:59:12 PDT)
Holly Freedman
Re: AMBER: igb and ibelly
(Fri May 30 2008 - 15:36:03 PDT)
RE: AMBER: igb and ibelly
(Fri May 30 2008 - 13:21:06 PDT)
AMBER: igb and ibelly
(Fri May 30 2008 - 12:23:21 PDT)
Hu, Shaowen (JSC-SK)[USRA]
RE: AMBER: Sander instead of PMEMD
(Fri May 30 2008 - 09:24:39 PDT)
Ian
AMBER: Ptraj | Multiple trajout commands?
(Fri May 30 2008 - 01:39:23 PDT)
Ibrahim Moustafa
Re: AMBER: VMD Movie 3
(Thu May 29 2008 - 14:03:16 PDT)
Re: AMBER: amber10 installation
(Thu May 22 2008 - 08:03:15 PDT)
Re: AMBER: distance
(Fri May 09 2008 - 07:49:37 PDT)
AMBER: DCCM correlation analysis
(Mon May 05 2008 - 13:21:37 PDT)
Idan Gabdank
Re: AMBER: Segmentation faults trying to run sander mpi
(Thu May 29 2008 - 07:57:07 PDT)
AMBER: Segmentation faults trying to run sander mpi
(Wed May 28 2008 - 03:59:09 PDT)
jacopo sgrignani
Re: AMBER: MM_PBSA problem in binding_energy
(Wed May 14 2008 - 11:43:55 PDT)
jacopo.sgrignani.unifi.it
RE: AMBER: from Gromax to AMBER
(Tue May 13 2008 - 06:19:19 PDT)
AMBER: molsurf
(Wed May 07 2008 - 04:11:34 PDT)
James Thomas
AMBER: Inquiry on B-factor of NMR
(Fri May 02 2008 - 12:31:09 PDT)
Jeffrey
Re: Re: AMBER: help to install AMBER9
(Mon May 12 2008 - 17:51:46 PDT)
Re: AMBER: help to install AMBER9
(Sun May 11 2008 - 02:12:18 PDT)
AMBER: help to install AMBER9
(Fri May 09 2008 - 07:47:16 PDT)
Jena M
AMBER: initial velocities of MD
(Tue May 13 2008 - 09:37:31 PDT)
AMBER: misplacement of TER by leap
(Mon May 05 2008 - 04:00:55 PDT)
Jennifer.Thomas.cbt.uhp-nancy.fr
Re: AMBER: self-diffusion coefficient and Berendsen
(Sun May 25 2008 - 03:47:22 PDT)
AMBER: self-diffusion coefficient and Berendsen
(Fri May 23 2008 - 01:03:49 PDT)
Jianyin Shao
Re: AMBER: Ptraj | Multiple trajout commands?
(Sat May 31 2008 - 17:02:17 PDT)
Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Fri May 30 2008 - 10:11:24 PDT)
Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Thu May 29 2008 - 14:47:43 PDT)
Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Thu May 29 2008 - 11:15:15 PDT)
Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Wed May 28 2008 - 21:07:18 PDT)
Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Wed May 28 2008 - 08:51:12 PDT)
Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Tue May 27 2008 - 12:29:43 PDT)
Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Tue May 27 2008 - 09:03:54 PDT)
Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Tue May 27 2008 - 08:37:57 PDT)
Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Fri May 09 2008 - 13:05:39 PDT)
Jiayun Pang
AMBER: RESP charges of an unusual substrate
(Fri May 16 2008 - 03:45:54 PDT)
jitrayut jitonnom
Re: AMBER: Mn2+ parameters in AMBER
(Fri May 23 2008 - 01:58:10 PDT)
Re: AMBER: AMBER Parallel test error
(Thu May 08 2008 - 02:10:49 PDT)
Re: AMBER: AMBER Parallel test error
(Tue May 06 2008 - 06:38:53 PDT)
Re: AMBER: AMBER Parallel test error
(Tue May 06 2008 - 06:09:10 PDT)
AMBER: AMBER Parallel test error
(Mon May 05 2008 - 11:37:39 PDT)
AMBER: Mn2+ parameters in AMBER
(Fri May 02 2008 - 11:46:25 PDT)
Joachim Reichelt
AMBER: Iron-Sulfur Cluster
(Fri May 30 2008 - 02:46:30 PDT)
AMBER: nab
(Fri May 30 2008 - 02:48:56 PDT)
Junmei Wang
Re: AMBER: Prepgen
(Thu May 15 2008 - 08:46:34 PDT)
Justin A. Lemkul
Re: AMBER: Installing PMEMD with Amber10
(Sat May 31 2008 - 05:24:30 PDT)
Re: AMBER: Installing PMEMD with Amber10
(Fri May 30 2008 - 03:42:53 PDT)
Re: AMBER: Installing PMEMD with Amber10
(Thu May 29 2008 - 13:41:30 PDT)
Re: AMBER: Installing PMEMD with Amber10
(Thu May 29 2008 - 12:12:26 PDT)
AMBER: Installing PMEMD with Amber10
(Thu May 29 2008 - 06:23:05 PDT)
Justine Condo
Re: AMBER: Iron-Sulfur Cluster
(Fri May 30 2008 - 10:52:24 PDT)
AMBER: Points on a Sphere
(Thu May 15 2008 - 09:27:06 PDT)
juyong Lee
AMBER: Installation error on IBM cluster
(Mon May 05 2008 - 01:40:59 PDT)
Re: AMBER: Amber10 Installation error - incorrect file suffix
(Sun May 04 2008 - 19:01:02 PDT)
AMBER: Amber10 Installation error - incorrect file suffix
(Sun May 04 2008 - 05:46:10 PDT)
AMBER: Compiling amber10 with xlf90 fortran compiler
(Fri May 02 2008 - 11:27:10 PDT)
AMBER: cfortran.h error with xlf90 compiler
(Fri May 02 2008 - 09:35:32 PDT)
Re: AMBER: Amber10 installation error
(Thu May 01 2008 - 21:52:10 PDT)
AMBER: Amber10 installation error
(Thu May 01 2008 - 19:28:07 PDT)
Karl Kirschner
Re: AMBER: AMBER file preparation for protein-carbohydrate complex
(Sun May 25 2008 - 02:25:35 PDT)
Kateryna Miroshnychenko
Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error
(Thu May 29 2008 - 00:22:17 PDT)
AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error
(Wed May 28 2008 - 08:08:19 PDT)
ke dong
AMBER: caculating nonpolar solvation energies
(Sat May 24 2008 - 07:53:17 PDT)
Re: AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params
(Sat May 24 2008 - 07:46:19 PDT)
Lachele Foley (Lists)
Re: AMBER: AMBER file preparation for protein-carbohydrate complex
(Thu May 22 2008 - 14:39:44 PDT)
Re: AMBER: atom type in glycam06
(Wed May 21 2008 - 06:37:51 PDT)
Lars Skjærven
AMBER: potassium ion
(Thu May 22 2008 - 06:09:59 PDT)
Re: AMBER: massively parallel computation
(Tue May 20 2008 - 07:28:24 PDT)
Lisa Perez
AMBER: neutral C-terminus and N-terminus parameters for amber
(Fri May 09 2008 - 10:32:13 PDT)
Lorenzo Gontrani
Re: AMBER: PGI amber9 problems
(Fri May 16 2008 - 05:02:53 PDT)
AMBER: PGI amber9 problems
(Fri May 16 2008 - 02:52:21 PDT)
luzhenw1.msu.edu
AMBER: how generate the final output file using mmpbsa
(Fri May 23 2008 - 13:49:33 PDT)
Lynn F. Ten Eyck
Re: AMBER: Problems installing Amber Tools for Amber 10
(Fri May 16 2008 - 08:12:49 PDT)
Re: AMBER: cannot read big .pdb files
(Sat May 10 2008 - 09:37:02 PDT)
M. L. Dodson
Re: AMBER: steered MD initial state
(Tue May 06 2008 - 10:39:04 PDT)
Re: AMBER: steered MD initial state
(Tue May 06 2008 - 10:27:03 PDT)
AMBER: steered MD initial state
(Tue May 06 2008 - 09:04:09 PDT)
Marcin Krol
AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params
(Tue May 13 2008 - 06:44:48 PDT)
Marina Grabar
Re: AMBER: anal
(Tue May 20 2008 - 02:20:04 PDT)
AMBER: anal
(Mon May 19 2008 - 06:30:13 PDT)
Mark Abraham
Re: AMBER: Which is best temperature controlling method
(Wed May 28 2008 - 00:02:14 PDT)
Re: AMBER: is in vacuo simulation neccessary?
(Sun May 25 2008 - 22:44:20 PDT)
AMBER: reading PDB trajectory
(Thu May 15 2008 - 20:49:55 PDT)
Markus Kaukonen
AMBER: Hydration free energies of charged ions using PME
(Tue May 27 2008 - 23:51:26 PDT)
Mathy Froeyen
Re: AMBER: Calculate number of ions
(Tue May 13 2008 - 00:50:29 PDT)
Miguel Ortiz-Lombardía
AMBER: ptraj analyze modes from nmode
(Sat May 31 2008 - 08:40:50 PDT)
Re: AMBER: how generate the final output file using mmpbsa
(Fri May 23 2008 - 23:40:40 PDT)
Mingfeng Yang
Re: AMBER: massively parallel computation
(Tue May 20 2008 - 09:58:56 PDT)
AMBER: massively parallel computation
(Tue May 20 2008 - 00:03:51 PDT)
mori.cerm.unifi.it
Re: AMBER: ligand unit charge is not zero
(Thu May 29 2008 - 02:17:55 PDT)
AMBER: MM_PBSA problem in binding_energy
(Wed May 14 2008 - 07:17:40 PDT)
AMBER: mm_pbsa problem: bad atom type: IP
(Thu May 08 2008 - 04:59:12 PDT)
n.gandhiau.gmail.com
Re: AMBER: AMBER file preparation for protein-carbohydrate complex
(Sun May 25 2008 - 00:17:55 PDT)
nag raj
RE: AMBER: Regarding binding free energy calculation using MM_PBSA method
(Thu May 22 2008 - 05:18:59 PDT)
AMBER: Regarding binding free energy calculation using MM_PBSA method
(Wed May 21 2008 - 00:01:14 PDT)
Navnit Kumar Mishra
Re: AMBER: MM-PBSA for carbohydrates
(Tue May 20 2008 - 04:25:20 PDT)
Re: AMBER: MM_PBSA output file
(Fri May 09 2008 - 09:21:17 PDT)
Neelanjana Sengupta
Re: AMBER: simulate dipole moment
(Wed May 14 2008 - 14:14:54 PDT)
Neha Gandhi
AMBER: AMBER file preparation for protein-carbohydrate complex
(Thu May 22 2008 - 07:31:50 PDT)
AMBER: MM-PBSA for carbohydrates
(Mon May 19 2008 - 19:07:24 PDT)
Neil Bruce
Re: AMBER: Discontinuous Constant pH Restarts
(Wed May 07 2008 - 13:21:28 PDT)
AMBER: Discontinuous Constant pH Restarts
(Thu May 01 2008 - 06:41:21 PDT)
Pavan G
AMBER: ptraj rmsd calculation
(Thu May 29 2008 - 11:08:36 PDT)
AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system
(Thu May 22 2008 - 08:37:56 PDT)
Peter Gannett
Re: AMBER: MMPBSA error
(Sat May 31 2008 - 07:15:40 PDT)
Peter Kiss
Re: AMBER: ff99 and ff03 forcefield parameters
(Fri May 23 2008 - 11:42:48 PDT)
Re: AMBER: ff99 and ff03 forcefield parameters
(Fri May 23 2008 - 07:27:15 PDT)
AMBER: ff99 and ff03 forcefield parameters
(Wed May 21 2008 - 14:01:47 PDT)
AMBER: parameters in ff03 and ff99
(Mon May 19 2008 - 04:21:21 PDT)
Piotr Cieplak
Re: AMBER: Weighting factors in RESP charge fitting
(Fri May 16 2008 - 11:46:51 PDT)
AMBER: printing dipoles in Amber10 (and earlier)
(Fri May 02 2008 - 13:29:49 PDT)
Pradipta Bandyopadhyay
Re: AMBER: calibration of constant pH simulations
(Wed Apr 30 2008 - 21:02:55 PDT)
priya priya
AMBER: calculating the energy from the restart file
(Sat May 24 2008 - 07:03:46 PDT)
Qi Yan
AMBER: MM_PBSA output file
(Fri May 09 2008 - 09:03:38 PDT)
RE: AMBER: How to transfer unformatted coordinates into formatted ones
(Wed May 07 2008 - 19:55:18 PDT)
AMBER: nmode: number of atoms limitation
(Wed May 07 2008 - 11:10:48 PDT)
AMBER: How to transfer unformatted coordinates into formatted ones
(Wed May 07 2008 - 12:44:10 PDT)
AMBER: nmode: number of atoms limitation
(Wed May 07 2008 - 11:25:58 PDT)
Qiuting Hong
AMBER: help MD running error
(Fri May 23 2008 - 01:40:12 PDT)
AMBER: build proline
(Fri May 16 2008 - 14:32:47 PDT)
AMBER: simulate dipole moment
(Wed May 14 2008 - 13:52:33 PDT)
Rabin
Re: AMBER: building quadruplex with nab
(Tue May 20 2008 - 15:30:17 PDT)
AMBER: building quadruplex with nab
(Tue May 13 2008 - 06:38:15 PDT)
Re: AMBER: nab
(Tue May 13 2008 - 06:17:51 PDT)
AMBER: nab
(Mon May 12 2008 - 17:40:54 PDT)
Re: AMBER: to unsubscribe email
(Mon May 12 2008 - 14:29:56 PDT)
AMBER: to unsubscribe email
(Mon May 12 2008 - 08:47:43 PDT)
AMBER: unable to compile AmberTools 1.0
(Mon May 05 2008 - 10:07:00 PDT)
Rahaman, Asif
RE: AMBER: velocity autocorrelation function for SPC felxible water model
(Thu May 08 2008 - 13:42:22 PDT)
AMBER: velocity autocorrelation function for SPC felxible water model
(Thu May 08 2008 - 10:07:41 PDT)
Rajendra P. OJHA
AMBER: Prepgen
(Wed May 14 2008 - 02:45:47 PDT)
AMBER: Prepgen does not give correct result?
(Fri May 09 2008 - 09:13:58 PDT)
Ray Luo
RE: AMBER: How to set a ZN atom radius for PB calculations
(Thu May 22 2008 - 13:41:36 PDT)
RE: AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params
(Thu May 22 2008 - 13:37:04 PDT)
rebeca
AMBER: analysis REMD
(Mon May 19 2008 - 11:41:15 PDT)
rebeca.mmb.pcb.ub.es
Re: AMBER: analysis REMD
(Wed May 21 2008 - 10:03:59 PDT)
Re: AMBER: analysis REMD
(Tue May 20 2008 - 11:31:30 PDT)
Re: AMBER: analysis REMD
(Tue May 20 2008 - 03:49:00 PDT)
Reena .....
Re: AMBER: Which is best temperature controlling method
(Tue May 27 2008 - 22:34:39 PDT)
Rima Chaudhuri
Re: AMBER: Cysteine sulphonic acid parameters
(Thu May 01 2008 - 08:43:48 PDT)
Robert Duke
Re: AMBER: Sander instead of PMEMD
(Fri May 30 2008 - 08:28:24 PDT)
Re: AMBER: Sander instead of PMEMD
(Fri May 30 2008 - 07:50:36 PDT)
Re: AMBER: Sander instead of PMEMD
(Fri May 30 2008 - 07:13:20 PDT)
Re: AMBER: Installing PMEMD with Amber10
(Thu May 29 2008 - 13:16:39 PDT)
Re: AMBER: Installing PMEMD with Amber10
(Thu May 29 2008 - 07:44:38 PDT)
Re: AMBER: Which is best temperature controlling method
(Thu May 29 2008 - 05:19:22 PDT)
Re: AMBER: massively parallel computation
(Wed May 21 2008 - 10:37:34 PDT)
Re: AMBER: massively parallel computation
(Tue May 20 2008 - 07:46:34 PDT)
Re: AMBER: massively parallel computation
(Tue May 20 2008 - 07:32:22 PDT)
Re: AMBER: massively parallel computation
(Tue May 20 2008 - 07:22:56 PDT)
Re: AMBER: STEERED MD
(Sat May 17 2008 - 06:21:10 PDT)
Re: AMBER: STEERED MD
(Fri May 16 2008 - 10:29:29 PDT)
Re: AMBER: STEERED MD
(Fri May 16 2008 - 10:15:40 PDT)
Re: AMBER: Compilation of PMEMD
(Thu May 08 2008 - 05:17:43 PDT)
Ross Walker
RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd'
(Sat May 31 2008 - 13:57:48 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Fri May 30 2008 - 15:41:51 PDT)
AMBER: SANDER and PMEMD with openmpi
(Fri May 30 2008 - 15:18:04 PDT)
RE: AMBER: igb and ibelly
(Fri May 30 2008 - 13:16:11 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Thu May 29 2008 - 21:50:30 PDT)
RE: AMBER: NTC and NTF
(Thu May 29 2008 - 12:30:28 PDT)
RE: AMBER: VMD Movie 3
(Thu May 29 2008 - 11:47:52 PDT)
RE: AMBER: solvatebox
(Thu May 29 2008 - 08:22:53 PDT)
RE: AMBER: error when read inpcrd
(Tue May 27 2008 - 13:50:23 PDT)
RE: AMBER: periodic boundary condition
(Fri May 23 2008 - 20:09:39 PDT)
RE: AMBER: how to extract energy
(Fri May 23 2008 - 20:07:41 PDT)
RE: AMBER: ff94 vs. ff03
(Fri May 23 2008 - 19:58:45 PDT)
RE: AMBER: Restart MD Simulation
(Fri May 23 2008 - 15:28:16 PDT)
RE: AMBER: help MD running error
(Fri May 23 2008 - 08:30:03 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Thu May 22 2008 - 15:40:54 PDT)
RE: AMBER: Force field in water and in vacuum ??
(Thu May 22 2008 - 09:06:36 PDT)
RE: AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system
(Thu May 22 2008 - 08:54:51 PDT)
RE: AMBER: amber10 installation
(Thu May 22 2008 - 08:40:20 PDT)
RE: AMBER: $AMBERHOME/dat/slko
(Thu May 22 2008 - 08:24:47 PDT)
RE: AMBER: about hydrogen bond in amber force field
(Wed May 21 2008 - 20:32:06 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Wed May 21 2008 - 11:05:20 PDT)
AMBER: 3rd Annual CMM Workshop on QM/MM Simulations
(Mon May 19 2008 - 16:33:55 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Mon May 19 2008 - 14:25:45 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Mon May 19 2008 - 10:19:37 PDT)
RE: AMBER: Hybrid REMD amber10
(Mon May 19 2008 - 08:51:13 PDT)
RE: Fw: RE: AMBER: MKL libraries/Amber10
(Mon May 19 2008 - 08:41:59 PDT)
RE: AMBER: MKL libraries/Amber10
(Fri May 16 2008 - 11:25:36 PDT)
RE: AMBER: PGI amber9 problems
(Fri May 16 2008 - 11:06:14 PDT)
AMBER: about addles:“forrtl: severe (71): integer divide by z
(Fri May 16 2008 - 11:00:34 PDT)
RE: AMBER: MKL libraries/Amber10
(Thu May 15 2008 - 19:59:16 PDT)
RE: AMBER: solvatebox error
(Thu May 15 2008 - 14:54:08 PDT)
AMBER: RE: AMBER: RE: AMBER: RE: AMBER: about addles:“forrtl: severe (71): integer divide by zero”.
(Thu May 15 2008 - 10:37:22 PDT)
RE: AMBER: simulate dipole moment
(Wed May 14 2008 - 14:25:33 PDT)
AMBER: RE: AMBER: about addles:“forrtl: severe (71): integer divide by zero”.
(Wed May 14 2008 - 09:30:51 PDT)
RE: AMBER: Amber10 testing problem
(Tue May 13 2008 - 14:20:53 PDT)
RE: AMBER: initial velocities of MD
(Tue May 13 2008 - 10:05:05 PDT)
RE: AMBER: Ligand energy minimization
(Tue May 13 2008 - 08:14:53 PDT)
RE: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Tue May 13 2008 - 08:08:08 PDT)
RE: AMBER: help to install AMBER9
(Fri May 09 2008 - 09:12:53 PDT)
RE: AMBER: drawing repeated units
(Fri May 09 2008 - 09:03:28 PDT)
RE: AMBER: can amber read .xyz files?
(Thu May 08 2008 - 10:23:16 PDT)
RE: AMBER: nmode "Atom out of bounds" for min of multiple ligands
(Thu May 08 2008 - 10:19:34 PDT)
RE: AMBER: Ewald error estimate
(Thu May 08 2008 - 08:27:15 PDT)
RE: AMBER: reset time and comments
(Thu May 08 2008 - 08:24:50 PDT)
RE: AMBER: nmode: number of atoms limitation
(Wed May 07 2008 - 14:39:44 PDT)
RE: AMBER: uninstall of AMBER
(Wed May 07 2008 - 10:05:20 PDT)
RE: AMBER: Minimization in Octahedric Box
(Tue May 06 2008 - 10:22:39 PDT)
RE: AMBER: AMBER Parallel test error
(Tue May 06 2008 - 08:25:46 PDT)
RE: AMBER: AMBER Parallel test error
(Mon May 05 2008 - 12:42:09 PDT)
RE: AMBER: Installation error on IBM cluster
(Mon May 05 2008 - 08:06:11 PDT)
RE: RE: AMBER: point charges
(Fri May 02 2008 - 16:03:08 PDT)
RE: AMBER: Installation problem of AMBER on cluster
(Fri May 02 2008 - 14:33:48 PDT)
RE: AMBER: point charges
(Fri May 02 2008 - 14:32:43 PDT)
RE: AMBER: Installation problem of AMBER on cluster
(Fri May 02 2008 - 14:18:48 PDT)
RE: AMBER: printing dipoles in Amber10 (and earlier)
(Fri May 02 2008 - 14:16:08 PDT)
RE: AMBER: Installation problem of AMBER on cluster
(Fri May 02 2008 - 12:07:10 PDT)
RE: AMBER: cfortran.h error with xlf90 compiler
(Fri May 02 2008 - 09:58:27 PDT)
RE: AMBER: test.parallel.QMMM problem
(Fri May 02 2008 - 08:50:31 PDT)
RE: AMBER: Installation problem of AMBER on cluster
(Fri May 02 2008 - 08:41:48 PDT)
RE: AMBER: Amber10 installation error
(Fri May 02 2008 - 08:33:43 PDT)
RE: AMBER: Amber10 installation error
(Thu May 01 2008 - 21:01:02 PDT)
Ruchi Sachdeva
Re: AMBER: Calculate number of ions
(Wed May 14 2008 - 00:24:08 PDT)
Sally Pias
Re: AMBER: B-factor calculation from data with different write frequencies
(Tue May 27 2008 - 20:42:13 PDT)
AMBER: B-factor calculation from data with different write frequencies
(Mon May 26 2008 - 21:19:42 PDT)
Sam Danziger
AMBER: How to set a ZN atom radius for PB calculations
(Tue May 20 2008 - 17:23:30 PDT)
Re: AMBER: Amber 10 ambpdb bug?
(Sun May 18 2008 - 20:41:43 PDT)
AMBER: Amber 10 ambpdb bug?
(Sat May 17 2008 - 19:17:44 PDT)
Re: AMBER: Problems installing Amber Tools for Amber 10
(Fri May 16 2008 - 11:29:32 PDT)
Re: AMBER: Problems installing Amber Tools for Amber 10
(Fri May 16 2008 - 10:41:31 PDT)
Re: AMBER: Problems installing Amber Tools for Amber 10
(Fri May 16 2008 - 10:06:05 PDT)
AMBER: Problems installing Amber Tools for Amber 10
(Mon May 12 2008 - 11:20:23 PDT)
Sara Alexandra Moura
Re: AMBER: bye
(Tue May 20 2008 - 07:14:51 PDT)
Sara J
AMBER: mbondi radii for gaff atom types
(Wed May 28 2008 - 08:03:52 PDT)
Sasha Buzko
Re: AMBER: xLeap compilation issues
(Wed May 21 2008 - 08:52:00 PDT)
AMBER: xLeap compilation issues
(Tue May 20 2008 - 16:41:49 PDT)
Scott Brozell
Re: AMBER: Problems installing Amber Tools for Amber 10
(Tue May 27 2008 - 10:17:19 PDT)
Re: AMBER: error in compilation elsize.cc
(Mon May 05 2008 - 11:55:49 PDT)
Seth Lilavivat
AMBER: ptraj analyze matrix
(Wed May 21 2008 - 07:53:28 PDT)
AMBER: RESP and Jaguar
(Thu May 15 2008 - 13:52:35 PDT)
AMBER: Free Energy Calculations - parameters for MM
(Tue May 13 2008 - 09:29:23 PDT)
Re: AMBER: nmode "Atom out of bounds" for min of multiple ligands
(Thu May 08 2008 - 13:01:45 PDT)
AMBER: nmode "Atom out of bounds" for min of multiple ligands
(Thu May 08 2008 - 07:30:24 PDT)
AMBER: mm_pbsa.pl not reading parameters for nmode
(Tue May 06 2008 - 10:50:18 PDT)
Re: AMBER: Help with NMODE
(Mon May 05 2008 - 12:39:06 PDT)
Re: AMBER: Help with NMODE
(Sun May 04 2008 - 15:15:53 PDT)
Re: AMBER: Help with NMODE
(Fri May 02 2008 - 11:05:19 PDT)
Re: AMBER: Help with NMODE
(Fri May 02 2008 - 09:50:35 PDT)
AMBER: Help with NMODE
(Fri May 02 2008 - 08:24:25 PDT)
Shultz, Jack
RE: AMBER: Harmonic Force Constant
(Thu May 08 2008 - 13:21:00 PDT)
AMBER: Harmonic Force Constant
(Wed May 07 2008 - 12:32:18 PDT)
AMBER: Amber Parameter Schema
(Tue May 06 2008 - 17:22:02 PDT)
AMBER: GAFF Schema
(Sun May 04 2008 - 15:11:37 PDT)
AMBER: Deriving Force Field Parameters
(Sun May 04 2008 - 14:32:03 PDT)
Smriti Sharma
Re: AMBER: Discontinuous Constant pH Restarts
(Thu May 08 2008 - 04:05:31 PDT)
Steve Seibold
AMBER: Water tracking
(Fri May 02 2008 - 08:09:35 PDT)
AMBER: Water residue tracking
(Thu May 01 2008 - 09:19:42 PDT)
sudipta sinha
Re: AMBER: Which is best temperature controlling method
(Wed May 28 2008 - 11:02:53 PDT)
Re: AMBER: Which is best temperature controlling method
(Tue May 27 2008 - 23:43:32 PDT)
AMBER: Which is best temperature controlling method
(Tue May 27 2008 - 03:25:02 PDT)
AMBER: Compilation of PMEMD
(Thu May 08 2008 - 04:07:28 PDT)
Re: AMBER: AMBER Parallel test error
(Wed May 07 2008 - 09:09:28 PDT)
AMBER: uninstall of AMBER
(Wed May 07 2008 - 08:50:37 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Mon May 05 2008 - 04:24:29 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Mon May 05 2008 - 02:47:38 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Sun May 04 2008 - 23:52:58 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Sun May 04 2008 - 05:31:22 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Fri May 02 2008 - 22:59:23 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Fri May 02 2008 - 13:29:38 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Fri May 02 2008 - 11:29:37 PDT)
Re: AMBER: Installation problem of AMBER on cluster
(Fri May 02 2008 - 00:39:09 PDT)
AMBER: Installation problem of AMBER on cluster
(Thu May 01 2008 - 11:16:44 PDT)
Swarup Gupta
Re: AMBER: ligand unit charge is not zero
(Thu May 29 2008 - 05:48:13 PDT)
Re: AMBER: how to overcome theunusual bonds formation
(Thu May 29 2008 - 05:27:36 PDT)
AMBER: ff94 vs. ff03
(Fri May 23 2008 - 17:26:46 PDT)
Re: AMBER: AMBER entropy calculation
(Wed May 14 2008 - 19:20:07 PDT)
sychen
AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
(Fri May 02 2008 - 07:22:50 PDT)
Syed Tarique Moin
AMBER: QM/MM
(Fri May 09 2008 - 01:28:06 PDT)
Taufik Al-Sarraj
Re: AMBER: drawing repeated units
(Fri May 09 2008 - 11:10:56 PDT)
AMBER: drawing repeated units
(Fri May 09 2008 - 08:10:19 PDT)
Re: AMBER: xleap (draw using edit)
(Thu May 08 2008 - 13:58:24 PDT)
AMBER: xleap (draw using edit)
(Wed May 07 2008 - 19:31:14 PDT)
Re: AMBER: single stranded DNA
(Tue May 06 2008 - 17:11:07 PDT)
AMBER: single stranded DNA
(Tue May 06 2008 - 15:37:41 PDT)
Thomas Cheatham
RE: AMBER: Ewald error estimate
(Wed May 07 2008 - 20:51:55 PDT)
Thomas Cheatham III
RE: AMBER: Ewald error estimate
(Thu May 08 2008 - 10:21:38 PDT)
Re: AMBER: Water tracking
(Fri May 02 2008 - 09:14:21 PDT)
Thomas Leonard
Re: AMBER: how to overcome theunusual bonds formation
(Thu May 29 2008 - 05:01:43 PDT)
AMBER: how to overcome theunusual bonds formation
(Thu May 29 2008 - 04:03:29 PDT)
AMBER: how to calculate delta G from IC50
(Mon May 19 2008 - 22:12:04 PDT)
AMBER: AMBER entropy calculation
(Wed May 14 2008 - 16:00:45 PDT)
AMBER: AMBER PBSA
(Wed May 14 2008 - 02:35:54 PDT)
Thomas Patko
Re: AMBER: MKL libraries/Amber10
(Fri May 16 2008 - 14:26:33 PDT)
Thomas Steinbrecher
Re: AMBER: NON-BONDED parameters
(Mon May 05 2008 - 11:14:59 PDT)
Tim Meyer
Re: AMBER: misplacement of TER by leap
(Mon May 05 2008 - 06:03:54 PDT)
tinni sona
AMBER: atom type in glycam06
(Mon May 19 2008 - 10:06:57 PDT)
Titus, Jamie \(bairdje\)
AMBER: Hydroxyprolines!!!
(Wed May 07 2008 - 11:54:03 PDT)
AMBER: GBSA SA calculation
(Wed May 07 2008 - 11:32:43 PDT)
Urszula Uciechowska
Re: AMBER: rms
(Mon May 12 2008 - 06:41:06 PDT)
AMBER: rms
(Mon May 12 2008 - 04:19:41 PDT)
AMBER: distance
(Fri May 09 2008 - 07:36:18 PDT)
Vijay Singh
AMBER: amber9 , ptraj vector commad issue
(Sat May 31 2008 - 16:34:23 PDT)
vijayaraj.clri.info
AMBER: amber10 installation
(Thu May 22 2008 - 07:22:47 PDT)
Re: AMBER: amber tools installation
(Thu May 22 2008 - 01:55:00 PDT)
AMBER: amber tools installation
(Wed May 21 2008 - 08:22:37 PDT)
Vlad Cojocaru
Re: AMBER: ff99 and ff03 forcefield parameters
(Fri May 23 2008 - 08:52:03 PDT)
Re: AMBER: ff99 and ff03 forcefield parameters
(Fri May 23 2008 - 02:43:38 PDT)
Re: AMBER: ff99 and ff03 forcefield parameters
(Fri May 23 2008 - 02:31:47 PDT)
AMBER: pressure regulation methods
(Wed May 21 2008 - 09:25:08 PDT)
Re: AMBER: rms
(Wed May 14 2008 - 07:01:17 PDT)
Re: AMBER: rms
(Mon May 12 2008 - 05:40:46 PDT)
Wang,Ying
AMBER: tleap error message
(Fri May 30 2008 - 09:08:14 PDT)
RE: AMBER: error when read inpcrd
(Tue May 27 2008 - 14:14:02 PDT)
AMBER: error when read inpcrd
(Tue May 27 2008 - 13:32:02 PDT)
RE: AMBER: how to extract energy
(Sun May 25 2008 - 06:57:20 PDT)
RE: AMBER: periodic boundary condition
(Sun May 25 2008 - 06:58:20 PDT)
AMBER: periodic bondary condition
(Fri May 23 2008 - 18:16:34 PDT)
AMBER: how to extract energy
(Fri May 23 2008 - 18:08:13 PDT)
AMBER: about hydrogen bond in amber force field
(Wed May 21 2008 - 19:24:47 PDT)
AMBER: nfft1-3 too large
(Mon May 19 2008 - 07:46:51 PDT)
RE: AMBER: solvatebox error
(Thu May 15 2008 - 15:16:17 PDT)
AMBER: solvatebox error
(Thu May 15 2008 - 14:47:06 PDT)
AMBER: periodic boundary condition
(Tue May 13 2008 - 06:55:00 PDT)
Re: AMBER: cannot read big .pdb files
(Tue May 13 2008 - 06:40:34 PDT)
Re: AMBER: cannot read big .pdb files
(Mon May 12 2008 - 12:42:27 PDT)
Re: AMBER: Ewald PARAMETER RANGE WRONG
(Mon May 12 2008 - 10:06:03 PDT)
Re: AMBER: cannot read big .pdb files
(Mon May 12 2008 - 07:37:24 PDT)
AMBER: Ewald PARAMETER RANGE WRONG
(Sun May 11 2008 - 11:01:09 PDT)
Re: AMBER: cannot read big .pdb files
(Sun May 11 2008 - 06:36:48 PDT)
Re: AMBER: cannot read big .pdb files
(Sun May 11 2008 - 06:38:41 PDT)
AMBER: cannot read big .pdb files
(Fri May 09 2008 - 19:00:29 PDT)
AMBER: can amber read .xyz files?
(Thu May 08 2008 - 08:29:57 PDT)
Re: AMBER: about glycam06
(Mon May 05 2008 - 07:30:19 PDT)
Re: AMBER: about glycam06
(Sat May 03 2008 - 19:40:14 PDT)
Re: AMBER: about glycam06
(Sat May 03 2008 - 19:35:05 PDT)
Re: AMBER: about glycam06
(Sat May 03 2008 - 16:57:35 PDT)
Re: AMBER: about glycam06
(Sat May 03 2008 - 16:55:11 PDT)
AMBER: about glycam06
(Sat May 03 2008 - 16:22:18 PDT)
wangluohuaxue
AMBER: subscribe amber
(Wed May 14 2008 - 07:40:04 PDT)
Wei Zhang
Re: AMBER: cannot read big .pdb files
(Mon May 12 2008 - 07:34:40 PDT)
Re: AMBER: AmberTools on OS X fails tests
(Thu May 08 2008 - 12:15:46 PDT)
wfli.biophy.nju.edu.cn
AMBER: energy pairwise decomposition in GB/SA simulation
(Wed May 28 2008 - 03:29:42 PDT)
Xioling Chuang
AMBER: bugfix (imin=5) in amber9
(Tue May 27 2008 - 21:23:09 PDT)
Yang, Lee-Wei
AMBER: About reading in heme and CO molecule together with myoglobin
(Mon May 05 2008 - 11:08:53 PDT)
Ye Mei
Re: AMBER: help to install AMBER9
(Fri May 09 2008 - 07:55:56 PDT)
yongleli
Re: Re: AMBER: Amber10:Compiling with gcc 2.4.1
(Thu May 15 2008 - 21:03:41 PDT)
Re: AMBER: MKL libraries/Amber10
(Thu May 15 2008 - 19:03:57 PDT)
Re: Re: AMBER: Prepgen
(Thu May 15 2008 - 09:18:31 PDT)
AMBER: Amber10:Compiling with gcc 2.4.1
(Thu May 15 2008 - 08:36:29 PDT)
Yu Chen
Re: AMBER: unable to compile AmberTools 1.0
(Mon May 05 2008 - 12:06:26 PDT)
yuan li
AMBER: simulating the pull out of Carbon Nanotube from polymer with AMBER
(Tue May 13 2008 - 19:53:10 PDT)
成全
AMBER: RE: AMBER: RE: AMBER: RE: AMBER: RE: AMBER: about addles:“forrtl: severe (71): integer divide by z
(Thu May 15 2008 - 23:56:34 PDT)
AMBER: RE: AMBER: RE: AMBER: about addles:“forrtl: severe (71): integer divide by zero”.
(Wed May 14 2008 - 17:18:05 PDT)
AMBER: about addles:“forrtl: severe (71): integer divide by zero”.
(Wed May 14 2008 - 07:57:25 PDT)
欧阳德方
RE: AMBER: Ewald error estimate
(Wed May 07 2008 - 22:04:05 PDT)
RE: AMBER: Ewald error estimate
(Wed May 07 2008 - 20:38:18 PDT)
AMBER: Ewald error estimate
(Wed May 07 2008 - 01:25:22 PDT)
Last message date
:
Sun Jun 01 2008 - 06:08:25 PDT
Archived on
: Wed Apr 24 2024 - 05:53:40 PDT
634 messages
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