Amber Archive Nov 2006 by author
492 messages
:
Starting
Sun Nov 05 2006 - 06:07:04 PST,
Ending
Sun Dec 03 2006 - 06:07:40 PST
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Re: AMBER: How to apply a force to some atom in a residues?
(Wed Nov 29 2006 - 22:45:04 PST)
AMBER: How to apply a force to some atom in a residues?
(Tue Nov 28 2006 - 19:36:15 PST)
AMBER: DNA helix end stable?
(Tue Nov 28 2006 - 19:35:11 PST)
Re: AMBER: nmode output with ptraj
(Tue Nov 28 2006 - 19:18:32 PST)
Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences?
(Mon Nov 27 2006 - 02:29:42 PST)
AMBER: Did Antechamber support tertiary amines? How can I get the prepin file for it?
(Mon Nov 27 2006 - 00:50:12 PST)
Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences?
(Fri Nov 24 2006 - 18:27:26 PST)
Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences?
(Fri Nov 24 2006 - 01:29:26 PST)
AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences?
(Thu Nov 23 2006 - 22:13:38 PST)
AMBER: saltconc for explicit solvent calculation.
(Thu Nov 09 2006 - 09:51:36 PST)
Adrian Roitberg
Re: AMBER: Unit of force
(Wed Nov 08 2006 - 04:57:00 PST)
Re: AMBER: PTRAJ RMS: dumping RMSd vs time data
(Sat Nov 04 2006 - 05:00:40 PST)
Re: AMBER: ab initio terminology query
(Wed Nov 01 2006 - 11:01:38 PST)
Re: AMBER: GBSA implicit chloroform
(Wed Nov 01 2006 - 09:22:14 PST)
Andreas Svrcek-Seiler
Re: AMBER: Langevin temperature control vs berendson heat bath
(Thu Nov 30 2006 - 04:06:22 PST)
Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5?
(Mon Nov 06 2006 - 09:13:37 PST)
Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5?
(Mon Nov 06 2006 - 01:17:11 PST)
Andres Palencia
Re: AMBER: Ptraj: radial distribution and correlation coefficient
(Tue Nov 14 2006 - 12:13:39 PST)
AMBER: Amber H-bond print?
(Thu Nov 09 2006 - 01:07:46 PST)
Andy Purkiss-Trew
Re: RE: AMBER: Radius of gyration
(Fri Nov 24 2006 - 11:38:28 PST)
RE: AMBER: Radius of gyration
(Fri Nov 24 2006 - 11:34:52 PST)
RE: AMBER: Radius of gyration
(Fri Nov 24 2006 - 04:58:53 PST)
Angelo
AMBER: Biomolecular Simulation 2007
(Thu Nov 09 2006 - 08:03:43 PST)
Re: AMBER: PCA results with explicit Vs Implicit solvation
(Mon Nov 06 2006 - 09:14:47 PST)
Re: AMBER: leap usage
(Thu Nov 02 2006 - 08:39:57 PST)
anna.schrey.gmx.de
AMBER: Confusion about PBC
(Wed Nov 29 2006 - 08:26:04 PST)
Austin B. Yongye
AMBER: Ptraj: correlation time
(Tue Nov 21 2006 - 13:05:52 PST)
AMBER: Ptraj: diffusion rate
(Tue Nov 21 2006 - 13:03:52 PST)
Re: AMBER: GLYCAM and ff98 atom-types]
(Thu Nov 16 2006 - 11:53:03 PST)
Re: AMBER: Ptraj: radial distribution and correlation coefficient
(Tue Nov 14 2006 - 11:02:27 PST)
Re: AMBER: Ptraj: radial distribution and correlation coefficient
(Tue Nov 14 2006 - 10:50:01 PST)
AMBER: Ptraj: radial distribution and correlation coefficient
(Tue Nov 14 2006 - 10:10:39 PST)
AYTUG TUNCEL
AMBER: error about the number of snapshots
(Tue Nov 07 2006 - 13:11:24 PST)
Bill Ross
RE: AMBER: Combining Residues in LEaP for Lipid Bilayers
(Mon Nov 20 2006 - 10:58:11 PST)
Re: AMBER: problems with saving self-built molecules parameters
(Mon Nov 20 2006 - 10:55:00 PST)
Re: AMBER: erroneous placement of TER card
(Thu Nov 16 2006 - 11:06:25 PST)
Re: AMBER: erroneous placement of TER card
(Thu Nov 16 2006 - 10:54:50 PST)
Re: AMBER: Restraints of the strand-endings?
(Tue Nov 14 2006 - 14:19:06 PST)
Re: AMBER: PTRAJ: radius of gyration
(Fri Nov 10 2006 - 11:04:06 PST)
Biswa Ranjan Meher
AMBER: klambda for TI method.
(Tue Nov 07 2006 - 04:59:15 PST)
Carles Jaime Cardiel
Re: RE: AMBER: Radius of gyration
(Fri Nov 24 2006 - 10:25:02 PST)
Carlos Simmerling
Re: AMBER: Langevin temperature control vs berendson heat bath
(Thu Nov 30 2006 - 04:23:24 PST)
Re: AMBER: How to apply a force to some atom in a residues?
(Thu Nov 30 2006 - 04:13:42 PST)
Re: AMBER: Langevin temperature control vs berendson heat bath
(Wed Nov 29 2006 - 11:02:20 PST)
Re: AMBER: DNA helix end stable?
(Wed Nov 29 2006 - 04:24:14 PST)
Re: AMBER: How to apply a force to some atom in a residues?
(Wed Nov 29 2006 - 04:26:19 PST)
Re: AMBER: ambpdb -pqr
(Tue Nov 28 2006 - 13:03:18 PST)
Re: AMBER: How to specify user defined force fields or its parameters in amber??
(Tue Nov 28 2006 - 06:07:18 PST)
Re: AMBER: How to specify user defined force fields or its parameters in amber??
(Tue Nov 28 2006 - 04:11:51 PST)
Re: AMBER: helices in GB simulations
(Mon Nov 27 2006 - 10:12:02 PST)
Re: AMBER: problem of the REMD with nmr constraints
(Fri Nov 24 2006 - 06:35:25 PST)
Re: AMBER: Snapshots (pdbs) from a trajectory.
(Thu Nov 23 2006 - 09:25:31 PST)
Re: Fwd: AMBER: sander error: rst file crash
(Sat Nov 11 2006 - 04:38:52 PST)
Re: AMBER: vlimit exceeded for step 0, vmax = infinity
(Fri Nov 10 2006 - 06:58:26 PST)
Re: AMBER: sander error: rst file crash
(Fri Nov 10 2006 - 05:26:16 PST)
Re: AMBER: saltconc for explicit solvent calculation.
(Thu Nov 09 2006 - 10:14:21 PST)
Re: AMBER: vlimit exceeded for step 0, vmax = infinity
(Wed Nov 08 2006 - 10:35:21 PST)
Re: AMBER: simulating a small chain protein in water box
(Wed Nov 08 2006 - 09:50:59 PST)
Re: AMBER: vlimit exceeded for step 0, vmax = infinity
(Wed Nov 08 2006 - 09:46:27 PST)
Re: AMBER: question about the topology file
(Wed Nov 08 2006 - 04:18:58 PST)
Re: AMBER: Potential Energy Calculation
(Mon Nov 06 2006 - 04:32:35 PST)
Re: AMBER: Zn metal library
(Mon Nov 06 2006 - 04:26:52 PST)
Re: AMBER: Simulation a small chain of amino acids - error in MD simulation
(Fri Nov 03 2006 - 10:05:22 PST)
Re: AMBER: ntt=1 in simulated annealing
(Fri Nov 03 2006 - 03:48:06 PST)
Re: AMBER: Can we use the distance restraint in Replica-exchange simulation with AMBER8
(Thu Nov 02 2006 - 12:28:33 PST)
Cenk Andac
Re: AMBER: NAD ??
(Mon Nov 13 2006 - 06:46:47 PST)
Re: AMBER: NAD ??
(Fri Nov 10 2006 - 15:27:35 PST)
Re: AMBER: NAD ??
(Fri Nov 10 2006 - 15:20:53 PST)
Re: AMBER: problem with NAD+ parameters
(Mon Nov 06 2006 - 14:05:52 PST)
Changge Ji
AMBER: Charge fitting in Amber
(Tue Nov 28 2006 - 08:50:20 PST)
AMBER: how can i treat with long "mask" in ptraj analysis.
(Sun Nov 26 2006 - 08:22:00 PST)
Chengwen Chen
AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes
(Thu Nov 30 2006 - 00:07:28 PST)
AMBER: How to run MD simulation of a silicon containing complex with AMBER9?
(Wed Nov 29 2006 - 23:06:54 PST)
AMBER: parameters for silicon atom
(Sun Nov 19 2006 - 23:45:07 PST)
AMBER: what to do with the counter ions when minimizing average structure of DNA?
(Tue Nov 14 2006 - 03:09:25 PST)
Chris Moth
AMBER: top2mol2.c scanf format string bug
(Mon Nov 06 2006 - 16:19:36 PST)
Christian Roth
RE: AMBER: error in tleap test
(Wed Nov 15 2006 - 10:18:07 PST)
AMBER: error in tleap test
(Tue Nov 14 2006 - 16:40:24 PST)
Christopher Gaughan
Re: AMBER: Problem with mask when using distance in ptraj
(Sun Nov 26 2006 - 06:28:29 PST)
AMBER: Problem with mask when using distance in ptraj
(Wed Nov 22 2006 - 11:36:23 PST)
cristian obiol
Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences?
(Fri Nov 24 2006 - 02:24:28 PST)
darden
Re: AMBER: too big EEL values in the minimisation output
(Thu Nov 02 2006 - 11:13:29 PST)
Re: AMBER: too big EEL values in the minimisation output
(Wed Nov 01 2006 - 10:08:27 PST)
Dave S Walker
Re: AMBER: NONB values adjusted?
(Tue Nov 28 2006 - 11:48:36 PST)
AMBER: NONB values adjusted?
(Mon Nov 27 2006 - 23:37:28 PST)
Dave, Sonya
AMBER: simulating a small chain protein in water box
(Wed Nov 08 2006 - 08:03:46 PST)
RE: AMBER: Simulation a small chain of amino acids - error in MD simulation
(Fri Nov 03 2006 - 11:20:55 PST)
AMBER: Simulation a small chain of amino acids - error in MD simulation
(Fri Nov 03 2006 - 09:54:06 PST)
David A. Case
Re: AMBER: amber9 parralel compiling
(Thu Nov 30 2006 - 15:54:08 PST)
Re: AMBER: How to recompile sander for single-processor use in AMBER 8?
(Thu Nov 30 2006 - 15:19:10 PST)
Re: AMBER: amber9 parralel compiling
(Thu Nov 30 2006 - 08:50:47 PST)
Re: AMBER: nmode output with ptraj
(Tue Nov 28 2006 - 18:36:33 PST)
Re: AMBER: Periodic simulations with net charge
(Tue Nov 28 2006 - 18:03:22 PST)
Re: AMBER: xleap
(Tue Nov 28 2006 - 08:02:13 PST)
Re: AMBER:
(Tue Nov 28 2006 - 07:53:48 PST)
Re: AMBER: minimization of Hydrogens with xLeaP
(Mon Nov 27 2006 - 18:19:48 PST)
Re: AMBER: Problem Installing Amber in SGI Irix 6.5
(Mon Nov 27 2006 - 17:56:14 PST)
Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences?
(Sat Nov 25 2006 - 00:51:06 PST)
Re: AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64
(Fri Nov 24 2006 - 16:43:20 PST)
Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences?
(Thu Nov 23 2006 - 23:02:21 PST)
Re: AMBER: Snapshots (pdbs) from a trajectory.
(Thu Nov 23 2006 - 19:58:34 PST)
Re: AMBER: SHAKE problem after minimization
(Wed Nov 22 2006 - 14:24:44 PST)
Re: AMBER: Ptraj syntax change Amber8->Amber9 ?
(Wed Nov 22 2006 - 13:22:37 PST)
Re: AMBER: Problem with mask when using distance in ptraj
(Wed Nov 22 2006 - 13:07:29 PST)
AMBER: Re: installation instructions
(Wed Nov 22 2006 - 08:48:17 PST)
Re: AMBER: Combining Residues in LEaP for Lipid Bilayers
(Tue Nov 21 2006 - 08:16:06 PST)
Re: AMBER: the energy and temperature both increasing during the simulation with NTT=0
(Mon Nov 20 2006 - 22:09:28 PST)
Re: AMBER: Combining Residues in LEaP for Lipid Bilayers
(Mon Nov 20 2006 - 09:35:04 PST)
Re: AMBER: problems with saving self-built molecules parameters
(Mon Nov 20 2006 - 09:33:25 PST)
Re: AMBER: erroneous placement of TER card
(Thu Nov 16 2006 - 10:59:28 PST)
Re: AMBER: Xleap woes
(Thu Nov 16 2006 - 10:39:39 PST)
Re: AMBER: pqr file
(Thu Nov 16 2006 - 08:53:46 PST)
Re: AMBER: erroneous placement of TER card
(Thu Nov 16 2006 - 08:20:32 PST)
Re: AMBER: Error in compliling LEAP on Fedora 5
(Wed Nov 15 2006 - 17:24:34 PST)
Re: AMBER: ntt=1 in simulated annealing
(Wed Nov 15 2006 - 08:46:58 PST)
Re: AMBER: how to remove the rotation of system in periodic condition?
(Wed Nov 15 2006 - 08:34:01 PST)
Re: Fwd: AMBER: sander error: rst file crash
(Sun Nov 12 2006 - 18:44:48 PST)
Re: AMBER: sander error: rst file crash
(Fri Nov 10 2006 - 13:11:15 PST)
Re: AMBER: vlimit exceeded for step 0, vmax = infinity
(Fri Nov 10 2006 - 08:34:45 PST)
Re: AMBER: saltconc for explicit solvent calculation.
(Thu Nov 09 2006 - 10:13:05 PST)
Re: AMBER:
(Thu Nov 09 2006 - 10:11:55 PST)
Re: AMBER: problem in calculating EGB using sander for ligand containing F atom
(Thu Nov 09 2006 - 08:14:06 PST)
Re: AMBER: vlimit exceeded for step 0, vmax = infinity
(Wed Nov 08 2006 - 13:35:10 PST)
Re: AMBER: vlimit exceeded for step 0, vmax = infinity
(Wed Nov 08 2006 - 08:48:01 PST)
Re: AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion
(Wed Nov 08 2006 - 08:35:24 PST)
Re: AMBER: NAD ??
(Wed Nov 08 2006 - 06:49:31 PST)
Re: AMBER: leap - compilation error
(Tue Nov 07 2006 - 18:25:37 PST)
Re: AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST)
(Tue Nov 07 2006 - 17:51:48 PST)
Re: AMBER: top2mol2.c scanf format string bug
(Tue Nov 07 2006 - 08:18:43 PST)
Re: AMBER: klambda for TI method.
(Tue Nov 07 2006 - 08:06:21 PST)
Re: AMBER: PTRAJ RMS: dumping RMSd vs time data
(Mon Nov 06 2006 - 23:26:13 PST)
Re: AMBER: How the ensemble average calculated in Gibbs, AMBER7?
(Sun Nov 05 2006 - 19:26:02 PST)
Re: AMBER: ab initio terminology query
(Wed Nov 01 2006 - 12:42:23 PST)
Re: AMBER: ab initio terminology query
(Wed Nov 01 2006 - 09:30:50 PST)
Re: AMBER: GBSA implicit chloroform
(Wed Nov 01 2006 - 08:56:07 PST)
Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft
(Wed Nov 01 2006 - 08:54:06 PST)
Ed Pate
AMBER: pmemd installation problem
(Fri Nov 03 2006 - 10:51:36 PST)
Einar Uggerud
AMBER: protonated phosphate
(Mon Nov 27 2006 - 23:11:46 PST)
Elijah Gregory
Re: RE: AMBER: Radius of gyration
(Fri Nov 24 2006 - 12:33:50 PST)
emilia wu
AMBER: optimatized structure is so much different from the original pdb structure
(Thu Nov 16 2006 - 21:38:18 PST)
Esther Brugger
AMBER: H-bond analysis (Ptraj)
(Thu Nov 30 2006 - 17:28:10 PST)
Re: AMBER: watershell and image commands
(Thu Nov 30 2006 - 16:04:04 PST)
AMBER: watershell command
(Thu Nov 30 2006 - 15:16:52 PST)
AMBER: watershell and image commands
(Thu Nov 30 2006 - 14:37:58 PST)
AMBER: ptraj----radial output files
(Wed Nov 29 2006 - 12:03:20 PST)
RE: AMBER: NEWPDB.PDB from antechamber
(Wed Nov 01 2006 - 11:10:20 PST)
AMBER: NEWPDB.PDB from antechamber
(Wed Nov 01 2006 - 08:59:29 PST)
Fenghui Fan
Re: AMBER: RE: Amber: ZN-complex file
(Tue Nov 28 2006 - 15:47:19 PST)
Re: AMBER: prepin file nan
(Tue Nov 28 2006 - 06:48:33 PST)
AMBER: prepin file nan
(Mon Nov 27 2006 - 19:28:16 PST)
AMBER: bond information
(Sun Nov 26 2006 - 20:10:42 PST)
Re: AMBER: respin file
(Sun Nov 26 2006 - 16:42:09 PST)
AMBER: ZN prepin
(Sun Nov 26 2006 - 14:29:31 PST)
Re: AMBER: respin file
(Sun Nov 26 2006 - 09:12:01 PST)
AMBER: how to get complete prepin file
(Sat Nov 25 2006 - 21:02:20 PST)
Re: AMBER: respin file
(Sat Nov 25 2006 - 19:15:53 PST)
Re: AMBER: respin file
(Sat Nov 25 2006 - 17:49:58 PST)
AMBER: respin file
(Sat Nov 25 2006 - 14:23:46 PST)
AMBER: resp
(Sat Nov 25 2006 - 13:03:00 PST)
AMBER: respin file
(Fri Nov 24 2006 - 23:06:49 PST)
AMBER: bondtype problem
(Fri Nov 24 2006 - 16:22:23 PST)
AMBER: Antechamber and gaussian questions
(Fri Nov 24 2006 - 14:04:40 PST)
Re: AMBER: ammonia parameters
(Thu Nov 23 2006 - 07:40:05 PST)
Re: AMBER: problems with saving self-built molecules parameters
(Mon Nov 20 2006 - 10:10:21 PST)
Re: AMBER: problems with saving self-built molecules parameters
(Mon Nov 20 2006 - 07:06:53 PST)
Re: AMBER: problems with saving self-built molecules parameters
(Mon Nov 20 2006 - 05:57:10 PST)
Re: AMBER: Xleap woes
(Thu Nov 16 2006 - 11:22:59 PST)
Re: AMBER: GLYCAM and ff98 atom-types
(Thu Nov 16 2006 - 11:16:34 PST)
Re: AMBER: gfortran/gcc versus ifort/icc
(Tue Nov 14 2006 - 09:40:13 PST)
AMBER: The plc.frcmod file in the old version tutorial
(Sun Nov 12 2006 - 18:50:29 PST)
AMBER: ZN-CYS prepin and frcmd file
(Sun Nov 12 2006 - 18:16:37 PST)
AMBER: bond command between Zn and a CYM residue in one chain of a protein complex
(Fri Nov 10 2006 - 21:25:01 PST)
Re: AMBER: antechamber:tutorial
(Thu Nov 09 2006 - 11:10:17 PST)
Re: AMBER: Building Library
(Thu Nov 09 2006 - 10:21:57 PST)
Re: AMBER: building a box
(Tue Nov 07 2006 - 09:49:54 PST)
AMBER: Zn metal library
(Sun Nov 05 2006 - 19:51:19 PST)
Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5?
(Sun Nov 05 2006 - 16:22:26 PST)
Re: AMBER: Combine amber-force field and gaff94 for one molecule?
(Sun Nov 05 2006 - 12:13:57 PST)
Re: AMBER: Combine amber-force field and gaff94 for one molecule?
(Sun Nov 05 2006 - 10:30:27 PST)
AMBER: trajout script
(Sun Nov 05 2006 - 08:23:57 PST)
RE: AMBER: Amber: disufide bond
(Sun Nov 05 2006 - 06:02:48 PST)
Re: AMBER: PTRAJ RMS: dumping RMSd vs time data
(Sat Nov 04 2006 - 22:31:25 PST)
AMBER: Amber: disufide bond
(Sat Nov 04 2006 - 20:29:57 PST)
FyD
Re: AMBER: RE: Amber: ZN-complex file
(Tue Nov 28 2006 - 23:21:19 PST)
Re: AMBER: Charge fitting in Amber
(Tue Nov 28 2006 - 23:16:38 PST)
Re: AMBER: Ethanol
(Wed Nov 22 2006 - 04:22:28 PST)
Re: AMBER: Ethanol
(Fri Nov 17 2006 - 06:19:15 PST)
Gabbar S. Daaku
Re: AMBER: optimatized structure is so much different from the original pdb structure
(Fri Nov 17 2006 - 09:13:04 PST)
AMBER: GLYCAM and ff98 atom-types
(Thu Nov 16 2006 - 10:11:05 PST)
Gobind Singh Bisht
AMBER: How to specify a box with few walls rigid and others with periodic boundary conditions and then apply a pressure gradient across it?
(Wed Nov 29 2006 - 23:34:28 PST)
Re: AMBER: How to specify user defined force fields or its parameters in amber??
(Tue Nov 28 2006 - 08:40:53 PST)
Re: AMBER: How to specify user defined force fields or its parameters in amber??
(Tue Nov 28 2006 - 06:34:36 PST)
Re: AMBER: How to specify user defined force fields or its parameters in amber??
(Tue Nov 28 2006 - 05:56:10 PST)
AMBER: How to specify user defined force fields or its parameters in amber??
(Tue Nov 28 2006 - 03:51:30 PST)
Gregory Sandala
AMBER: erroneous placement of TER card
(Thu Nov 16 2006 - 01:12:43 PST)
Gustavo Seabra
Re: AMBER: How to specify user defined force fields or its parameters in amber??
(Thu Nov 30 2006 - 07:46:42 PST)
Re: AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes
(Thu Nov 30 2006 - 07:20:00 PST)
Re: AMBER: How to specify user defined force fields or its parameters in amber??
(Tue Nov 28 2006 - 07:18:49 PST)
Re: AMBER: <kein Betreff>
(Mon Nov 13 2006 - 09:52:55 PST)
Re: AMBER: ab initio terminology query
(Wed Nov 01 2006 - 08:50:27 PST)
Hannes Loeffler
AMBER: ptraj grid
(Sun Nov 26 2006 - 20:05:05 PST)
harianto
Re: AMBER: ambpdb -pqr
(Tue Nov 28 2006 - 13:03:26 PST)
hayden
RE: AMBER: Amber: disufide bond
(Sun Nov 05 2006 - 05:03:23 PST)
Hayden Eastwood
RE: AMBER: Langevin temperature control vs berendson heat bath
(Thu Nov 30 2006 - 03:23:37 PST)
AMBER: Langevin temperature control vs berendson heat bath
(Wed Nov 29 2006 - 10:12:16 PST)
RE: AMBER: SHAKE problem after minimization
(Wed Nov 22 2006 - 12:47:09 PST)
RE: AMBER: SHAKE problem after minimization
(Wed Nov 22 2006 - 12:33:17 PST)
RE: AMBER: SHAKE problem after minimization
(Wed Nov 22 2006 - 11:13:24 PST)
RE: AMBER: Potential Energy Calculation
(Mon Nov 06 2006 - 04:47:00 PST)
RE: AMBER: ab initio terminology query
(Wed Nov 01 2006 - 12:12:49 PST)
hbluo
AMBER: Performing Interactive Essential Dynamics in Ptraj
(Thu Nov 30 2006 - 16:58:11 PST)
AMBER: how to choose the parameter for the production/sampling run after the equilibration run
(Fri Nov 03 2006 - 17:57:01 PST)
HL Eastwood
AMBER: ab initio terminology query
(Wed Nov 01 2006 - 03:38:24 PST)
Holly Freedman
Re: AMBER: mm_pbsa does not terminate
(Wed Nov 01 2006 - 11:34:17 PST)
Re: AMBER: mm_pbsa does not terminate
(Wed Nov 01 2006 - 09:56:28 PST)
Igor Schapiro
Re: AMBER: dihedral angle equation
(Fri Nov 17 2006 - 06:24:29 PST)
Re: AMBER: dihedral angle equation
(Fri Nov 17 2006 - 06:15:47 PST)
Ilyas Yildirim
Re: AMBER: ambpdb -pqr
(Tue Nov 28 2006 - 13:02:39 PST)
Re: AMBER: helices in GB simulations
(Mon Nov 27 2006 - 14:09:04 PST)
Re: AMBER: respin file
(Sun Nov 26 2006 - 09:45:20 PST)
Re: AMBER: respin file
(Sun Nov 26 2006 - 00:03:33 PST)
Re: AMBER: respin file
(Sat Nov 25 2006 - 18:45:37 PST)
Re: AMBER: respin file
(Sat Nov 25 2006 - 17:07:04 PST)
Re: AMBER: H-Bond Terms in amber force field
(Wed Nov 15 2006 - 16:05:13 PST)
AMBER: H-Bond Terms in amber force field
(Wed Nov 15 2006 - 11:28:06 PST)
RE: AMBER: ab initio terminology query
(Wed Nov 01 2006 - 12:38:58 PST)
In Hee Park
AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64
(Fri Nov 24 2006 - 14:50:54 PST)
Ivelin Georgiev
AMBER: Solvation Energies
(Wed Nov 29 2006 - 06:31:13 PST)
J. Zhang
Re: Re: AMBER: question about the topology file
(Sun Nov 12 2006 - 17:42:20 PST)
AMBER: question about the topology file
(Wed Nov 08 2006 - 01:24:10 PST)
Jardas sucuriba
AMBER: matrix correl
(Tue Nov 21 2006 - 05:05:41 PST)
Jennie Thomas
AMBER: Periodic simulations with net charge
(Tue Nov 28 2006 - 16:47:32 PST)
Jianhui
AMBER: ptraj and mdvel question
(Wed Nov 15 2006 - 11:07:06 PST)
Jiri Sponer
Re: AMBER: Quantifying pi-pi interactions
(Tue Nov 21 2006 - 08:14:32 PST)
Re: AMBER: H-Bond Terms in amber force field
(Wed Nov 15 2006 - 16:30:48 PST)
Re: AMBER: H-Bond Terms in amber force field
(Wed Nov 15 2006 - 15:20:18 PST)
Re: AMBER: Combine amber-force field and gaff94 for one molecule?
(Sun Nov 05 2006 - 14:01:27 PST)
Re: AMBER: ab initio terminology query
(Wed Nov 01 2006 - 11:43:13 PST)
Re: AMBER: ab initio terminology query
(Wed Nov 01 2006 - 10:34:57 PST)
Re: AMBER: ab initio terminology query
(Wed Nov 01 2006 - 10:27:44 PST)
Re: AMBER: ab initio terminology query
(Wed Nov 01 2006 - 03:59:04 PST)
jitrayut jitonnom
AMBER: Some warning !!! during SANDER ?
(Wed Nov 22 2006 - 00:20:36 PST)
Re: AMBER: sander error: rst file crash
(Sat Nov 11 2006 - 09:22:20 PST)
Fwd: AMBER: sander error: rst file crash
(Sat Nov 11 2006 - 03:16:37 PST)
Fwd: AMBER: sander error: rst file crash
(Fri Nov 10 2006 - 07:52:00 PST)
AMBER: sander error: rst file crash
(Fri Nov 10 2006 - 04:52:19 PST)
Joe Nolan
Re: AMBER: Problem Installing Amber in SGI Irix 6.5
(Wed Nov 29 2006 - 04:40:58 PST)
jojartb.pharm.u-szeged.hu
Re: AMBER: reading psf file
(Sat Nov 18 2006 - 01:40:37 PST)
Re: AMBER: reading psf file
(Sat Nov 18 2006 - 00:38:26 PST)
AMBER: reading psf file
(Fri Nov 17 2006 - 15:24:24 PST)
Jordi Camps
RE: AMBER: gfortran/gcc versus ifort/icc
(Thu Nov 16 2006 - 08:22:55 PST)
RE: AMBER: gfortran/gcc versus ifort/icc
(Wed Nov 15 2006 - 09:50:54 PST)
Jordi Rodrigo De Losada
AMBER: Snapshots (pdbs) from a trajectory.
(Thu Nov 23 2006 - 09:11:18 PST)
Joshua
AMBER: strange temperature behavior when changing to constant pressure
(Thu Nov 09 2006 - 11:52:33 PST)
Junmei Wang
RE: AMBER: RE: Amber: ZN-complex file
(Tue Nov 28 2006 - 15:54:56 PST)
AMBER: RE: Amber: ZN-complex file
(Tue Nov 28 2006 - 15:21:40 PST)
RE: AMBER: bond information
(Tue Nov 28 2006 - 14:16:03 PST)
RE: AMBER: Problem about dummy atoms when running antechamber
(Tue Nov 28 2006 - 13:54:42 PST)
RE: AMBER: prepin file nan
(Tue Nov 28 2006 - 13:47:03 PST)
RE: AMBER: NEWPDB.PDB from antechamber
(Wed Nov 01 2006 - 11:42:42 PST)
RE: AMBER: NEWPDB.PDB from antechamber
(Wed Nov 01 2006 - 09:19:27 PST)
Kakali Sen
Re: AMBER: Unit of force
(Wed Nov 08 2006 - 05:12:41 PST)
AMBER: Unit of force
(Wed Nov 08 2006 - 03:06:16 PST)
AMBER: Re: Unit of force
(Tue Nov 07 2006 - 22:41:30 PST)
Keerthi Gottipati
AMBER: Amber9 installation error
(Fri Nov 17 2006 - 16:12:53 PST)
AMBER: PCA results with explicit Vs Implicit solvation
(Mon Nov 06 2006 - 08:32:16 PST)
kepa koldo burusco
RE: AMBER: Radius of gyration
(Fri Nov 24 2006 - 09:45:55 PST)
RE: AMBER: Combining Residues in LEaP for Lipid Bilayers
(Fri Nov 24 2006 - 03:38:06 PST)
RE: AMBER: Radius of gyration
(Fri Nov 24 2006 - 02:27:01 PST)
Re: AMBER: ntt=1 in simulated annealing
(Wed Nov 15 2006 - 03:53:27 PST)
AMBER: PTRAJ: radius of gyration
(Fri Nov 10 2006 - 09:05:09 PST)
Re: AMBER: building a box
(Wed Nov 08 2006 - 04:08:32 PST)
AMBER: building a box
(Tue Nov 07 2006 - 08:52:28 PST)
Lachele Foley (Lists)
AMBER: phantom sander8 in dmesg
(Mon Nov 27 2006 - 13:25:57 PST)
Re: AMBER: gfortran/gcc versus ifort/icc
(Thu Nov 16 2006 - 12:49:23 PST)
Re: AMBER: gfortran/gcc versus ifort/icc
(Wed Nov 15 2006 - 07:37:27 PST)
AMBER: gfortran/gcc versus ifort/icc
(Tue Nov 14 2006 - 06:35:21 PST)
Lee Kyung-koo
[RE]AMBER: RE: I got the error meassage in testcase of QMMM
(Tue Nov 07 2006 - 08:59:16 PST)
[RE]AMBER: RE: I got the error meassage in testcase of QMMM
(Tue Nov 07 2006 - 08:46:25 PST)
AMBER: I got the error meassage in testcase of QMMM
(Fri Nov 03 2006 - 21:33:44 PST)
[RE]RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version
(Thu Nov 02 2006 - 00:53:53 PST)
[RE]RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version
(Wed Nov 01 2006 - 15:25:25 PST)
AMBER: Problem of QM/MM calculation with amber 9 parallel version
(Wed Nov 01 2006 - 11:50:28 PST)
linfu
Re: AMBER: prepin file nan
(Tue Nov 28 2006 - 01:00:30 PST)
Luis Gracia
Re: AMBER: gfortran/gcc versus ifort/icc
(Wed Nov 15 2006 - 10:34:36 PST)
Lwin, ThuZar
RE: AMBER: antechamber:tutorial. .
(Thu Nov 09 2006 - 12:02:28 PST)
AMBER: FW: antechamber:tutorial
(Thu Nov 09 2006 - 11:03:46 PST)
AMBER: antechamber:tutorial
(Thu Nov 09 2006 - 10:48:58 PST)
M. L. Dodson
Re: AMBER: respin file
(Sun Nov 26 2006 - 10:05:33 PST)
Re: AMBER: respin file
(Sat Nov 25 2006 - 06:37:05 PST)
AMBER: gfortran and amber9 success on FreeBSD
(Sat Nov 18 2006 - 14:02:16 PST)
Re: AMBER: Xleap woes
(Thu Nov 16 2006 - 12:14:07 PST)
Re: AMBER: Combine amber-force field and gaff94 for one molecule?
(Sun Nov 05 2006 - 12:47:22 PST)
Re: AMBER: Combine amber-force field and gaff94 for one molecule?
(Sun Nov 05 2006 - 11:35:34 PST)
mahdi fathi
RE: AMBER: ff03 GLY HAs atom type
(Tue Nov 21 2006 - 21:46:22 PST)
Margaret S. Cheung
Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5?
(Mon Nov 06 2006 - 07:23:29 PST)
AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5?
(Sun Nov 05 2006 - 15:16:34 PST)
Marie-Pierre Durrieu
AMBER: helices in GB simulations
(Mon Nov 27 2006 - 09:43:41 PST)
Mark Williamson
Re: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1
(Tue Nov 28 2006 - 13:04:06 PST)
Re: AMBER: Unable to find mopac charges in divcon.out
(Fri Nov 24 2006 - 05:54:34 PST)
Re: AMBER: Unable to find mopac charges in divcon.out
(Thu Nov 23 2006 - 14:06:35 PST)
Re: AMBER: antechamber:tutorial
(Thu Nov 09 2006 - 11:06:24 PST)
Re: AMBER: leap usage
(Thu Nov 02 2006 - 07:26:42 PST)
Markus Kaukonen
AMBER: Ptraj syntax change Amber8->Amber9 ?
(Wed Nov 22 2006 - 02:35:26 PST)
Markus Weingarth
AMBER: Problems with equilibrating the starting density
(Fri Nov 03 2006 - 09:32:20 PST)
Martin Peters
Re: AMBER: compile amber8 on IBM-sp4
(Thu Nov 23 2006 - 09:22:06 PST)
Matthew Tessier
RE: AMBER: Combining Residues in LEaP for Lipid Bilayers
(Mon Nov 20 2006 - 09:48:32 PST)
AMBER: Combining Residues in LEaP for Lipid Bilayers
(Mon Nov 20 2006 - 09:09:13 PST)
Michael John Hanby
RE: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1
(Tue Nov 28 2006 - 13:43:06 PST)
RE: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1
(Tue Nov 28 2006 - 12:59:48 PST)
AMBER: Amber9 patch bugfix.all issue on SunOS 5.1
(Tue Nov 28 2006 - 10:06:16 PST)
Michel Becker
AMBER: Restraints of the strand-endings?
(Tue Nov 14 2006 - 12:22:36 PST)
AMBER: <kein Betreff>
(Mon Nov 13 2006 - 03:21:58 PST)
AMBER: Combine amber-force field and gaff94 for one molecule?
(Sun Nov 05 2006 - 09:45:05 PST)
Miguel Ferreira
AMBER: PCA and projections
(Wed Nov 01 2006 - 06:11:57 PST)
Mingfeng Yang
Re: AMBER: Potential Energy Calculation
(Mon Nov 06 2006 - 13:06:18 PST)
nadiav.soton.ac.uk
AMBER: nmode output with ptraj
(Tue Nov 28 2006 - 07:59:02 PST)
Re: AMBER: GBSA implicit chloroform
(Wed Nov 01 2006 - 09:13:22 PST)
AMBER: GBSA implicit chloroform
(Wed Nov 01 2006 - 08:41:18 PST)
Nicolas Lux Fawzi
Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines
(Fri Nov 24 2006 - 11:16:01 PST)
Nikola Trbovic
Re: AMBER: amber9 parralel compiling
(Thu Nov 30 2006 - 09:06:12 PST)
AMBER: amber9 parralel compiling
(Thu Nov 30 2006 - 08:31:22 PST)
Nitin Bhardwaj
AMBER: Atom Exclusion
(Tue Nov 07 2006 - 21:44:30 PST)
AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST)
(Tue Nov 07 2006 - 13:08:42 PST)
Re: AMBER: Mutual exclusion of atoms
(Mon Nov 06 2006 - 14:27:49 PST)
AMBER: Mutual exclusion of atoms
(Mon Nov 06 2006 - 13:40:50 PST)
AMBER: Mutual exclusion of atoms
(Sun Nov 05 2006 - 21:59:38 PST)
nur avneet
AMBER: How to start a Simulation of a peptide in bilayer
(Wed Nov 01 2006 - 01:28:31 PST)
Pankaj Daga
AMBER: Error in compliling LEAP on Fedora 5
(Wed Nov 15 2006 - 14:56:58 PST)
Peter Anderson
AMBER: How to recompile sander for single-processor use in AMBER 8?
(Thu Nov 30 2006 - 13:41:27 PST)
Peter Gannett
Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5?
(Sun Nov 05 2006 - 15:40:18 PST)
Peter Trodler
AMBER: ammonia parameters
(Thu Nov 23 2006 - 00:51:39 PST)
Philip Cheung
AMBER: Re: Fluorine and Bromine Parameters in Amber 9
(Fri Nov 03 2006 - 11:56:52 PST)
r. a.
Re: RE: AMBER: Radius of gyration
(Mon Nov 27 2006 - 20:20:32 PST)
AMBER: Radius of gyration
(Wed Nov 22 2006 - 02:11:14 PST)
Re: AMBER: PTRAJ RMS: dumping RMSd vs time data
(Mon Nov 06 2006 - 23:41:35 PST)
Re: AMBER: PTRAJ RMS: dumping RMSd vs time data
(Mon Nov 06 2006 - 22:44:35 PST)
AMBER: PTRAJ RMS: dumping RMSd vs time data
(Sat Nov 04 2006 - 00:58:25 PST)
AMBER: PTRAJ RMS: dumping RMSd vs time data
(Sat Nov 04 2006 - 00:45:25 PST)
Rachel
Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines
(Fri Nov 24 2006 - 11:53:29 PST)
AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines
(Fri Nov 24 2006 - 09:58:53 PST)
Re: AMBER: Unable to find mopac charges in divcon.out
(Thu Nov 23 2006 - 15:22:06 PST)
AMBER: Unable to find mopac charges in divcon.out
(Thu Nov 23 2006 - 11:31:55 PST)
Re: AMBER: SHAKE problem after minimization
(Thu Nov 23 2006 - 10:37:24 PST)
Re: AMBER: compile amber8 on IBM-sp4
(Thu Nov 23 2006 - 09:45:04 PST)
Re: AMBER: compile amber8 on IBM-sp4
(Thu Nov 23 2006 - 08:37:18 PST)
Re: AMBER: compile amber8 on IBM-sp4
(Thu Nov 23 2006 - 05:14:09 PST)
Re: AMBER: compile amber8 on IBM-sp4
(Thu Nov 23 2006 - 01:56:53 PST)
Re: AMBER: SHAKE problem after minimization
(Wed Nov 22 2006 - 11:37:15 PST)
Re: AMBER: SHAKE problem after minimization
(Wed Nov 22 2006 - 10:43:50 PST)
Re: AMBER: compile amber8 on IBM-sp4
(Wed Nov 22 2006 - 10:34:19 PST)
Re: AMBER: SHAKE problem after minimization
(Wed Nov 22 2006 - 07:42:34 PST)
AMBER: SHAKE problem after minimization
(Wed Nov 22 2006 - 03:39:18 PST)
Re: AMBER: compile amber8 on IBM-sp4
(Wed Nov 22 2006 - 02:08:42 PST)
AMBER: compile amber8 on IBM-sp4
(Tue Nov 21 2006 - 09:56:13 PST)
Re: AMBER: problems with saving self-built molecules parameters
(Mon Nov 20 2006 - 10:42:10 PST)
Re: AMBER: problems with saving self-built molecules parameters
(Mon Nov 20 2006 - 09:18:00 PST)
Re: AMBER: problems with saving self-built molecules parameters
(Mon Nov 20 2006 - 06:23:30 PST)
AMBER: problems with saving self-built molecules parameters
(Mon Nov 20 2006 - 04:59:07 PST)
Re: AMBER: vlimit exceeded for step 0, vmax = infinity
(Tue Nov 14 2006 - 14:44:44 PST)
Re: AMBER: vlimit exceeded for step 0, vmax = infinity
(Mon Nov 13 2006 - 09:09:22 PST)
Re: AMBER: vlimit exceeded for step 0, vmax = infinity
(Fri Nov 10 2006 - 07:54:26 PST)
Re: AMBER: vlimit exceeded for step 0, vmax = infinity
(Fri Nov 10 2006 - 06:42:31 PST)
Re: AMBER: vlimit exceeded for step 0, vmax = infinity
(Wed Nov 08 2006 - 09:31:12 PST)
AMBER: big bond energy change from minimization and md (heating)
(Wed Nov 08 2006 - 08:40:12 PST)
AMBER: vlimit exceeded for step 0, vmax = infinity
(Wed Nov 08 2006 - 04:59:00 PST)
Re: AMBER: too big EEL values in the minimisation output
(Fri Nov 03 2006 - 04:09:54 PST)
Re: AMBER: too big EEL values in the minimisation output
(Thu Nov 02 2006 - 10:08:00 PST)
AMBER: too big EEL values in the minimisation output
(Wed Nov 01 2006 - 09:01:17 PST)
Rafi Ahmad
AMBER: Probelm with running Amber 9 parallelly
(Thu Nov 09 2006 - 04:59:56 PST)
RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version
(Thu Nov 02 2006 - 01:51:18 PST)
Rajesh Murarka
AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion
(Wed Nov 08 2006 - 07:59:36 PST)
Rama krishnan
AMBER: Unable to find solution for an error - "cannot successfully assign bond type"
(Sat Nov 04 2006 - 02:06:51 PST)
rebeca.mmb.pcb.ub.es
AMBER: minimization of Hydrogens with xLeaP
(Mon Nov 27 2006 - 10:38:04 PST)
Rita Cassia
Re: AMBER: Ethanol
(Wed Nov 22 2006 - 01:33:24 PST)
AMBER: Ethanol
(Fri Nov 17 2006 - 04:13:14 PST)
Robert Duke
Re: AMBER: erroneous placement of TER card
(Thu Nov 16 2006 - 08:47:23 PST)
Re: AMBER: erroneous placement of TER card
(Thu Nov 16 2006 - 05:56:11 PST)
Re: AMBER: pmemd installation problem
(Fri Nov 03 2006 - 11:09:52 PST)
Ross Walker
RE: AMBER: SHAKE problem after minimization
(Wed Nov 22 2006 - 09:59:58 PST)
RE: AMBER: compile amber8 on IBM-sp4
(Wed Nov 22 2006 - 09:55:45 PST)
RE: AMBER: Some warning !!! during SANDER ?
(Wed Nov 22 2006 - 08:48:55 PST)
RE: AMBER: Amber9 installation error
(Sat Nov 18 2006 - 09:20:39 PST)
RE: AMBER: <kein Betreff>
(Mon Nov 13 2006 - 08:44:03 PST)
RE: AMBER: The plc.frcmod file in the old version tutorial
(Mon Nov 13 2006 - 08:29:26 PST)
RE: AMBER: Zn metal library
(Sun Nov 05 2006 - 22:08:20 PST)
AMBER: RE: I got the error meassage in testcase of QMMM
(Sat Nov 04 2006 - 10:09:13 PST)
AMBER:
(Sat Nov 04 2006 - 09:35:43 PST)
RE: AMBER: ntt=1 in simulated annealing
(Fri Nov 03 2006 - 18:04:08 PST)
RE: AMBER: Problems with equilibrating the starting density
(Fri Nov 03 2006 - 11:41:55 PST)
RE: AMBER: Simulation a small chain of amino acids - error in MD simulation
(Fri Nov 03 2006 - 10:32:27 PST)
Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft
(Fri Nov 03 2006 - 08:39:22 PST)
RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version
(Thu Nov 02 2006 - 09:17:42 PST)
RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version
(Thu Nov 02 2006 - 09:05:38 PST)
RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version
(Wed Nov 01 2006 - 16:04:28 PST)
RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version
(Wed Nov 01 2006 - 13:36:17 PST)
RE: AMBER: ab initio terminology query
(Wed Nov 01 2006 - 12:51:43 PST)
RE: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft
(Wed Nov 01 2006 - 09:21:02 PST)
RE: AMBER: ab initio terminology query
(Wed Nov 01 2006 - 08:44:22 PST)
Sandro Fornili
AMBER: ff03 GLY HAs atom type
(Tue Nov 21 2006 - 08:21:01 PST)
sangeeta
AMBER: Potential Energy Calculation
(Mon Nov 06 2006 - 04:11:30 PST)
Sayandeep Purkayasth
Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
(Wed Nov 01 2006 - 22:48:03 PST)
Scott Brozell
Re: AMBER: compile amber8 on IBM-sp4
(Tue Nov 21 2006 - 10:38:49 PST)
Re: AMBER: error in tleap test
(Wed Nov 15 2006 - 09:55:07 PST)
Scott Pendley
Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5?
(Mon Nov 06 2006 - 09:28:48 PST)
Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5?
(Mon Nov 06 2006 - 09:20:43 PST)
Seongeun Yang
AMBER: energy minimizations in amber8 vs. amber9
(Mon Nov 27 2006 - 23:43:35 PST)
Sergey Samsonov
AMBER: Restarting with new topology
(Thu Nov 23 2006 - 08:39:53 PST)
Re: AMBER: ntt=1 in simulated annealing
(Tue Nov 14 2006 - 23:09:15 PST)
Re: AMBER: Problems amber mask in distance?
(Wed Nov 08 2006 - 08:57:20 PST)
AMBER: Problems amber mask in distance?
(Wed Nov 08 2006 - 08:39:18 PST)
Re: AMBER: grid output
(Tue Nov 07 2006 - 08:46:07 PST)
Re: AMBER: grid output
(Tue Nov 07 2006 - 00:35:28 PST)
Re: AMBER: Mass weights
(Tue Nov 07 2006 - 00:06:14 PST)
AMBER: grid output
(Wed Nov 01 2006 - 08:31:34 PST)
Re: AMBER: Closest(closest water)
(Wed Nov 01 2006 - 00:38:55 PST)
AMBER: Mass weights
(Wed Nov 01 2006 - 00:41:33 PST)
SERGIO MIGUEL FERNANDES DOS SANTOS
AMBER: Acetone box
(Tue Nov 14 2006 - 10:34:24 PST)
Seth Lilavivat
AMBER: ambpdb -pqr
(Tue Nov 28 2006 - 12:52:10 PST)
AMBER: Modifying a Force Field
(Tue Nov 28 2006 - 07:27:08 PST)
AMBER: pqr file
(Thu Nov 16 2006 - 08:43:55 PST)
Shozeb Haider
AMBER: Xleap woes
(Thu Nov 16 2006 - 15:07:01 PST)
Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
AMBER: leap usage
(Thu Nov 02 2006 - 01:41:34 PST)
Steve Seibold
AMBER: xleap
(Tue Nov 28 2006 - 06:33:48 PST)
AMBER: Building Library
(Thu Nov 09 2006 - 11:40:30 PST)
AMBER:
(Thu Nov 09 2006 - 09:03:14 PST)
AMBER: Building Library
(Thu Nov 09 2006 - 08:52:08 PST)
Steven Winfield
Re: AMBER: SHAKE problem after minimization
(Wed Nov 22 2006 - 13:53:07 PST)
Re: AMBER: Error in compliling LEAP on Fedora 5
(Wed Nov 15 2006 - 16:10:33 PST)
Re: AMBER: ntt=1 in simulated annealing
(Tue Nov 07 2006 - 03:26:28 PST)
Tanya Johannsen
Re: AMBER: ntt=1 in simulated annealing
(Tue Nov 14 2006 - 15:59:04 PST)
Re: AMBER: ntt=1 in simulated annealing
(Fri Nov 03 2006 - 16:38:38 PST)
AMBER: ntt=1 in simulated annealing
(Thu Nov 02 2006 - 19:44:19 PST)
Thomas Cheatham
Re: AMBER: watershell and image commands
(Thu Nov 30 2006 - 15:22:59 PST)
Re: AMBER: Problem with mask when using distance in ptraj
(Wed Nov 22 2006 - 13:17:12 PST)
Re: AMBER: reading psf file
(Fri Nov 17 2006 - 16:28:45 PST)
Re: AMBER: H-Bond Terms in amber force field
(Wed Nov 15 2006 - 15:51:36 PST)
Re: AMBER: ptraj and mdvel question
(Wed Nov 15 2006 - 15:37:13 PST)
Re: AMBER: Ptraj: radial distribution and correlation coefficient
(Tue Nov 14 2006 - 11:17:40 PST)
Re: AMBER: Ptraj: radial distribution and correlation coefficient
(Tue Nov 14 2006 - 10:34:57 PST)
Re: AMBER: grid output
(Tue Nov 07 2006 - 08:25:39 PST)
Re: AMBER: Mass weights
(Mon Nov 06 2006 - 20:58:54 PST)
Re: AMBER: grid output
(Mon Nov 06 2006 - 20:30:25 PST)
Re: AMBER: PTRAJ RMS: dumping RMSd vs time data
(Mon Nov 06 2006 - 20:18:20 PST)
Re: AMBER: trajout script
(Mon Nov 06 2006 - 12:39:04 PST)
AMBER: ACS Chicago potential symposia and OASYS abstracts
(Sat Nov 04 2006 - 13:04:47 PST)
Thomas Steinbrecher
Re: AMBER: Confusion about PBC
(Wed Nov 29 2006 - 08:40:05 PST)
Re: AMBER: NONB values adjusted?
(Tue Nov 28 2006 - 08:31:33 PST)
Re: AMBER: MM_PBSA
(Thu Nov 16 2006 - 08:21:55 PST)
Re: AMBER: Mutual exclusion of atoms
(Mon Nov 06 2006 - 14:02:47 PST)
Tomas Kubar
AMBER: leap - compilation error
(Tue Nov 07 2006 - 01:47:33 PST)
trudy.uoguelph.ca
Re: AMBER: Problem Installing Amber in SGI Irix 6.5
(Thu Nov 30 2006 - 07:31:02 PST)
Re: AMBER: Problem Installing Amber in SGI Irix 6.5
(Wed Nov 29 2006 - 06:50:51 PST)
Re: AMBER: Problem Installing Amber in SGI Irix 6.5
(Tue Nov 28 2006 - 07:41:07 PST)
AMBER: Problem Installing Amber in SGI Irix 6.5
(Mon Nov 27 2006 - 12:29:53 PST)
uccadco.ucl.ac.uk
AMBER:
(Tue Nov 28 2006 - 06:48:08 PST)
Urszula Uciechowska
Re: AMBER: NAD ??
(Mon Nov 13 2006 - 01:08:45 PST)
Re: AMBER: NAD ??
(Fri Nov 10 2006 - 01:36:15 PST)
AMBER: NAD ??
(Wed Nov 08 2006 - 05:40:15 PST)
AMBER: problem with NAD+ parameters
(Mon Nov 06 2006 - 06:27:16 PST)
VANDANA KUMARI
AMBER: problem in calculating EGB using sander for ligand containing F atom
(Wed Nov 08 2006 - 19:36:52 PST)
Varsha Goyal
AMBER: MM_PBSA
(Wed Nov 15 2006 - 18:27:15 PST)
Re: AMBER: Interaction Energy Calculation
(Thu Nov 02 2006 - 15:04:12 PST)
AMBER: Interaction Energy Calculation
(Thu Nov 02 2006 - 13:34:28 PST)
Viktor Hornak
Re: AMBER: Problems amber mask in distance?
(Wed Nov 08 2006 - 08:50:59 PST)
Vitor Manuel Sousa F?x
AMBER: dihedral angle equation
(Fri Nov 17 2006 - 04:41:25 PST)
AMBER: opls_aa in amber
(Thu Nov 16 2006 - 06:29:45 PST)
Re: AMBER: Interaction Energy Calculation
(Thu Nov 02 2006 - 14:08:01 PST)
wenfei Li
Re: AMBER: problem of the REMD with nmr constraints
(Sat Nov 25 2006 - 17:56:05 PST)
AMBER: problem of the REMD with nmr constraints
(Wed Nov 22 2006 - 17:57:32 PST)
AMBER: Can we use the distance restraint in Replica-exchange simulation with AMBER8
(Thu Nov 02 2006 - 04:44:18 PST)
Xiaowei (David) Li
AMBER: the energy and temperature both increasing during the simulation with NTT=0
(Mon Nov 20 2006 - 10:50:00 PST)
Xuebin Qiao
Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines
(Fri Nov 24 2006 - 20:55:14 PST)
Re: AMBER: compile amber8 on IBM-sp4
(Thu Nov 23 2006 - 06:23:36 PST)
Re: AMBER: compile amber8 on IBM-sp4
(Thu Nov 23 2006 - 04:21:07 PST)
Re: AMBER: compile amber8 on IBM-sp4
(Thu Nov 23 2006 - 04:26:12 PST)
Re: AMBER: compile amber8 on IBM-sp4
(Wed Nov 22 2006 - 19:51:57 PST)
yipinl.umich.edu
AMBER: parameters for beta peptides
(Thu Nov 16 2006 - 11:29:08 PST)
Yong Duan
RE: AMBER: ff03 GLY HAs atom type
(Tue Nov 21 2006 - 09:41:17 PST)
RE: AMBER: vlimit exceeded for step 0, vmax = infinity
(Tue Nov 14 2006 - 15:05:08 PST)
RE: AMBER: vlimit exceeded for step 0, vmax = infinity
(Mon Nov 13 2006 - 17:56:29 PST)
RE: AMBER: vlimit exceeded for step 0, vmax = infinity
(Fri Nov 10 2006 - 13:55:23 PST)
RE: AMBER: ab initio terminology query
(Wed Nov 01 2006 - 15:17:43 PST)
RE: AMBER: ab initio terminology query
(Wed Nov 01 2006 - 10:53:39 PST)
Yongmei Pan
AMBER: How the ensemble average calculated in Gibbs, AMBER7?
(Wed Nov 01 2006 - 14:06:09 PST)
Yu Chen
Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft
(Fri Nov 03 2006 - 11:05:55 PST)
Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft
(Fri Nov 03 2006 - 07:18:35 PST)
Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft
(Wed Nov 01 2006 - 09:02:26 PST)
AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft
(Wed Nov 01 2006 - 08:22:54 PST)
zachary hartman
AMBER: Quantifying pi-pi interactions
(Tue Nov 21 2006 - 07:51:30 PST)
张勇
AMBER: how to remove the rotation of system in periodic condition?
(Tue Nov 14 2006 - 04:10:22 PST)
한 민우
AMBER: Problem about dummy atoms when running antechamber
(Mon Nov 27 2006 - 19:30:27 PST)
Last message date
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Sun Dec 03 2006 - 06:07:40 PST
Archived on
: Fri Nov 22 2024 - 05:53:31 PST
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