Amber Archive Aug 2006 by author
390 messages
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Starting
Wed Aug 02 2006 - 06:07:09 PDT,
Ending
Sun Sep 03 2006 - 06:07:18 PDT
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AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp
(Tue Aug 29 2006 - 03:15:07 PDT)
AMBER: Can I run RED/RESP for Platinum Complexes?
(Thu Aug 24 2006 - 02:50:42 PDT)
AMBER: (no subject)
(Tue Aug 15 2006 - 03:13:49 PDT)
RE: AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number?
(Mon Aug 14 2006 - 22:48:49 PDT)
AMBER: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number?
(Mon Aug 14 2006 - 04:25:31 PDT)
Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What canI do next?
(Sun Aug 13 2006 - 21:29:59 PDT)
Re: AMBER: Phosphated Tyrosine, not a type (xleap)?
(Thu Aug 10 2006 - 19:38:47 PDT)
Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next?
(Thu Aug 10 2006 - 19:39:54 PDT)
AMBER: Phosphated Tyrosine, not a type (xleap)?
(Thu Aug 10 2006 - 02:22:27 PDT)
AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next?
(Thu Aug 10 2006 - 02:26:01 PDT)
Abhilash
AMBER: how to do a molecular dynamic study on a trimer
(Fri Aug 11 2006 - 08:05:44 PDT)
Adrian Roitberg
Re: AMBER: Temperature fluctuation with Langevin Temperature control
(Sun Aug 27 2006 - 14:07:07 PDT)
Re: AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9
(Fri Aug 11 2006 - 13:23:10 PDT)
Re: AMBER: Re: Confusion re AMBER SMD output
(Tue Aug 01 2006 - 04:07:03 PDT)
Akshay Patny
RE: AMBER: GAFF parameters: DPPC Bilayer
(Wed Aug 09 2006 - 14:08:00 PDT)
AMBER: GAFF parameters: DPPC Bilayer
(Tue Aug 08 2006 - 12:53:49 PDT)
Amarda Shehu
Re: ***SPAM*** Re: AMBER: problem imposing arbitrary peptide bonds through leap
(Mon Aug 14 2006 - 09:56:31 PDT)
AMBER: problem imposing arbitrary peptide bonds through leap
(Mon Aug 14 2006 - 09:27:24 PDT)
Amber admin
RE: AMBER: compiling parallel amber 9 in linux
(Thu Aug 24 2006 - 17:10:57 PDT)
Re: AMBER: increase force constants
(Thu Aug 24 2006 - 17:15:24 PDT)
AMBER: compiling parallel amber 9 in linux
(Wed Aug 23 2006 - 12:00:08 PDT)
Andrea Bortolato
AMBER: TI vlimit exceeded
(Thu Aug 24 2006 - 06:42:21 PDT)
Andreas Svrcek-Seiler
Re: AMBER: building AMBER9 with gfortran/cygwin
(Fri Aug 25 2006 - 03:39:08 PDT)
Re: AMBER: Maximum system size in simulated annealing
(Thu Aug 03 2006 - 02:23:13 PDT)
anna.schrey.gmx.de
AMBER: problems with ptraj
(Thu Aug 03 2006 - 07:49:39 PDT)
Arvind Marathe
AMBER: regarding diffusion command output
(Tue Aug 01 2006 - 03:45:21 PDT)
Atro Tossavainen
Re: AMBER: nmode memory problem
(Fri Aug 25 2006 - 03:10:50 PDT)
Austin B. Yongye
AMBER: REMD: Hybrid topology file
(Wed Aug 30 2006 - 07:30:34 PDT)
AYTUG TUNCEL
AMBER: nmode: number of atoms limitation
(Mon Aug 28 2006 - 16:15:04 PDT)
AMBER: mm_pbsa calculation allocation error
(Mon Aug 21 2006 - 06:15:31 PDT)
AMBER: input conversion error mm_pbsa
(Tue Aug 15 2006 - 15:23:28 PDT)
AMBER: brookhaven to amber pdb format
(Wed Aug 02 2006 - 02:08:50 PDT)
AMBER: pdb error
(Tue Aug 01 2006 - 12:36:39 PDT)
backy
Re: AMBER: DIELC?
(Sat Aug 19 2006 - 01:04:14 PDT)
AMBER: DIELC?
(Sat Aug 12 2006 - 05:16:47 PDT)
AMBER: Could mm_pbsa decompose energy only for the receptor ?
(Fri Aug 11 2006 - 07:10:52 PDT)
Re: AMBER: Energy differecnes as using igb=1 and igb=0
(Wed Aug 09 2006 - 23:47:37 PDT)
AMBER: Energy differecnes as using igb=1 and igb=0
(Wed Aug 09 2006 - 07:46:56 PDT)
bala
AMBER: parallel pmemd with intel 9 fc
(Sat Aug 12 2006 - 08:56:15 PDT)
Bill Ross
Re: AMBER: 1-4 interaction in AMBER8
(Wed Aug 30 2006 - 14:17:10 PDT)
Re: AMBER: 1-4 interaction in AMBER8
(Wed Aug 30 2006 - 14:05:27 PDT)
Re: AMBER: how to limit the simulation space
(Mon Aug 28 2006 - 18:04:39 PDT)
Re: AMBER: Periodic boundary condition (PBC)
(Mon Aug 28 2006 - 16:21:57 PDT)
Re: AMBER: How to create a modified NA in leap
(Sat Aug 26 2006 - 17:21:41 PDT)
Re: AMBER: How to create a modified NA in leap
(Fri Aug 25 2006 - 14:52:40 PDT)
Re: AMBER: Carnal: Internal error: stream file name 2 out of range
(Wed Aug 23 2006 - 14:16:16 PDT)
Re: AMBER: holding a pair of residues fixed during minimization
(Wed Aug 23 2006 - 13:45:13 PDT)
Re: AMBER: amber naming conventions for structure files
(Tue Aug 22 2006 - 15:00:10 PDT)
Re: AMBER: Execution time discrepancies
(Thu Aug 17 2006 - 18:24:13 PDT)
Re: AMBER: help with leap
(Wed Aug 16 2006 - 17:51:56 PDT)
Biswa Ranjan Meher
AMBER: TI-FEP for ILE--->VAL.
(Wed Aug 02 2006 - 22:26:22 PDT)
Björn C-G. Karlsson
AMBER: Calculate interaction energy between small organic molecules
(Wed Aug 23 2006 - 23:17:56 PDT)
AMBER: Calculate interaction energy between small organic molecules
(Sun Aug 20 2006 - 23:37:24 PDT)
Brent Krueger
Re: AMBER: DOTA-Lanthanide complexes in Amber
(Wed Aug 16 2006 - 13:08:57 PDT)
Carlos Simmerling
Re: AMBER: reference of ff99
(Thu Aug 31 2006 - 09:18:09 PDT)
Re: AMBER: 1-4 interaction in AMBER8
(Wed Aug 30 2006 - 14:23:26 PDT)
Re: AMBER: 1-4 interaction in AMBER8
(Wed Aug 30 2006 - 14:15:23 PDT)
Re: AMBER: 1-4 interaction in AMBER8
(Wed Aug 30 2006 - 12:22:13 PDT)
Re: AMBER: REMD: Hybrid topology file
(Wed Aug 30 2006 - 07:48:20 PDT)
Re: AMBER: Periodic boundary condition (PBC)
(Mon Aug 28 2006 - 13:40:05 PDT)
Re: AMBER: TI, mutation
(Mon Aug 28 2006 - 05:18:56 PDT)
Re: AMBER: missing values in md.out
(Fri Aug 25 2006 - 05:53:26 PDT)
Re: AMBER: missing values in md.out
(Thu Aug 24 2006 - 09:24:28 PDT)
Re: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8
(Wed Aug 23 2006 - 05:18:03 PDT)
Re: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8
(Mon Aug 21 2006 - 07:19:10 PDT)
AMBER: Re: Simulated annealing
(Thu Aug 10 2006 - 04:40:24 PDT)
Re: AMBER: Energy differecnes as using igb=1 and igb=0
(Thu Aug 10 2006 - 03:09:23 PDT)
Re: AMBER: Energy differecnes as using igb=1 and igb=0
(Wed Aug 09 2006 - 08:01:27 PDT)
Re: AMBER: Format of mdcrd files
(Wed Aug 09 2006 - 07:24:35 PDT)
Re: AMBER: cutting the box after "solvatebox"
(Tue Aug 08 2006 - 05:43:47 PDT)
Re: AMBER: Problem with restarting MD simulation
(Tue Aug 08 2006 - 04:08:27 PDT)
Re: AMBER: SURFTEN in GB (mm_pbsa calculations)
(Thu Aug 03 2006 - 12:38:59 PDT)
Re: AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms
(Thu Aug 03 2006 - 08:33:34 PDT)
AMBER: ff03 and ff99SB force fields
(Thu Aug 03 2006 - 03:59:11 PDT)
Re: AMBER: Maximum system size in simulated annealing
(Thu Aug 03 2006 - 03:26:58 PDT)
Re: AMBER: Ignoring every other frame in a .crd trajectory in Ptraj
(Tue Aug 01 2006 - 11:13:07 PDT)
Re: AMBER: How to set Bondi Radii using xleap
(Tue Aug 01 2006 - 10:43:04 PDT)
Cenk Andac
Re: AMBER: nmode: number of atoms limitation
(Wed Aug 30 2006 - 06:01:58 PDT)
Changge Ji
Re: Re: AMBER: nmode: number of atoms limitation
(Mon Aug 28 2006 - 23:33:27 PDT)
Cheng Luo, Ph.D.
AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9
(Fri Aug 11 2006 - 13:41:32 PDT)
Chris Moth
AMBER: Missing LES reference in Amber 9 manual
(Tue Aug 29 2006 - 11:43:12 PDT)
Christophe Guilbert
AMBER: antechamber charge calculation very sensitive to conformations ?
(Wed Aug 23 2006 - 18:59:08 PDT)
Chunhu Tan
AMBER: 答复: AMBER: pmf input files
(Thu Aug 17 2006 - 09:36:30 PDT)
Claire Zerafa
Fw: AMBER: HBOND ANALYSIS
(Sat Aug 05 2006 - 12:45:10 PDT)
AMBER: HBOND ANALYSIS
(Fri Aug 04 2006 - 07:35:50 PDT)
Come On
AMBER: to do tutorial 4 using tleap
(Fri Aug 04 2006 - 09:50:53 PDT)
cristian obiol
AMBER: counterions and particle-mesh-ewald
(Tue Aug 29 2006 - 01:06:20 PDT)
darden
Re: AMBER: counterions and particle-mesh-ewald
(Wed Aug 30 2006 - 15:59:32 PDT)
David A. Case
Re: AMBER: Question about free energy with mm_pbsa
(Thu Aug 31 2006 - 22:32:54 PDT)
Re: AMBER: reference of ff99
(Thu Aug 31 2006 - 09:43:50 PDT)
Re: AMBER: counterions and particle-mesh-ewald
(Wed Aug 30 2006 - 13:14:40 PDT)
Re: AMBER: Missing LES reference in Amber 9 manual
(Wed Aug 30 2006 - 09:03:34 PDT)
Re: AMBER:
(Tue Aug 29 2006 - 08:09:23 PDT)
Re: AMBER: nmode: number of atoms limitation
(Mon Aug 28 2006 - 22:55:53 PDT)
Re: AMBER: Periodic boundary condition (PBC)
(Mon Aug 28 2006 - 17:17:42 PDT)
Re: AMBER: preparing ligand/rna structure for MD
(Mon Aug 28 2006 - 17:11:34 PDT)
Re: AMBER: Temperature fluctuation with Langevin Temperature control
(Mon Aug 28 2006 - 10:32:08 PDT)
Re: AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine
(Sun Aug 27 2006 - 09:03:54 PDT)
Re: AMBER: TI vlimit exceeded
(Sat Aug 26 2006 - 10:38:58 PDT)
Re: AMBER: building AMBER9 with gfortran/cygwin
(Fri Aug 25 2006 - 09:39:40 PDT)
Re: AMBER: building AMBER9 with gfortran/cygwin
(Fri Aug 25 2006 - 08:41:49 PDT)
Re: AMBER: Installation amber 9 on IBM SP4
(Fri Aug 25 2006 - 08:03:10 PDT)
Re: AMBER: increase force constants
(Thu Aug 24 2006 - 15:56:33 PDT)
Re: AMBER: how to use AddPdbAtomMap
(Thu Aug 24 2006 - 15:47:50 PDT)
Re: AMBER: Backbone & Sidechain atoms: Definition
(Thu Aug 24 2006 - 08:15:44 PDT)
Re: AMBER: 0 steps the same as 1 step?
(Wed Aug 23 2006 - 18:14:53 PDT)
Re: AMBER: holding a pair of residues fixed during minimization
(Wed Aug 23 2006 - 13:05:25 PDT)
Re: AMBER: compiling parallel amber 9 in linux
(Wed Aug 23 2006 - 13:01:35 PDT)
Re: AMBER: Calculate interaction energy between small organic molecules
(Mon Aug 21 2006 - 23:14:15 PDT)
Re: AMBER: GBSA EGB = NaN
(Mon Aug 21 2006 - 11:21:10 PDT)
Re: AMBER: GBSA EGB = NaN
(Mon Aug 21 2006 - 10:10:24 PDT)
Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system
(Fri Aug 18 2006 - 11:35:04 PDT)
Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system
(Fri Aug 18 2006 - 10:50:32 PDT)
Re: AMBER: generate "template" frcmod from standard residues?
(Thu Aug 17 2006 - 11:01:45 PDT)
Re: AMBER: generate "template" frcmod from standard residues?
(Thu Aug 17 2006 - 09:04:22 PDT)
Re: AMBER: reading ff file into XLeap
(Wed Aug 16 2006 - 10:21:47 PDT)
Re: AMBER: DOTA-Lanthanide complexes in Amber
(Wed Aug 16 2006 - 09:59:22 PDT)
Re: AMBER: MM_PBSA : Question about Stability?
(Wed Aug 16 2006 - 09:24:48 PDT)
Re: AMBER: MMPBSA: positive energies during nmode
(Wed Aug 16 2006 - 09:10:29 PDT)
Re: AMBER: TI tutorial
(Tue Aug 15 2006 - 16:34:58 PDT)
Re: AMBER: antechamber failure on FMN
(Tue Aug 15 2006 - 16:14:41 PDT)
Re: AMBER: (Another) Question about using antechamber with G03
(Tue Aug 15 2006 - 16:09:56 PDT)
Re: AMBER: input conversion error mm_pbsa
(Tue Aug 15 2006 - 15:47:19 PDT)
Re: AMBER: Question about using antechamber with G03
(Tue Aug 15 2006 - 14:15:26 PDT)
Re: AMBER: amber9 Test Failer
(Tue Aug 15 2006 - 08:05:54 PDT)
Re: AMBER: Problem with sander in Linux
(Mon Aug 14 2006 - 09:49:53 PDT)
Re: AMBER: klambda
(Mon Aug 14 2006 - 09:48:30 PDT)
Re: AMBER: problem imposing arbitrary peptide bonds through leap
(Mon Aug 14 2006 - 09:45:48 PDT)
Re: AMBER: how to do a molecular dynamic study on a trimer
(Sun Aug 13 2006 - 09:37:03 PDT)
Re: AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file
(Sun Aug 13 2006 - 09:49:27 PDT)
Re: AMBER: DIELC?
(Sun Aug 13 2006 - 09:43:58 PDT)
Re: AMBER: Middlebury College Cluster and Amber 8
(Fri Aug 11 2006 - 11:30:46 PDT)
Re: AMBER: how to do a molecular dynamic study on a trimer
(Fri Aug 11 2006 - 09:05:12 PDT)
Re: AMBER: Leap adds hydrogens but cannot resolve their type.
(Thu Aug 10 2006 - 13:15:16 PDT)
Re: AMBER: Phosphated Tyrosine, not a type (xleap)?
(Thu Aug 10 2006 - 09:07:09 PDT)
Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition
(Wed Aug 09 2006 - 13:45:42 PDT)
Re: AMBER: how to reassign charges
(Wed Aug 09 2006 - 13:43:07 PDT)
Re: AMBER: Amber Installation Help
(Tue Aug 08 2006 - 08:25:49 PDT)
Re: AMBER: Info regarding reduced cysteines
(Mon Aug 07 2006 - 08:02:57 PDT)
Re: AMBER: question on chargning free energy in solvent vs vacuum
(Fri Aug 04 2006 - 09:18:53 PDT)
Re: AMBER: problems with ptraj
(Thu Aug 03 2006 - 09:46:19 PDT)
Re: AMBER: TI-FEP for ILE--->VAL.
(Thu Aug 03 2006 - 09:43:44 PDT)
Re: AMBER: about Silica's polarizability
(Thu Aug 03 2006 - 09:16:40 PDT)
Re: AMBER: brookhaven to amber pdb format
(Wed Aug 02 2006 - 07:48:23 PDT)
Re: AMBER: any work-around for 80 character mask string limit?
(Tue Aug 01 2006 - 14:37:36 PDT)
Re: AMBER: Using a trajectory and some PDB files as input for PCA
(Tue Aug 01 2006 - 10:10:29 PDT)
Re: AMBER: How to set Bondi Radii using xleap
(Tue Aug 01 2006 - 10:17:38 PDT)
Re: AMBER: GB tutorials and disulphide bonds
(Tue Aug 01 2006 - 10:14:20 PDT)
David LeBard
Re: AMBER: Calculate interaction energy between small organic molecules
(Thu Aug 24 2006 - 14:01:16 PDT)
David Mobley
Re: AMBER: antechamber charge calculation very sensitive to conformations ?
(Fri Aug 25 2006 - 08:08:44 PDT)
Re: AMBER: Calculate interaction energy between small organic molecules
(Thu Aug 24 2006 - 13:07:57 PDT)
Re: AMBER: Calculate interaction energy between small organic molecules
(Mon Aug 21 2006 - 07:20:42 PDT)
AMBER: Re: antechamber failure on FMN
(Fri Aug 18 2006 - 11:46:58 PDT)
Re: AMBER: generate "template" frcmod from standard residues?
(Fri Aug 18 2006 - 09:13:08 PDT)
Re: AMBER: generate "template" frcmod from standard residues?
(Wed Aug 16 2006 - 14:51:47 PDT)
Re: AMBER: antechamber failure on FMN
(Tue Aug 15 2006 - 11:16:47 PDT)
AMBER: antechamber failure on FMN
(Tue Aug 15 2006 - 11:04:42 PDT)
Re: AMBER: how to reassign charges
(Wed Aug 09 2006 - 13:03:10 PDT)
AMBER: antechamber bond typing questions
(Mon Aug 07 2006 - 13:14:42 PDT)
Don.Bashford.stjude.org
Re: AMBER: How to set Bondi Radii using xleap. .
(Tue Aug 01 2006 - 10:23:51 PDT)
Eric Hu
AMBER: how to limit the simulation space
(Mon Aug 28 2006 - 17:55:11 PDT)
Re: AMBER: transition state
(Mon Aug 21 2006 - 17:06:22 PDT)
Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition
(Wed Aug 09 2006 - 14:30:04 PDT)
Re: AMBER: transition state
(Wed Aug 09 2006 - 12:05:14 PDT)
AMBER: build box info for acetonitrile in the simulation with periodic boundary condition
(Wed Aug 09 2006 - 11:06:30 PDT)
eric.henon.univ-reims.fr
Re: AMBER: TI, mutation
(Tue Aug 29 2006 - 01:43:04 PDT)
AMBER: TI, mutation
(Mon Aug 28 2006 - 05:39:48 PDT)
Evan Kelly
AMBER: Please DISREGARD previous message (restraint=0.0000)
(Thu Aug 03 2006 - 10:57:46 PDT)
AMBER: restraint=0.0000 during minimization?
(Thu Aug 03 2006 - 10:48:17 PDT)
Fabian Boes
Re: AMBER: amber 9 intel 9.1 ia64
(Tue Aug 15 2006 - 06:59:39 PDT)
Fabián Alejandro Rodríguez
Re: AMBER: from traj to crd
(Tue Aug 01 2006 - 08:41:22 PDT)
Re: AMBER: Xmgr in Windows
(Tue Aug 01 2006 - 04:39:19 PDT)
Feng X Zhou
AMBER: Advice on linux cluster sought
(Mon Aug 14 2006 - 11:34:16 PDT)
Florian Haberl
Re: AMBER: Xmgr in Windows
(Tue Aug 01 2006 - 05:11:44 PDT)
Franck_Vendeix.ncsu.edu
Re: AMBER: help with leap
(Thu Aug 17 2006 - 07:46:07 PDT)
FyD
Re: AMBER: Details about Gaussian basis set for Cobalt complex
(Mon Aug 21 2006 - 05:28:49 PDT)
Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next?
(Sat Aug 12 2006 - 12:09:29 PDT)
Re: AMBER: neutral N-terminal amino-acid parameters for ff03
(Sat Aug 05 2006 - 01:16:23 PDT)
Glass, Kevin A
AMBER: Execution time discrepancies
(Thu Aug 17 2006 - 17:18:20 PDT)
AMBER:
(Mon Aug 07 2006 - 13:09:02 PDT)
Gloria T. Anderle
AMBER: Residue connection points on prep.in
(Fri Aug 04 2006 - 09:10:53 PDT)
Gobind Bisht
AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine
(Sat Aug 26 2006 - 22:24:12 PDT)
Re: AMBER: how to do a molecular dynamic study on a trimer
(Sat Aug 12 2006 - 10:05:29 PDT)
AMBER: Format of mdcrd files
(Wed Aug 09 2006 - 06:56:18 PDT)
AMBER: Problem with restarting MD simulation
(Mon Aug 07 2006 - 22:02:56 PDT)
Gobind Singh Bisht
AMBER: Temperature fluctuation with Langevin Temperature control
(Sun Aug 27 2006 - 12:06:49 PDT)
Guanglei Cui
Re: AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files
(Fri Aug 11 2006 - 06:57:46 PDT)
Re: AMBER: cutting the box after "solvatebox"
(Tue Aug 08 2006 - 07:38:06 PDT)
Re: AMBER: from traj to crd
(Tue Aug 01 2006 - 08:30:59 PDT)
Re: AMBER: Distance between two regions
(Tue Aug 01 2006 - 08:35:54 PDT)
Guillaume Bollot
AMBER: MM_PBSA : Question about Stability?
(Wed Aug 16 2006 - 00:00:15 PDT)
Gustavo Seabra
Re: AMBER: Question about using antechamber with G03
(Wed Aug 16 2006 - 06:49:42 PDT)
AMBER: (Another) Question about using antechamber with G03
(Tue Aug 15 2006 - 10:51:16 PDT)
AMBER: Question about using antechamber with G03
(Tue Aug 15 2006 - 08:58:40 PDT)
Ilyas Yildirim
Re: AMBER: minimization with my own charges
(Thu Aug 31 2006 - 20:37:18 PDT)
Re: AMBER: minimization with my own charges
(Thu Aug 31 2006 - 16:47:54 PDT)
Re: AMBER: minimization with my own charges
(Thu Aug 31 2006 - 15:50:26 PDT)
Re: AMBER: minimization with my own charges
(Thu Aug 31 2006 - 15:12:24 PDT)
Re: AMBER: how to use AddPdbAtomMap
(Thu Aug 24 2006 - 13:27:41 PDT)
Re: AMBER: GBSA EGB = NaN
(Mon Aug 21 2006 - 09:14:54 PDT)
Re: AMBER: cutting the box after "solvatebox"
(Thu Aug 17 2006 - 12:28:55 PDT)
Re: AMBER: klambda
(Mon Aug 14 2006 - 10:31:24 PDT)
Re: AMBER: TI-FEP for ILE--->VAL.
(Wed Aug 02 2006 - 23:15:10 PDT)
Re: AMBER: brookhaven to amber pdb format
(Wed Aug 02 2006 - 11:55:38 PDT)
Re: AMBER: pdb error
(Tue Aug 01 2006 - 12:23:30 PDT)
AMBER: How to set Bondi Radii using xleap
(Mon Jul 31 2006 - 22:40:15 PDT)
Re: AMBER: Xmgr in Windows
(Mon Jul 31 2006 - 22:33:38 PDT)
Isherwood, James
AMBER: Nature of QM scanning protocol for parameter development
(Fri Aug 11 2006 - 09:17:01 PDT)
Jardas sucuriba
RE: AMBER: RDF output
(Wed Aug 30 2006 - 14:31:08 PDT)
AMBER: RDF output
(Tue Aug 29 2006 - 07:48:29 PDT)
AMBER: waters closest to specific residues
(Sat Aug 26 2006 - 08:39:35 PDT)
Re: AMBER: missing values in md.out
(Fri Aug 25 2006 - 05:36:45 PDT)
AMBER: missing values in md.out
(Thu Aug 24 2006 - 09:15:40 PDT)
AMBER: ptraj script
(Fri Aug 18 2006 - 13:08:31 PDT)
Jianhui
Re: AMBER: 1-4 interaction in AMBER8
(Wed Aug 30 2006 - 12:48:28 PDT)
AMBER: 1-4 interaction in AMBER8
(Wed Aug 30 2006 - 12:08:09 PDT)
AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file
(Fri Aug 11 2006 - 11:50:54 PDT)
Jianyin Shao
Re: AMBER: mm_pbsa_statistical.pl
(Wed Aug 30 2006 - 10:52:56 PDT)
Jing Huang
AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files
(Fri Aug 11 2006 - 06:35:12 PDT)
John Chuang莊曜遠老師
Re: AMBER: transition state
(Mon Aug 14 2006 - 15:20:20 PDT)
AMBER: transition state
(Mon Aug 07 2006 - 09:06:50 PDT)
Joseph Nachman
AMBER: ptraj: nofit option for rmsd
(Tue Aug 08 2006 - 08:27:41 PDT)
JunJun Liu
AMBER: parameter for Cd2+?
(Fri Aug 04 2006 - 08:50:46 PDT)
Junmei Wang
RE: AMBER: antechamber charge calculation very sensitive to conformations ?
(Thu Aug 24 2006 - 19:51:07 PDT)
AMBER: RE: antechamber failure on FMN
(Thu Aug 17 2006 - 16:14:47 PDT)
RE: AMBER: antechamber error -> metals
(Wed Aug 16 2006 - 19:29:46 PDT)
AMBER: RE: antechamber bond typing questions
(Mon Aug 07 2006 - 18:43:05 PDT)
Juraj Kotulic Bunta
AMBER: Maximum system size in simulated annealing
(Wed Aug 02 2006 - 19:03:11 PDT)
Jyh-Shyong Ho
Re: AMBER: Installation amber 9 on IBM SP4
(Fri Aug 25 2006 - 19:11:21 PDT)
AMBER: building AMBER9 with gfortran/cygwin
(Thu Aug 24 2006 - 19:30:02 PDT)
Kateryna Miroshnychenko
AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number?
(Mon Aug 14 2006 - 06:19:46 PDT)
kawamura_hiro.riken.jp
AMBER: amber9 Test Failer
(Tue Aug 15 2006 - 05:21:49 PDT)
Kirk Hevener
AMBER: Amber Installation Help
(Mon Aug 07 2006 - 05:43:25 PDT)
Knut Langsestmo
Re: AMBER: nmode memory problem
(Thu Aug 24 2006 - 09:17:04 PDT)
Lauren O'Neil
AMBER: pmf input files
(Wed Aug 16 2006 - 10:20:45 PDT)
Lubans, Peter S
AMBER: Middlebury College Cluster and Amber 8
(Fri Aug 11 2006 - 09:55:19 PDT)
Lwin, ThuZar
AMBER: how to reassign charges
(Wed Aug 09 2006 - 11:16:01 PDT)
RE: AMBER: question on chargning free energy in solvent vs vacuum. .
(Fri Aug 04 2006 - 12:02:10 PDT)
AMBER: how to take care of toluene system neutrality
(Fri Aug 04 2006 - 11:31:53 PDT)
AMBER: how to take care of toluene system neutrality
(Fri Aug 04 2006 - 11:27:39 PDT)
AMBER: question on chargning free energy in solvent vs vacuum
(Thu Aug 03 2006 - 10:08:07 PDT)
AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms
(Thu Aug 03 2006 - 08:14:28 PDT)
Mahalakshmi Sahasranaman
AMBER: increase force constants
(Thu Aug 24 2006 - 06:45:28 PDT)
Marcelo Puiatti
AMBER: Heme parameters
(Wed Aug 09 2006 - 15:58:35 PDT)
Mark Williamson
Re: AMBER: Format of mdcrd files
(Wed Aug 09 2006 - 07:32:06 PDT)
Markus Kaukonen
AMBER: ptraj dumpq feature/bug
(Thu Aug 24 2006 - 01:31:51 PDT)
mernst.tricity.wsu.edu
Re: AMBER: generate "template" frcmod from standard residues?
(Thu Aug 17 2006 - 10:06:07 PDT)
AMBER: generate "template" frcmod from standard residues?
(Wed Aug 16 2006 - 11:41:02 PDT)
Miguel Ferreira
AMBER: atomifluct
(Fri Aug 25 2006 - 04:09:03 PDT)
Mingfeng Yang
AMBER: TI tutorial
(Tue Aug 15 2006 - 15:22:10 PDT)
Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction
(Mon Aug 14 2006 - 12:06:56 PDT)
AMBER: Modify charges to increase/decrease hydrogen bond interaction
(Mon Aug 14 2006 - 11:25:19 PDT)
Myunggi Yi
Re: AMBER: minimization with my own charges
(Thu Aug 31 2006 - 18:16:49 PDT)
Re: AMBER: minimization with my own charges
(Thu Aug 31 2006 - 16:13:29 PDT)
Re: AMBER: minimization with my own charges
(Thu Aug 31 2006 - 15:22:08 PDT)
AMBER: minimization with my own charges
(Thu Aug 31 2006 - 15:01:24 PDT)
Re: AMBER: reference of ff99
(Thu Aug 31 2006 - 09:26:09 PDT)
Re: AMBER: reference of ff99
(Thu Aug 31 2006 - 09:21:59 PDT)
AMBER: reference of ff99
(Thu Aug 31 2006 - 08:59:51 PDT)
Re: AMBER: Installation amber 9 on IBM SP4
(Fri Aug 25 2006 - 19:41:46 PDT)
Re: AMBER: Installation amber 9 on IBM SP4
(Fri Aug 25 2006 - 18:20:47 PDT)
Re: AMBER: Installation amber 9 on IBM SP4
(Thu Aug 24 2006 - 20:20:12 PDT)
Re: AMBER: Installation amber 9 on IBM SP4
(Thu Aug 24 2006 - 20:09:29 PDT)
Re: AMBER: Installation amber 9 on IBM SP4
(Thu Aug 24 2006 - 19:59:09 PDT)
Re: AMBER: Installation amber 9 on IBM SP4
(Thu Aug 24 2006 - 19:48:07 PDT)
Re: AMBER: Installation amber 9 on IBM SP4
(Thu Aug 24 2006 - 19:39:43 PDT)
Re: AMBER: Installation amber 9 on IBM SP4
(Thu Aug 24 2006 - 18:29:58 PDT)
Re: AMBER: Installation amber 9 on IBM SP4
(Thu Aug 24 2006 - 12:00:04 PDT)
AMBER: Installation amber 9 on IBM SP4
(Thu Aug 24 2006 - 09:05:50 PDT)
Navnit Kumar Mishra
Re: AMBER: (no subject)
(Tue Aug 15 2006 - 05:51:49 PDT)
Nitin Bhardwaj
Re: AMBER: GAFF parameters: DPPC Bilayer
(Tue Aug 08 2006 - 12:58:59 PDT)
opitz.che.udel.edu
Re: AMBER: DOTA-Lanthanide complexes in Amber
(Wed Aug 16 2006 - 10:27:23 PDT)
AMBER: DOTA-Lanthanide complexes in Amber
(Tue Aug 15 2006 - 10:48:23 PDT)
Paul R Brenner
Re: AMBER: Leap adds hydrogens but cannot resolve their type.
(Tue Aug 15 2006 - 08:39:08 PDT)
AMBER: Leap adds hydrogens but cannot resolve their type.
(Thu Aug 10 2006 - 12:23:55 PDT)
Petr Jerabek
AMBER: reading ff file into XLeap
(Wed Aug 16 2006 - 09:21:00 PDT)
Petr Kulhanek
AMBER: AMBER8 - RDF bug
(Fri Aug 11 2006 - 09:00:57 PDT)
Piotr Cieplak
Re: AMBER: impose command in leap problem
(Mon Aug 14 2006 - 13:44:02 PDT)
AMBER: impose command in leap problem
(Fri Aug 11 2006 - 17:56:40 PDT)
pkb bioinfo
Re: AMBER: mm_pbsa.pl fails to start in linux cluster
(Wed Aug 02 2006 - 06:58:48 PDT)
AMBER: mm_pbsa.pl fails to start in linux cluster
(Wed Aug 02 2006 - 05:07:22 PDT)
Pradipta Bandyopadhyay
Re: AMBER: TI, mutation
(Mon Aug 28 2006 - 05:46:43 PDT)
Prashanth Athri
AMBER: amidine group/ gaff parameters
(Fri Aug 18 2006 - 12:00:17 PDT)
priya priya
RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8
(Tue Aug 22 2006 - 21:16:42 PDT)
AMBER: problem relating all atom structure prediction and folding simulations on AMBER8
(Mon Aug 21 2006 - 00:46:29 PDT)
Qingning Shu
Re: Re: AMBER:
(Tue Aug 29 2006 - 09:26:34 PDT)
AMBER:
(Tue Aug 29 2006 - 06:01:58 PDT)
Rafi Ahmad
AMBER: Info regarding reduced cysteines
(Mon Aug 07 2006 - 07:06:40 PDT)
Rahaman, Asif
RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj
(Thu Aug 31 2006 - 15:29:25 PDT)
RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj
(Thu Aug 31 2006 - 14:34:50 PDT)
RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj
(Thu Aug 31 2006 - 13:24:43 PDT)
AMBER: Periodic boundary condition (PBC)
(Mon Aug 28 2006 - 13:24:19 PDT)
Ray Luo
Re: AMBER: mm_pbsa calculation allocation error
(Mon Aug 21 2006 - 09:37:14 PDT)
Re: AMBER: ff03 and ff99SB force fields
(Thu Aug 03 2006 - 05:21:03 PDT)
Robert Duke
Re: AMBER: parallel pmemd with intel 9 fc
(Sat Aug 12 2006 - 11:58:59 PDT)
Re: AMBER: Middlebury College Cluster and Amber 8
(Fri Aug 11 2006 - 10:33:13 PDT)
AMBER: Bugfixes available for pmemd iwrap problem
(Wed Aug 02 2006 - 10:05:32 PDT)
Ross Walker
RE: AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp
(Wed Aug 30 2006 - 19:04:36 PDT)
RE: AMBER: Installation amber 9 on IBM SP4
(Fri Aug 25 2006 - 09:16:13 PDT)
RE: AMBER: Installation amber 9 on IBM SP4
(Thu Aug 24 2006 - 15:08:03 PDT)
RE: AMBER: nmode memory problem
(Thu Aug 24 2006 - 10:57:12 PDT)
RE: AMBER: Installation amber 9 on IBM SP4
(Thu Aug 24 2006 - 10:23:02 PDT)
RE: AMBER: compiling parallel amber 9 in linux
(Wed Aug 23 2006 - 12:54:39 PDT)
RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8
(Mon Aug 21 2006 - 08:48:00 PDT)
RE: AMBER: GBSA EGB = NaN
(Fri Aug 18 2006 - 15:11:52 PDT)
RE: AMBER: Execution time discrepancies
(Thu Aug 17 2006 - 20:00:29 PDT)
RE: AMBER: GBSA EGB = NaN
(Thu Aug 17 2006 - 19:57:29 PDT)
RE: AMBER: identical high energies
(Thu Aug 17 2006 - 19:52:38 PDT)
S. Jamal Rahi
AMBER: 0 steps the same as 1 step?
(Wed Aug 23 2006 - 14:25:44 PDT)
S.Sundar Raman
Re: AMBER: Details about Gaussian basis set for Cobalt complex
(Sat Aug 26 2006 - 03:51:04 PDT)
AMBER: Details about Gaussian basis set for Cobalt complex
(Sun Aug 20 2006 - 07:07:57 PDT)
sangeeta
AMBER: H-bonds of peptide with water
(Fri Aug 04 2006 - 06:20:13 PDT)
Scott Brozell
Re: AMBER: Installation amber 9 on IBM SP4
(Thu Aug 24 2006 - 23:45:09 PDT)
Re: AMBER: Installation amber 9 on IBM SP4
(Thu Aug 24 2006 - 23:28:35 PDT)
Re: AMBER: Installation amber 9 on IBM SP4
(Thu Aug 24 2006 - 19:58:20 PDT)
Re: AMBER: Installation amber 9 on IBM SP4; bugfix 12
(Thu Aug 24 2006 - 19:57:03 PDT)
Re: AMBER: Installation amber 9 on IBM SP4
(Thu Aug 24 2006 - 18:50:31 PDT)
Re: AMBER: antechamber error -> metals
(Sun Aug 13 2006 - 14:58:14 PDT)
Re: AMBER: impose command in leap problem
(Fri Aug 11 2006 - 18:57:21 PDT)
Re: AMBER: Amber Installation Help; link woes
(Tue Aug 08 2006 - 12:36:32 PDT)
Re: AMBER:
(Mon Aug 07 2006 - 17:37:19 PDT)
Scott Pendley
Re: AMBER: Ptraj selecting specific atoms in specific residues
(Wed Aug 16 2006 - 10:19:31 PDT)
Re: AMBER: H-bonds of peptide with water
(Mon Aug 07 2006 - 12:56:04 PDT)
Seth Lilavivat
AMBER: holding a pair of residues fixed during minimization
(Tue Aug 22 2006 - 20:22:06 PDT)
sethl.gatech.edu
AMBER: preparing ligand/rna structure for MD
(Mon Aug 28 2006 - 11:45:17 PDT)
Re: AMBER: How to create a modified NA in leap
(Sat Aug 26 2006 - 13:13:10 PDT)
AMBER: How to create a modified NA in leap
(Fri Aug 25 2006 - 13:20:35 PDT)
AMBER: how to use AddPdbAtomMap
(Thu Aug 24 2006 - 13:03:59 PDT)
AMBER: amber naming conventions for structure files
(Tue Aug 22 2006 - 14:36:56 PDT)
AMBER: help with leap
(Wed Aug 16 2006 - 16:24:42 PDT)
Shawn yy
AMBER: ptraj quasiharmonic analysis question
(Fri Aug 11 2006 - 07:45:21 PDT)
Shuting Wei
AMBER: Carnal: Internal error: stream file name 2 out of range
(Wed Aug 23 2006 - 13:43:31 PDT)
AMBER: SURFTEN in GB (mm_pbsa calculations)
(Thu Aug 03 2006 - 12:18:10 PDT)
Steve Seibold
AMBER: checkmask
(Wed Aug 16 2006 - 11:14:29 PDT)
RE: AMBER: Ptraj selecting specific atoms in specific residues
(Wed Aug 16 2006 - 10:50:16 PDT)
AMBER: Ptraj selecting specific atoms in specific residues
(Wed Aug 16 2006 - 10:05:16 PDT)
Suxin Zheng
Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system
(Fri Aug 18 2006 - 11:23:17 PDT)
AMBER: The PB GB energy from mm_pbsa will be positive on high charged system
(Wed Aug 16 2006 - 11:23:44 PDT)
Tanya Johannsen
AMBER: identical high energies
(Thu Aug 17 2006 - 19:22:40 PDT)
AMBER: any work-around for 80 character mask string limit?
(Tue Aug 01 2006 - 13:12:22 PDT)
Thomas Cheatham
RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj
(Thu Aug 31 2006 - 21:38:02 PDT)
Re: AMBER: minimization with my own charges
(Thu Aug 31 2006 - 21:07:40 PDT)
RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj
(Thu Aug 31 2006 - 14:50:33 PDT)
RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj
(Thu Aug 31 2006 - 13:49:42 PDT)
Re: AMBER: RDF output
(Wed Aug 30 2006 - 15:18:29 PDT)
Re: AMBER: Details about Gaussian basis set for Cobalt complex
(Fri Aug 25 2006 - 11:21:07 PDT)
Re: AMBER: ptraj dumpq feature/bug
(Thu Aug 24 2006 - 13:16:23 PDT)
Re: AMBER: identical high energies
(Thu Aug 17 2006 - 19:57:23 PDT)
Re: AMBER: Ptraj selecting specific atoms in specific residues
(Wed Aug 16 2006 - 10:32:24 PDT)
Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction
(Mon Aug 14 2006 - 11:42:52 PDT)
Re: AMBER: source code
(Mon Aug 14 2006 - 11:31:08 PDT)
Re: AMBER: HBOND ANALYSIS
(Thu Aug 10 2006 - 16:57:34 PDT)
Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next?
(Thu Aug 10 2006 - 15:18:00 PDT)
Re: AMBER: problems with ptraj
(Thu Aug 10 2006 - 12:25:18 PDT)
Tim Robinson
AMBER: amber 9 intel 9.1 ia64
(Tue Aug 15 2006 - 06:45:16 PDT)
Vitor Manuel Sousa F?x
AMBER: klambda
(Mon Aug 14 2006 - 03:45:10 PDT)
Vlad Cojocaru
Re: AMBER: PCA: can't complete projection
(Tue Aug 08 2006 - 07:56:49 PDT)
Re: AMBER: cutting the box after "solvatebox"
(Tue Aug 08 2006 - 05:52:39 PDT)
AMBER: cutting the box after "solvatebox"
(Tue Aug 08 2006 - 05:12:37 PDT)
Re: AMBER: ff03 and ff99SB force fields
(Fri Aug 04 2006 - 01:17:59 PDT)
Re: AMBER: PhosphoThreonine Parms for use with ff03
(Thu Aug 03 2006 - 03:07:48 PDT)
AMBER: neutral N-terminal amino-acid parameters for ff03
(Wed Aug 02 2006 - 07:21:31 PDT)
Weihua Li
Re: AMBER: Heme parameters
(Wed Aug 09 2006 - 19:44:15 PDT)
William Lianhu Wei
AMBER: GBSA EGB = NaN
(Thu Aug 17 2006 - 19:30:50 PDT)
William Wei
AMBER: Question about free energy with mm_pbsa
(Thu Aug 31 2006 - 11:50:11 PDT)
Re: AMBER: mm_pbsa_statistical.pl
(Wed Aug 30 2006 - 14:11:51 PDT)
AMBER: mm_pbsa_statistical.pl
(Tue Aug 29 2006 - 14:02:32 PDT)
Re: AMBER: nmode memory problem
(Thu Aug 24 2006 - 14:05:55 PDT)
Re: AMBER: nmode memory problem
(Thu Aug 24 2006 - 10:04:59 PDT)
AMBER: nmode memory problem
(Thu Aug 24 2006 - 08:29:13 PDT)
Re: AMBER: GBSA EGB = NaN
(Mon Aug 21 2006 - 11:00:21 PDT)
Re: AMBER: GBSA EGB = NaN
(Mon Aug 21 2006 - 09:37:47 PDT)
Re: AMBER: GBSA EGB = NaN
(Mon Aug 21 2006 - 09:04:26 PDT)
Re: AMBER: GBSA EGB = NaN
(Mon Aug 21 2006 - 09:04:36 PDT)
Re: AMBER: GBSA EGB = NaN
(Fri Aug 18 2006 - 08:12:10 PDT)
Wimal
AMBER: Problem with sander in Linux
(Mon Aug 14 2006 - 01:14:00 PDT)
Xiaojian Deng
Re: AMBER: Ignoring every other frame in a .crd trajectory in Ptraj
(Tue Aug 01 2006 - 11:02:22 PDT)
AMBER: Ignoring every other frame in a .crd trajectory in Ptraj
(Tue Aug 01 2006 - 10:55:31 PDT)
Yannick Bomble
AMBER: source code
(Mon Aug 14 2006 - 11:09:31 PDT)
Yong Duan
RE: AMBER: how to reassign charges
(Wed Aug 09 2006 - 14:26:10 PDT)
RE: AMBER: GAFF parameters: DPPC Bilayer
(Tue Aug 08 2006 - 13:42:50 PDT)
RE: AMBER: ff03 and ff99SB force fields
(Fri Aug 04 2006 - 04:58:51 PDT)
RE: AMBER: ff03 and ff99SB force fields
(Thu Aug 03 2006 - 12:29:51 PDT)
yxiong99
AMBER: about Silica's polarizability
(Thu Aug 03 2006 - 08:20:19 PDT)
AMBER: where can I find the force field paramete r for Silica
(Wed Aug 02 2006 - 12:53:33 PDT)
Zu Thur Yew
Re: AMBER: Backbone & Sidechain atoms: Definition
(Thu Aug 24 2006 - 10:32:14 PDT)
AMBER: Backbone & Sidechain atoms: Definition
(Thu Aug 24 2006 - 06:13:14 PDT)
AMBER: MMPBSA: positive energies during nmode
(Wed Aug 16 2006 - 07:15:11 PDT)
Re: AMBER: PCA: can't complete projection
(Tue Aug 08 2006 - 09:42:04 PDT)
AMBER: PCA: can't complete projection
(Tue Aug 08 2006 - 07:17:31 PDT)
Last message date
:
Sun Sep 03 2006 - 06:07:18 PDT
Archived on
: Fri Nov 22 2024 - 05:53:29 PST
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