Amber Archive Mar 2012 by author
598 messages
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Starting
Thu Mar 01 2012 - 01:00:02 PST,
Ending
Sat Mar 31 2012 - 23:30:03 PDT
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abinayar.imsc.res.in
[AMBER] Query on error :Atom does not have a type
(Fri Mar 30 2012 - 05:52:49 PDT)
[AMBER] Query on error
(Fri Mar 30 2012 - 05:39:19 PDT)
Acoot Brett
[AMBER] test failure in the AMBERTOOL installation
(Sat Mar 31 2012 - 23:26:34 PDT)
Adam Jion
Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi
(Fri Mar 30 2012 - 04:08:07 PDT)
[AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi
(Thu Mar 29 2012 - 17:05:16 PDT)
Re: [AMBER] Problems with pmemd.cuda.mpi (again!)
(Mon Mar 26 2012 - 10:25:30 PDT)
Re: [AMBER] Problems with pmemd.cuda.mpi (again!)
(Mon Mar 26 2012 - 09:13:05 PDT)
Re: [AMBER] Problems with pmemd.cuda.mpi (again!)
(Sun Mar 25 2012 - 09:58:48 PDT)
Re: [AMBER] Problems with pmemd.cuda.mpi (again!)
(Sun Mar 25 2012 - 07:34:28 PDT)
[AMBER] Problems with pmemd.cuda.mpi (again!)
(Sun Mar 25 2012 - 04:51:53 PDT)
Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs)
(Sat Mar 24 2012 - 20:28:04 PDT)
[AMBER] Problems testing pmemd.cuda.MPI
(Sat Mar 24 2012 - 19:21:02 PDT)
Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs)
(Sat Mar 24 2012 - 17:45:47 PDT)
Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs)
(Sat Mar 24 2012 - 17:12:48 PDT)
Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs)
(Sat Mar 24 2012 - 10:29:09 PDT)
Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs)
(Sat Mar 24 2012 - 09:38:16 PDT)
[AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs)
(Sat Mar 24 2012 - 06:03:58 PDT)
Re: [AMBER] Conflict between AmberTools 1.5 and Cuda
(Sat Mar 24 2012 - 04:26:21 PDT)
Re: [AMBER] Problems compiling pmemd.cuda - undefined reference to ...
(Fri Mar 23 2012 - 10:22:40 PDT)
Re: [AMBER] Conflict between AmberTools 1.5 and Cuda
(Fri Mar 23 2012 - 10:09:32 PDT)
[AMBER] Conflict between AmberTools 1.5 and Cuda
(Fri Mar 23 2012 - 08:18:55 PDT)
[AMBER] Problems compiling pmemd.cuda - undefined reference to ...
(Fri Mar 23 2012 - 07:15:28 PDT)
[AMBER] Converting Gromacs coordinate file to Amber input files for molecular dynamics
(Wed Mar 21 2012 - 10:00:23 PDT)
[AMBER] Amber 11 Compilation Error (again!)
(Wed Mar 21 2012 - 04:57:37 PDT)
Aditya Padhi
Re: [AMBER] Implicit MD run
(Tue Mar 20 2012 - 04:12:04 PDT)
Re: [AMBER] Implicit MD run
(Mon Mar 19 2012 - 22:52:57 PDT)
Re: [AMBER] Implicit MD run
(Mon Mar 19 2012 - 04:11:35 PDT)
Re: [AMBER] Implicit MD run
(Sun Mar 18 2012 - 21:30:51 PDT)
Re: [AMBER] Implicit MD run
(Fri Mar 16 2012 - 23:19:21 PDT)
Re: [AMBER] Implicit MD run
(Fri Mar 16 2012 - 22:57:20 PDT)
[AMBER] Implicit MD run
(Fri Mar 16 2012 - 21:29:00 PDT)
Adrian Roitberg
Re: [AMBER] Amber and Short Bonds
(Mon Mar 26 2012 - 17:08:47 PDT)
Re: [AMBER] Replica Exchange
(Wed Mar 14 2012 - 08:40:46 PDT)
Re: [AMBER] Extra Bonds For Water
(Tue Mar 13 2012 - 15:44:59 PDT)
Re: [AMBER] Harmonic Restraint in pmemd.cuda
(Wed Mar 07 2012 - 15:16:33 PST)
Re: [AMBER] Harmonic Restraint in pmemd.cuda
(Wed Mar 07 2012 - 15:10:07 PST)
Re: [AMBER] Velocity
(Wed Mar 07 2012 - 11:05:50 PST)
Agostino Bruno
Re: [AMBER] Segmentation fault
(Thu Mar 29 2012 - 01:06:09 PDT)
[AMBER] Segmentation fault
(Wed Mar 28 2012 - 08:33:15 PDT)
akshar bhosale
Re: [AMBER] slow : amber job
(Sat Mar 03 2012 - 19:21:33 PST)
Re: [AMBER] slow : amber job
(Sat Mar 03 2012 - 10:26:45 PST)
Re: [AMBER] slow : amber job
(Fri Mar 02 2012 - 19:14:20 PST)
[AMBER] slow : amber job
(Thu Mar 01 2012 - 09:44:09 PST)
Albert
Re: [AMBER] RED resp step failed
(Wed Mar 07 2012 - 22:24:46 PST)
[AMBER] how to keep atom restrained in R.E.D?
(Tue Mar 06 2012 - 22:45:37 PST)
[AMBER] RED resp step failed
(Tue Mar 06 2012 - 11:38:11 PST)
Alex Rodriguez
Re: [AMBER] Converting Gromacs coordinate file to Amber input files for molecular dynamics
(Wed Mar 21 2012 - 10:13:23 PDT)
Re: [AMBER] is GB/SA suitable for nonaqueous solvent?
(Mon Mar 19 2012 - 10:25:15 PDT)
Re: [AMBER] Replica Exchange
(Wed Mar 14 2012 - 08:32:40 PDT)
amir abbasi
[AMBER] both parallel and serial
(Wed Mar 14 2012 - 06:57:34 PDT)
Re: [AMBER] Base stacking
(Thu Mar 08 2012 - 11:10:11 PST)
Re: [AMBER] Base stacking
(Thu Mar 08 2012 - 10:11:12 PST)
[AMBER] Base stacking
(Thu Mar 08 2012 - 03:13:51 PST)
[AMBER] performance dependency on OS
(Tue Mar 06 2012 - 02:41:18 PST)
Re: [AMBER] md sticking!
(Sat Mar 03 2012 - 04:37:25 PST)
amirhossein taghavi
Re: [AMBER] Base stacking
(Fri Mar 09 2012 - 07:33:51 PST)
Re: [AMBER] Base stacking
(Thu Mar 08 2012 - 09:18:27 PST)
Re: [AMBER] Base stacking
(Thu Mar 08 2012 - 09:17:06 PST)
Andrew Petersen
[AMBER] Amber11 Intel compiler version 12 make parallel fail
(Fri Mar 09 2012 - 14:34:32 PST)
Andy Ballard
[AMBER] turning off solute-solvent interactions
(Mon Mar 05 2012 - 13:22:17 PST)
[AMBER] using GAFF with TIP3P model for simulation of solvated organic molecule
(Sun Mar 04 2012 - 12:19:22 PST)
Re: [AMBER] Help with solvating organic molecule with input .prmtop file
(Thu Mar 01 2012 - 09:28:23 PST)
Anselm Horn
[AMBER] ptraj: SegFault during SOM clustering
(Fri Mar 30 2012 - 09:47:34 PDT)
Antonija Tomić
[AMBER] MM-PBSA: different dielectric constants for ligand and receptor?
(Mon Mar 05 2012 - 02:07:38 PST)
Aron Broom
Re: [AMBER] Asking About Differences between amber force field ff10 and ff03
(Fri Mar 30 2012 - 07:21:30 PDT)
Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi
(Thu Mar 29 2012 - 17:35:33 PDT)
Re: [AMBER] GTX680
(Wed Mar 28 2012 - 15:11:26 PDT)
Re: [AMBER] GTX680
(Wed Mar 28 2012 - 10:45:45 PDT)
Re: [AMBER] GTX680
(Wed Mar 28 2012 - 10:30:30 PDT)
Re: [AMBER] GTX680
(Wed Mar 28 2012 - 09:54:11 PDT)
Re: [AMBER] ABMD in pmemd.cuda in AMBER 12
(Mon Mar 26 2012 - 10:39:36 PDT)
Re: [AMBER] on the AMBER advanced tutorial 3 MM-PBSA
(Sat Mar 17 2012 - 11:40:25 PDT)
Re: [AMBER] Implicit MD run
(Fri Mar 16 2012 - 23:06:13 PDT)
Re: [AMBER] Implicit MD run
(Fri Mar 16 2012 - 22:53:08 PDT)
Re: [AMBER] MMPBSA
(Tue Mar 13 2012 - 10:13:04 PDT)
Re: [AMBER] saltconc and string parameters in MM/PB(GB)SA
(Thu Mar 08 2012 - 11:21:44 PST)
Re: [AMBER] How to convert multiple mdcrd files to single files with minimium size?
(Thu Mar 08 2012 - 08:08:47 PST)
Re: [AMBER] Harmonic Restraint in pmemd.cuda
(Wed Mar 07 2012 - 15:14:40 PST)
[AMBER] Harmonic Restraint in pmemd.cuda
(Wed Mar 07 2012 - 15:01:37 PST)
Re: [AMBER] Assignment of partial charge to a molecule
(Tue Mar 06 2012 - 10:18:47 PST)
Re: [AMBER] slow : amber job
(Sat Mar 03 2012 - 20:03:51 PST)
Re: [AMBER] PDB trajectory format
(Sat Mar 03 2012 - 08:45:16 PST)
Re: [AMBER] top and crd file error
(Thu Mar 01 2012 - 23:34:47 PST)
Re: [AMBER] top and crd file error
(Thu Mar 01 2012 - 23:13:01 PST)
Re: [AMBER] ABMD in pmemd.cuda in AMBER 12
(Thu Mar 01 2012 - 10:45:37 PST)
[AMBER] ABMD in pmemd.cuda in AMBER 12
(Thu Mar 01 2012 - 10:08:52 PST)
Re: [AMBER] slow : amber job
(Thu Mar 01 2012 - 10:02:55 PST)
Aronica, Pietro
Re: [AMBER] Amber and Short Bonds
(Tue Mar 27 2012 - 05:24:43 PDT)
Re: [AMBER] Amber and Short Bonds
(Mon Mar 26 2012 - 17:02:02 PDT)
Re: [AMBER] Amber and Short Bonds
(Mon Mar 26 2012 - 16:18:35 PDT)
Re: [AMBER] Amber and Short Bonds
(Mon Mar 26 2012 - 10:05:41 PDT)
[AMBER] Amber and Short Bonds
(Mon Mar 26 2012 - 08:04:45 PDT)
Ashutosh Shandilya
Re: [AMBER] Problem in creating topology of NAD
(Thu Mar 01 2012 - 22:55:25 PST)
[AMBER] Problem in creating topology of NAD
(Thu Mar 01 2012 - 22:50:06 PST)
ashwini gupta
Re: [AMBER] atom type of Sulphur in CYS/CYM (MCPB)
(Sun Mar 25 2012 - 21:33:53 PDT)
[AMBER] atom type of Sulphur in CYS/CYM (MCPB)
(Thu Mar 22 2012 - 23:39:03 PDT)
[AMBER] Non - integral charge o unperturbed unit
(Thu Mar 22 2012 - 03:08:44 PDT)
Re: [AMBER] Water coordinated with transition metal
(Wed Mar 21 2012 - 04:40:32 PDT)
Re: [AMBER] Water coordinated with transition metal
(Wed Mar 21 2012 - 03:33:29 PDT)
Re: [AMBER] Water coordinated with transition metal
(Wed Mar 21 2012 - 02:09:04 PDT)
[AMBER] Water coordinated with transition metal
(Tue Mar 20 2012 - 23:36:40 PDT)
Bala Subramani
Re: [AMBER] how to measure atom distance in md trajectories using ptraj program
(Wed Mar 28 2012 - 11:25:41 PDT)
[AMBER] how to measure atom distance in md trajectories using ptraj program
(Wed Mar 28 2012 - 10:26:21 PDT)
Bala subramanian
Re: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues
(Mon Mar 26 2012 - 12:05:29 PDT)
[AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues
(Mon Mar 26 2012 - 08:23:49 PDT)
BALASUBRAMANI G L
[AMBER] how to merge 10 trajectory files
(Wed Mar 28 2012 - 21:35:42 PDT)
Beale, John
[AMBER] SASA Plot
(Tue Mar 06 2012 - 03:08:06 PST)
Re: [AMBER] Distance plot
(Fri Mar 02 2012 - 06:50:18 PST)
[AMBER] Distance plot
(Fri Mar 02 2012 - 05:57:35 PST)
Ben Ahmady
Re: [AMBER] Best way to implement PBC
(Wed Mar 07 2012 - 07:26:35 PST)
Ben Roberts
Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi
(Thu Mar 29 2012 - 17:38:00 PDT)
Re: [AMBER] Segmentation fault
(Thu Mar 29 2012 - 02:37:53 PDT)
Re: [AMBER] how to merge 10 trajectory files
(Wed Mar 28 2012 - 21:42:41 PDT)
Re: [AMBER] Segmentation fault
(Wed Mar 28 2012 - 13:22:06 PDT)
Re: [AMBER] MP2 for RESP
(Mon Mar 26 2012 - 13:26:07 PDT)
Re: [AMBER] Problems testing pmemd.cuda.MPI
(Sun Mar 25 2012 - 16:14:18 PDT)
Re: [AMBER] atom type of Sulphur in CYS/CYM (MCPB)
(Sun Mar 25 2012 - 11:02:04 PDT)
Re: [AMBER] Water coordinated with transition metal
(Wed Mar 21 2012 - 03:41:10 PDT)
Re: [AMBER] Water coordinated with transition metal
(Wed Mar 21 2012 - 02:40:50 PDT)
Re: [AMBER] Water coordinated with transition metal
(Wed Mar 21 2012 - 00:21:35 PDT)
Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW
(Mon Mar 19 2012 - 01:30:42 PDT)
Re: [AMBER] asking about mden
(Sun Mar 11 2012 - 23:35:11 PDT)
Bill Miller III
Re: [AMBER] error in nmode calculations
(Wed Mar 28 2012 - 12:05:14 PDT)
Re: [AMBER] on the AMBER advanced tutorial 3 MM-PBSA
(Sat Mar 17 2012 - 11:19:03 PDT)
bin wang
Re: [AMBER] How to calculate the energy contributed by hydrogen bonds?
(Wed Mar 21 2012 - 20:58:22 PDT)
Re: [AMBER] How to calculate the energy contributed by hydrogen bonds?
(Tue Mar 20 2012 - 07:17:29 PDT)
[AMBER] How to calculate the energy contributed by hydrogen bonds?
(Mon Mar 19 2012 - 14:00:51 PDT)
Brian Radak
Re: [AMBER] AMBER force calculations
(Fri Mar 16 2012 - 13:10:53 PDT)
Re: [AMBER] puting restrains
(Thu Mar 15 2012 - 06:59:11 PDT)
Re: [AMBER] AM1
(Wed Mar 07 2012 - 07:33:33 PST)
Re: [AMBER] turning off solute-solvent interactions
(Mon Mar 05 2012 - 14:01:27 PST)
Re: [AMBER] Alkali and Halide Monovalent Ion : paper
(Mon Mar 05 2012 - 09:28:40 PST)
Re: [AMBER] AMBER force calculations
(Fri Mar 02 2012 - 06:47:43 PST)
Brian Wolfe
Re: [AMBER] NAB segmentation fault
(Tue Mar 20 2012 - 17:34:19 PDT)
Bruno Luís Pinto de Oliveira
Re: [AMBER] SASA Plot
(Tue Mar 06 2012 - 07:00:49 PST)
c00jsw00.nchc.narl.org.tw
Re: [AMBER] covert CHARMM format PDB file to AMBER formart
(Wed Mar 07 2012 - 03:11:32 PST)
Cannon, John F.
Re: [AMBER] error in nmode calculations
(Wed Mar 28 2012 - 13:11:03 PDT)
Re: [AMBER] MMPB(GB)SA: two questions
(Mon Mar 05 2012 - 05:37:16 PST)
Re: [AMBER] Distance plot
(Fri Mar 02 2012 - 06:42:27 PST)
Re: [AMBER] slow : amber job
(Thu Mar 01 2012 - 10:27:29 PST)
caobb0214
Re: [AMBER] glycine sidechain contribution in MM-GBSA decompostion
(Mon Mar 26 2012 - 18:56:22 PDT)
[AMBER] glycine sidechain contribution in MM-GBSA decompostion
(Mon Mar 26 2012 - 18:05:04 PDT)
Carlos Simmerling
Re: [AMBER] Large Energy Jump in TMD simulation - Regarding
(Fri Mar 30 2012 - 08:57:53 PDT)
Re: [AMBER] Large Energy Jump in TMD simulation - Regarding
(Fri Mar 30 2012 - 06:41:13 PDT)
Re: [AMBER] Large Energy Jump in TMD simulation - Regarding
(Fri Mar 30 2012 - 05:52:35 PDT)
Re: [AMBER] AmberGS forcefield
(Tue Mar 27 2012 - 08:17:19 PDT)
Re: [AMBER] glycine sidechain contribution in MM-GBSA decompostion
(Tue Mar 27 2012 - 03:01:13 PDT)
Re: [AMBER] glycine sidechain contribution in MM-GBSA decompostion
(Mon Mar 26 2012 - 18:08:33 PDT)
Re: [AMBER] GBSA - surface tension question for calculation of ΔGnonpolar
(Wed Mar 21 2012 - 04:08:30 PDT)
Re: [AMBER] GBSA - surface tension question for calculation of ΔGnonpolar
(Tue Mar 20 2012 - 10:44:37 PDT)
Re: [AMBER] Implicit MD run
(Tue Mar 20 2012 - 04:02:13 PDT)
Re: [AMBER] Implicit MD run
(Mon Mar 19 2012 - 05:42:34 PDT)
Re: [AMBER] Implicit MD run
(Mon Mar 19 2012 - 03:30:27 PDT)
Re: [AMBER] is GB/SA suitable for nonaqueous solvent?
(Sun Mar 18 2012 - 07:25:35 PDT)
Re: [AMBER] Implicit MD run
(Sat Mar 17 2012 - 04:20:00 PDT)
Re: [AMBER] Replica Exchange
(Wed Mar 14 2012 - 08:29:16 PDT)
Re: [AMBER] MMGBSA residue-wise decomposition
(Wed Mar 14 2012 - 06:05:01 PDT)
[AMBER] April 3 deadline for application for ACS computational chemistry awards for the Fall 2012 national meeting
(Mon Mar 12 2012 - 10:02:19 PDT)
Re: [AMBER] Question about Simulated Annealing procedure
(Mon Mar 05 2012 - 05:19:43 PST)
Re: [AMBER] implicit and explicit
(Sun Mar 04 2012 - 04:35:12 PST)
Re: [AMBER] slow : amber job
(Sat Mar 03 2012 - 10:35:22 PST)
Carlos Sosa
Re: [AMBER] mpi-allreduce in AMBER11
(Fri Mar 16 2012 - 09:36:59 PDT)
[AMBER] mpi-allreduce in AMBER11
(Fri Mar 16 2012 - 06:23:16 PDT)
case
Re: [AMBER] NAB segmentation fault
(Tue Mar 20 2012 - 18:26:52 PDT)
Re: [AMBER] Problems with tetrahedral Al in antechamber
(Mon Mar 19 2012 - 05:11:32 PDT)
Re: [AMBER] Question about output files
(Wed Mar 07 2012 - 14:59:08 PST)
Re: [AMBER] SHAKE not available for parallel runs
(Wed Mar 07 2012 - 14:55:54 PST)
Re: [AMBER] covert CHARMM format PDB file to AMBER formart
(Wed Mar 07 2012 - 05:09:19 PST)
Re: [AMBER] Residual Dipolar Coupling
(Wed Mar 07 2012 - 05:04:23 PST)
Catein Catherine
[AMBER] Is it possible to cluster several mdcrd files based on a dihedral angles of a particular residues?
(Thu Mar 15 2012 - 07:16:56 PDT)
[AMBER] How to convert multiple mdcrd files to single files with minimium size?
(Thu Mar 08 2012 - 07:47:26 PST)
CHAMI F.
Re: [AMBER] Use of SLEF1 force field in Amber
(Wed Mar 14 2012 - 11:52:05 PDT)
Re: [AMBER] Dihedral analysis
(Thu Mar 08 2012 - 08:47:45 PST)
[AMBER] SHAKE not available for parallel runs
(Wed Mar 07 2012 - 12:30:51 PST)
Re: [AMBER] Alkali and Halide Monovalent Ion : paper
(Tue Mar 06 2012 - 07:27:17 PST)
[AMBER] Alkali and Halide Monovalent Ion : paper
(Mon Mar 05 2012 - 09:18:17 PST)
Chris Bryant
[AMBER] Defining sulfonyl halide atom type
(Fri Mar 02 2012 - 09:03:08 PST)
Daniel Roe
Re: [AMBER] ptraj removes my ligands
(Fri Mar 30 2012 - 11:36:23 PDT)
Re: [AMBER] how to measure atom distance in md trajectories using ptraj program
(Wed Mar 28 2012 - 12:37:04 PDT)
Re: [AMBER] how to measure atom distance in md trajectories using ptraj program
(Wed Mar 28 2012 - 10:33:39 PDT)
Re: [AMBER] ptraj removes my ligands
(Mon Mar 26 2012 - 21:10:01 PDT)
Re: [AMBER] cpptraj hbond
(Mon Mar 26 2012 - 12:06:57 PDT)
Re: [AMBER] Problems compiling pmemd.cuda - undefined reference to ...
(Fri Mar 23 2012 - 11:10:19 PDT)
Re: [AMBER] Conflict between AmberTools 1.5 and Cuda
(Fri Mar 23 2012 - 09:16:55 PDT)
Re: [AMBER] PDB trajectory format
(Fri Mar 16 2012 - 09:30:34 PDT)
Re: [AMBER] PDB trajectory format
(Fri Mar 16 2012 - 08:43:20 PDT)
Re: [AMBER] PDB trajectory format
(Thu Mar 15 2012 - 09:46:40 PDT)
Re: [AMBER] Amber10 parallel installation test example run error
(Thu Mar 15 2012 - 03:16:25 PDT)
Re: [AMBER] Hydrogen bond analysis
(Fri Mar 09 2012 - 04:34:41 PST)
Re: [AMBER] SASA Plot
(Wed Mar 07 2012 - 09:27:56 PST)
Re: [AMBER] cpptraj surf Segmentation fault
(Wed Mar 07 2012 - 08:12:46 PST)
Re: [AMBER] SASA Plot
(Tue Mar 06 2012 - 04:05:16 PST)
Re: [AMBER] PDB trajectory format
(Sat Mar 03 2012 - 10:53:39 PST)
David A Case
Re: [AMBER] Issue with running sander
(Fri Mar 30 2012 - 09:39:47 PDT)
Re: [AMBER] Asking About Differences between amber force field ff10 and ff03
(Fri Mar 30 2012 - 09:27:54 PDT)
Re: [AMBER] Fwd: V limit
(Thu Mar 29 2012 - 13:20:05 PDT)
Re: [AMBER] Fwd: V limit
(Thu Mar 29 2012 - 09:18:59 PDT)
Re: [AMBER] rfree: Error decoding variable 1 3 from:
(Thu Mar 29 2012 - 07:47:25 PDT)
Re: [AMBER] Conflict between AmberTools 1.5 and Cuda
(Fri Mar 23 2012 - 11:11:32 PDT)
Re: [AMBER] Amber10 parallel installation test example
(Fri Mar 23 2012 - 05:21:38 PDT)
Re: [AMBER] Is it possible to just calculate translational and rotational entropy?
(Thu Mar 22 2012 - 05:23:10 PDT)
Re: [AMBER] Problem in Amber installation
(Thu Mar 22 2012 - 05:18:32 PDT)
Re: [AMBER] About ANAL problem: Amber
(Thu Mar 22 2012 - 05:14:10 PDT)
Re: [AMBER] About ANAL problem: Amber
(Wed Mar 21 2012 - 04:55:01 PDT)
Re: [AMBER] Fast ibelly?
(Tue Mar 20 2012 - 13:22:15 PDT)
Re: [AMBER] Amber 10 parallel installation error
(Fri Mar 16 2012 - 05:20:17 PDT)
Re: [AMBER] antechamber error
(Fri Mar 16 2012 - 05:16:22 PDT)
Re: [AMBER] rigid body simulation
(Thu Mar 15 2012 - 12:30:40 PDT)
Re: [AMBER] Amber10 parallel installation test error
(Thu Mar 15 2012 - 12:29:09 PDT)
Re: [AMBER] binding free energy
(Thu Mar 15 2012 - 05:51:43 PDT)
Re: [AMBER] separated thermostat in AMBER
(Fri Mar 09 2012 - 06:54:24 PST)
Re: [AMBER] Dedication from Ibrahim - Manchester/Minia
(Wed Mar 07 2012 - 12:01:38 PST)
Re: [AMBER-Developers] [AMBER] Alkali and Halide Monovalent Ion : paper
(Tue Mar 06 2012 - 09:42:15 PST)
Re: [AMBER] Error in amber output files
(Tue Mar 06 2012 - 04:50:08 PST)
Re: [AMBER] ./nab -c dna3.nab,nab2c failed!
(Mon Mar 05 2012 - 06:54:20 PST)
Re: [AMBER] Free Energy Calculate
(Mon Mar 05 2012 - 05:24:28 PST)
Re: [AMBER] MM-PBSA: different dielectric constants for ligand and receptor?
(Mon Mar 05 2012 - 05:20:10 PST)
Re: [AMBER] different residues use different force to restrict
(Mon Mar 05 2012 - 05:15:04 PST)
Re: [AMBER] problem with MMPBSA script
(Thu Mar 01 2012 - 05:14:41 PST)
Re: [AMBER] MMPBSA and explicit ions: what should I do?
(Thu Mar 01 2012 - 05:11:42 PST)
David A. Case
Re: [AMBER] error in nmode calculations
(Thu Mar 29 2012 - 06:09:53 PDT)
Re: [AMBER] COM
(Wed Mar 28 2012 - 12:25:45 PDT)
Re: [AMBER] COM
(Wed Mar 28 2012 - 07:53:38 PDT)
Re: [AMBER] About ANAL
(Sun Mar 25 2012 - 07:47:38 PDT)
Re: [AMBER] Energy and Coordinate Outputs
(Wed Mar 14 2012 - 14:49:53 PDT)
Re: [AMBER] binding free energy
(Wed Mar 14 2012 - 14:49:23 PDT)
Re: [AMBER] binding free energy
(Wed Mar 14 2012 - 14:16:20 PDT)
Re: [AMBER] Energy and Coordinate Outputs
(Wed Mar 14 2012 - 14:15:58 PDT)
Re: [AMBER] NAB segmentation fault
(Tue Mar 13 2012 - 00:28:08 PDT)
Re: [AMBER] NAB segmentation fault
(Sun Mar 11 2012 - 10:57:16 PDT)
Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint."
(Sun Mar 11 2012 - 10:54:23 PDT)
Re: [AMBER] Energy and Coordinate Outputs
(Sat Mar 10 2012 - 10:13:00 PST)
David Case
Re: [AMBER] Amber11 Intel compiler version 12 make parallel fail
(Fri Mar 09 2012 - 17:44:03 PST)
Re: [AMBER] Energy and Coordinate Outputs
(Fri Mar 09 2012 - 17:37:45 PST)
David Condon
Re: [AMBER] AMBER force calculations
(Fri Mar 16 2012 - 13:30:45 PDT)
Re: [AMBER] AMBER force calculations
(Fri Mar 16 2012 - 13:03:29 PDT)
[AMBER] AMBER force calculations
(Fri Mar 02 2012 - 06:25:10 PST)
David Minh
Re: [AMBER] Fast ibelly?
(Wed Mar 21 2012 - 07:22:59 PDT)
Re: [AMBER] Fast ibelly?
(Tue Mar 20 2012 - 11:10:15 PDT)
[AMBER] Fast ibelly?
(Tue Mar 20 2012 - 08:29:00 PDT)
[AMBER] PB with inp=2 doesn't recognize ff10 atom types?
(Sat Mar 17 2012 - 11:10:45 PDT)
Re: [AMBER] Energy and Coordinate Outputs
(Sat Mar 17 2012 - 05:03:28 PDT)
Re: [AMBER] Energy and Coordinate Outputs
(Mon Mar 12 2012 - 08:55:38 PDT)
Re: [AMBER] Energy and Coordinate Outputs
(Fri Mar 09 2012 - 18:26:39 PST)
[AMBER] Energy and Coordinate Outputs
(Fri Mar 09 2012 - 13:47:53 PST)
Dean Cuebas
Re: [AMBER] is GB/SA suitable for nonaqueous solvent?
(Mon Mar 19 2012 - 09:51:28 PDT)
DENILSON FERREIRA DE OLIVEIRA
[AMBER] ptraj removes my ligands
(Mon Mar 26 2012 - 19:22:48 PDT)
Dmitry Mukha
Re: [AMBER] Replica Exchange
(Tue Mar 13 2012 - 13:34:23 PDT)
Re: [AMBER] MMPBSA
(Tue Mar 13 2012 - 13:15:21 PDT)
Re: [AMBER] MMPBSA
(Tue Mar 13 2012 - 12:19:19 PDT)
Dmitry Osolodkin
Re: [AMBER] PDB trajectory format
(Fri Mar 16 2012 - 09:11:26 PDT)
Re: [AMBER] PDB trajectory format
(Fri Mar 16 2012 - 08:08:48 PDT)
Re: [AMBER] PDB trajectory format
(Thu Mar 15 2012 - 09:15:21 PDT)
[AMBER] PDB trajectory format
(Sat Mar 03 2012 - 08:10:46 PST)
Elisa Frezza
Re: [AMBER] rfree: Error decoding variable 1 3 from:
(Thu Mar 29 2012 - 06:46:30 PDT)
[AMBER] rfree: Error decoding variable 1 3 from:
(Thu Mar 29 2012 - 06:04:47 PDT)
Re: [AMBER] amber12
(Tue Mar 27 2012 - 05:35:44 PDT)
[AMBER] angle restraint
(Tue Mar 27 2012 - 02:28:46 PDT)
[AMBER] amber12
(Mon Mar 26 2012 - 02:26:39 PDT)
Enrico Caldarulo
[AMBER] tleap and water molecules
(Tue Mar 13 2012 - 03:05:36 PDT)
Fati
[AMBER] simulation with metal-containing ligands
(Thu Mar 15 2012 - 05:01:04 PDT)
Fenley, Andrew
Re: [AMBER] GTX680
(Wed Mar 28 2012 - 19:33:53 PDT)
Fernando Blanco
[AMBER] MMPBSA, in parallel?
(Fri Mar 16 2012 - 05:30:17 PDT)
filip fratev
[AMBER] GTX680
(Fri Mar 23 2012 - 11:37:02 PDT)
Re: [AMBER] Question about Simulated Annealing procedure
(Mon Mar 05 2012 - 06:08:35 PST)
[AMBER] Question about Simulated Annealing procedure
(Sun Mar 04 2012 - 18:29:13 PST)
francesco oteri
Re: [AMBER] Base stacking
(Thu Mar 08 2012 - 11:00:49 PST)
Re: [AMBER] Viewing with VMD bonds set by the "bond" command
(Thu Mar 08 2012 - 06:27:46 PST)
Francesco Pietra
[AMBER] Fwd: vmd-l: Re: Viewing with VMD bonds set by the "bond" command
(Thu Mar 08 2012 - 23:39:17 PST)
Re: [AMBER] Viewing with VMD bonds set by the "bond" command
(Thu Mar 08 2012 - 10:27:58 PST)
Re: [AMBER] Viewing with VMD bonds set by the "bond" command
(Thu Mar 08 2012 - 03:30:29 PST)
Re: [AMBER] Viewing with VMD bonds set by the "bond" command
(Thu Mar 08 2012 - 03:01:34 PST)
Re: [AMBER] Viewing with VMD bonds set by the "bond" command
(Thu Mar 08 2012 - 01:48:48 PST)
[AMBER] Viewing with VMD bonds set by the "bond" command
(Wed Mar 07 2012 - 23:59:23 PST)
Fredrick Devadoss
Re: [AMBER] Large Energy Jump in TMD simulation - Regarding
(Fri Mar 30 2012 - 15:15:50 PDT)
Re: [AMBER] Large Energy Jump in TMD simulation - Regarding
(Fri Mar 30 2012 - 11:06:02 PDT)
Re: [AMBER] Large Energy Jump in TMD simulation - Regarding
(Fri Mar 30 2012 - 06:49:21 PDT)
Re: [AMBER] Large Energy Jump in TMD simulation - Regarding
(Fri Mar 30 2012 - 06:34:11 PDT)
[AMBER] Large Energy Jump in TMD simulation - Regarding
(Fri Mar 30 2012 - 05:19:56 PDT)
FyD
Re: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues
(Tue Mar 27 2012 - 06:30:52 PDT)
Re: [AMBER] assignment of partial charge to fullerene2160
(Tue Mar 27 2012 - 05:55:04 PDT)
Re: [AMBER] parameters for Lys-sugar P2N file
(Mon Mar 26 2012 - 05:47:17 PDT)
Re: [AMBER] parameters for Lys-sugar
(Sat Mar 24 2012 - 01:14:17 PDT)
Re: [AMBER] parameters for Lys-sugar
(Fri Mar 23 2012 - 09:11:51 PDT)
Re: [AMBER] parameters for Lys-sugar
(Fri Mar 23 2012 - 08:06:35 PDT)
Re: [AMBER] esp and resp comparison
(Fri Mar 23 2012 - 08:01:27 PDT)
Re: [AMBER] Non - integral charge o unperturbed unit
(Fri Mar 23 2012 - 07:58:26 PDT)
Re: [AMBER] charges for ion and surrounding residues at the active site
(Wed Mar 21 2012 - 00:02:44 PDT)
Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW
(Tue Mar 20 2012 - 09:26:58 PDT)
Re: [AMBER] charges for ion and surrounding residues at the active site
(Tue Mar 20 2012 - 04:55:07 PDT)
Re: [AMBER] Viewing with VMD bonds set by the "bond" command
(Fri Mar 09 2012 - 10:10:27 PST)
Re: [AMBER] Viewing with VMD bonds set by the "bond" command
(Thu Mar 08 2012 - 03:48:31 PST)
Re: [AMBER] Viewing with VMD bonds set by the "bond" command
(Thu Mar 08 2012 - 03:22:40 PST)
Re: [AMBER] [q4md-fft] Re: RED resp step failed
(Wed Mar 07 2012 - 23:30:59 PST)
Re: [AMBER] [q4md-fft] how to keep atom restrained in R.E.D?
(Wed Mar 07 2012 - 01:01:44 PST)
Re: [AMBER] Modified phosphotyrosine parameters
(Tue Mar 06 2012 - 02:18:37 PST)
Re: [AMBER] Parameters
(Tue Mar 06 2012 - 01:48:22 PST)
Re: [AMBER] ATP minimization
(Tue Mar 06 2012 - 01:17:28 PST)
Re: [AMBER] Defining sulfonyl halide atom type
(Sat Mar 03 2012 - 10:39:04 PST)
Re: [AMBER] Problem in creating topology of NAD
(Thu Mar 01 2012 - 23:18:29 PST)
Re: [AMBER] Problem in creating topology of NAD
(Thu Mar 01 2012 - 23:05:26 PST)
g t
Re: [AMBER] problem in output file of the awk script in tutorial A6
(Thu Mar 22 2012 - 00:24:30 PDT)
Re: [AMBER] Test if MD converged or not.
(Thu Mar 22 2012 - 00:14:36 PDT)
Re: [AMBER] GBSA - surface tension question for calculation of ΔGnonpolar
(Wed Mar 21 2012 - 23:18:34 PDT)
Re: [AMBER] GBSA - surface tension question for calculation of ΔGnonpolar
(Tue Mar 20 2012 - 16:02:06 PDT)
[AMBER] GBSA - surface tension question for calculation of ΔGnonpolar
(Tue Mar 20 2012 - 10:34:48 PDT)
Re: [AMBER] ptraj: Sort trajectory based on protein-ligand distance
(Wed Mar 14 2012 - 11:37:31 PDT)
Re: [AMBER] Dihedral analysis
(Tue Mar 13 2012 - 10:41:45 PDT)
Re: [AMBER] How to get the information of hydrophobic contact?
(Tue Mar 13 2012 - 10:39:44 PDT)
Re: [AMBER] mm_pbsa error: Flag "RADII" not found in PARM file
(Thu Mar 01 2012 - 08:32:45 PST)
Re: [AMBER] mm_pbsa error: Flag "RADII" not found in PARM file
(Thu Mar 01 2012 - 06:59:07 PST)
Re: [AMBER] mm_pbsa error: Flag "RADII" not found in PARM file
(Thu Mar 01 2012 - 06:40:24 PST)
gargi borgohai
[AMBER] assignment of partial charge to fullerene2160
(Tue Mar 27 2012 - 00:15:21 PDT)
[AMBER] Assignment of partial charge to a molecule
(Tue Mar 06 2012 - 10:05:07 PST)
George Tzotzos
Re: [AMBER] cpptraj hbond
(Mon Mar 26 2012 - 12:10:43 PDT)
Re: [AMBER] cpptraj hbond
(Mon Mar 26 2012 - 11:13:55 PDT)
[AMBER] cpptraj hbond
(Mon Mar 26 2012 - 07:26:28 PDT)
Re: [AMBER] ptraj atomicfluct
(Sat Mar 24 2012 - 14:54:48 PDT)
[AMBER] ptraj atomicfluct
(Sat Mar 24 2012 - 14:12:11 PDT)
Re: [AMBER] disulfide bond warnings
(Tue Mar 20 2012 - 16:19:41 PDT)
[AMBER] disulfide bond warnings
(Tue Mar 20 2012 - 11:30:29 PDT)
Re: [AMBER] MMPBSA.py - Internal energy
(Fri Mar 16 2012 - 12:13:40 PDT)
[AMBER] MMPBSA.py - Internal energy
(Fri Mar 16 2012 - 11:58:40 PDT)
[AMBER] Amber for Cuda on Mac OSX
(Fri Mar 16 2012 - 07:35:38 PDT)
Re: [AMBER] MMPBSA
(Tue Mar 13 2012 - 13:43:36 PDT)
Re: [AMBER] MMPBSA
(Tue Mar 13 2012 - 12:28:12 PDT)
Re: [AMBER] MMPBSA
(Tue Mar 13 2012 - 10:26:43 PDT)
[AMBER] MMPBSA
(Tue Mar 13 2012 - 10:08:47 PDT)
[AMBER] MMPBSA
(Tue Mar 13 2012 - 10:06:14 PDT)
[AMBER] Mac OSX 10.7
(Thu Mar 08 2012 - 11:05:05 PST)
Re: [AMBER] MMPB(GB)SA: two questions
(Mon Mar 05 2012 - 09:23:06 PST)
[AMBER] MMPB(GB)SA: two questions
(Sat Mar 03 2012 - 05:05:05 PST)
Giovanni Pavan
[AMBER] R: tleap and water molecules
(Tue Mar 13 2012 - 03:19:05 PDT)
Gonzalo Jimenez
[AMBER] Problems with tetrahedral Al in antechamber
(Mon Mar 19 2012 - 02:16:35 PDT)
[AMBER] Problems with tetrahedral Al in antechamber
(Mon Mar 19 2012 - 01:44:19 PDT)
Re: [AMBER] Use of SLEF1 force field in Amber
(Wed Mar 14 2012 - 16:40:40 PDT)
[AMBER] Use of SLEF1 force field in Amber
(Tue Mar 13 2012 - 00:56:54 PDT)
Gould, Ian R
Re: [AMBER] GPU performance and GPU Direct
(Wed Mar 07 2012 - 06:14:08 PST)
Guillermo Mulliert Carlín
[AMBER] cpptraj surf Segmentation fault
(Wed Mar 07 2012 - 07:51:07 PST)
Gurunath Katagi
[AMBER] amber parameters for cytochrome c
(Thu Mar 22 2012 - 19:42:03 PDT)
Hannes Loeffler
[AMBER] Announcement: Large biomolecule benchmark report
(Thu Mar 15 2012 - 05:50:10 PDT)
Ibrahim Moustafa
Re: [AMBER] Dihedral analysis
(Thu Mar 08 2012 - 08:06:33 PST)
[AMBER] Dihedral analysis
(Wed Mar 07 2012 - 10:05:00 PST)
Ilya Belalov
[AMBER] Modified phosphotyrosine parameters
(Mon Mar 05 2012 - 17:32:44 PST)
Ilyas Yildirim
Re: [AMBER] rigid body simulation
(Thu Mar 15 2012 - 12:36:48 PDT)
Re: [AMBER] Base stacking
(Thu Mar 08 2012 - 10:39:13 PST)
Indrajit Deb
Re: [AMBER] Replica Exchange
(Wed Mar 14 2012 - 08:29:19 PDT)
Ismail, Mohd F.
Re: [AMBER] External Force Method in pmemd.cuda
(Wed Mar 21 2012 - 10:46:59 PDT)
[AMBER] External Force Method in pmemd.cuda
(Wed Mar 21 2012 - 10:28:43 PDT)
Re: [AMBER] Force Field Parameterization -- Torsion Potentials
(Thu Mar 15 2012 - 22:31:02 PDT)
Re: [AMBER] Force Field Parameterization -- Torsion Potentials
(Tue Mar 13 2012 - 15:14:08 PDT)
Re: [AMBER] Force Field Parameterization -- Torsion Potentials
(Tue Mar 13 2012 - 15:08:48 PDT)
Re: [AMBER] RED resp step failed
(Tue Mar 06 2012 - 13:41:45 PST)
Jacopo Sgrignani
Re: [AMBER] AM1
(Wed Mar 07 2012 - 23:23:57 PST)
[AMBER] AM1
(Wed Mar 07 2012 - 03:17:51 PST)
Jan-Philip Gehrcke
Re: [AMBER] Conflict between AmberTools 1.5 and Cuda
(Sat Mar 24 2012 - 05:23:38 PDT)
Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint."
(Fri Mar 09 2012 - 06:28:38 PST)
[AMBER] non-linear PB solver within MMPBSA: questions regarding EEL, eneopt and cutnb
(Wed Mar 07 2012 - 08:23:32 PST)
Jason Swails
Re: [AMBER] Large Energy Jump in TMD simulation - Regarding
(Fri Mar 30 2012 - 15:51:50 PDT)
Re: [AMBER] Large Energy Jump in TMD simulation - Regarding
(Fri Mar 30 2012 - 12:25:40 PDT)
Re: [AMBER] Issue with running sander
(Fri Mar 30 2012 - 10:56:15 PDT)
Re: [AMBER] Query on error :Atom does not have a type
(Fri Mar 30 2012 - 07:15:33 PDT)
Re: [AMBER] Issue with running sander
(Fri Mar 30 2012 - 07:13:14 PDT)
Re: [AMBER] Problem in Amber installation
(Fri Mar 30 2012 - 07:09:11 PDT)
Re: [AMBER] Fwd: V limit
(Thu Mar 29 2012 - 12:04:41 PDT)
Re: [AMBER] rfree: Error decoding variable 1 3 from:
(Thu Mar 29 2012 - 11:42:44 PDT)
Re: [AMBER] rfree: Error decoding variable 1 3 from:
(Thu Mar 29 2012 - 06:33:42 PDT)
Re: [AMBER] Problem in Amber installation
(Thu Mar 29 2012 - 04:49:37 PDT)
Re: [AMBER] error in nmode calculations
(Wed Mar 28 2012 - 14:46:54 PDT)
Re: [AMBER] how to measure atom distance in md trajectories using ptraj program
(Wed Mar 28 2012 - 12:23:30 PDT)
Re: [AMBER] amber12
(Tue Mar 27 2012 - 06:16:40 PDT)
Re: [AMBER] Amber and Short Bonds
(Tue Mar 27 2012 - 05:59:12 PDT)
Re: [AMBER] glycine sidechain contribution in MM-GBSA decompostion
(Mon Mar 26 2012 - 21:52:10 PDT)
Re: [AMBER] Amber and Short Bonds
(Mon Mar 26 2012 - 16:47:36 PDT)
Re: [AMBER] Amber and Short Bonds
(Mon Mar 26 2012 - 13:15:55 PDT)
Re: [AMBER] compiling failure on ibm
(Mon Mar 26 2012 - 12:51:48 PDT)
Re: [AMBER] Problems with pmemd.cuda.mpi (again!)
(Mon Mar 26 2012 - 09:51:13 PDT)
Re: [AMBER] amber12
(Mon Mar 26 2012 - 08:32:45 PDT)
Re: [AMBER] Problems with pmemd.cuda.mpi (again!)
(Mon Mar 26 2012 - 07:24:35 PDT)
Re: [AMBER] Problems with pmemd.cuda.mpi (again!)
(Sun Mar 25 2012 - 08:24:26 PDT)
Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs)
(Sat Mar 24 2012 - 19:33:37 PDT)
Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs)
(Sat Mar 24 2012 - 17:15:42 PDT)
Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs)
(Sat Mar 24 2012 - 10:06:02 PDT)
Re: [AMBER] Problems compiling pmemd.cuda - undefined reference to ...
(Sat Mar 24 2012 - 09:06:43 PDT)
Re: [AMBER] amber parameters for cytochrome c
(Sat Mar 24 2012 - 08:49:23 PDT)
Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs)
(Sat Mar 24 2012 - 08:17:58 PDT)
Re: [AMBER] Problem in Amber installation
(Thu Mar 22 2012 - 06:09:39 PDT)
Re: [AMBER] External Force Method in pmemd.cuda
(Wed Mar 21 2012 - 10:35:52 PDT)
Re: [AMBER] Amber 11 Compilation Error (again!)
(Wed Mar 21 2012 - 05:16:25 PDT)
Re: [AMBER] disulfide bond warnings
(Tue Mar 20 2012 - 18:45:32 PDT)
Re: [AMBER] disulfide bond warnings
(Tue Mar 20 2012 - 16:01:09 PDT)
Re: [AMBER] To generate more than one structure using ptraj
(Tue Mar 20 2012 - 10:04:48 PDT)
Re: [AMBER] How to calculate the energy contributed by hydrogen bonds?
(Tue Mar 20 2012 - 10:01:24 PDT)
Re: [AMBER] How to calculate the energy contributed by hydrogen bonds?
(Mon Mar 19 2012 - 19:27:01 PDT)
Re: [AMBER] To generate more than one structure using ptraj
(Mon Mar 19 2012 - 08:17:12 PDT)
Re: [AMBER] AMBER force calculations
(Fri Mar 16 2012 - 15:01:19 PDT)
Re: [AMBER] MMPBSA.py - Internal energy
(Fri Mar 16 2012 - 12:05:58 PDT)
Re: [AMBER] Amber for Cuda on Mac OSX
(Fri Mar 16 2012 - 12:03:52 PDT)
Re: [AMBER] MMPBSA, in parallel?
(Fri Mar 16 2012 - 06:41:07 PDT)
Re: [AMBER] mpi-allreduce in AMBER11
(Fri Mar 16 2012 - 06:38:40 PDT)
Re: [AMBER] MMGBSA residue-wise decomposition
(Thu Mar 15 2012 - 07:10:50 PDT)
Re: [AMBER] both parallel and serial
(Wed Mar 14 2012 - 07:10:59 PDT)
Re: [AMBER] MMGBSA residue-wise decomposition
(Wed Mar 14 2012 - 06:34:40 PDT)
Re: [AMBER] Energy and Coordinate Outputs
(Tue Mar 13 2012 - 15:22:11 PDT)
Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint."
(Sun Mar 11 2012 - 14:42:36 PDT)
Re: [AMBER] non-linear PB solver within MMPBSA: questions regarding EEL, eneopt and cutnb
(Sat Mar 10 2012 - 13:36:04 PST)
Re: [AMBER] Amber10 paralel installation
(Sat Mar 10 2012 - 13:08:21 PST)
Re: [AMBER] Comparison of the results
(Thu Mar 08 2012 - 14:00:20 PST)
Re: [AMBER] Can I use Amber 10 PRMTOP with Amber 11?
(Thu Mar 08 2012 - 12:41:53 PST)
Re: [AMBER] Mac OSX 10.7
(Thu Mar 08 2012 - 12:36:00 PST)
Re: [AMBER] correct inconsistencies in [DR]NA_CI.lib
(Tue Mar 06 2012 - 20:38:09 PST)
Re: [AMBER] Error in amber output files
(Tue Mar 06 2012 - 07:44:32 PST)
Re: [AMBER] Error in amber output files
(Mon Mar 05 2012 - 13:34:51 PST)
Re: [AMBER] using GAFF with TIP3P model for simulation of solvated organic molecule
(Sun Mar 04 2012 - 17:46:13 PST)
Re: [AMBER] slow : amber job
(Sat Mar 03 2012 - 04:34:23 PST)
Re: [AMBER] ABMD in pmemd.cuda in AMBER 12
(Thu Mar 01 2012 - 12:35:47 PST)
Re: [AMBER] Help with solvating organic molecule with input .prmtop file
(Thu Mar 01 2012 - 12:33:32 PST)
Re: [AMBER] ABMD in pmemd.cuda in AMBER 12
(Thu Mar 01 2012 - 10:18:17 PST)
Re: [AMBER] mm_pbsa error: Flag "RADII" not found in PARM file
(Thu Mar 01 2012 - 07:24:57 PST)
Jesper Sørensen
Re: [AMBER] PBSA sprob question
(Wed Mar 14 2012 - 08:57:50 PDT)
Re: [AMBER] PBSA sprob question
(Tue Mar 13 2012 - 15:58:18 PDT)
[AMBER] PBSA sprob question
(Tue Mar 13 2012 - 13:49:09 PDT)
JiYuan Liu
[AMBER] Which methodology could estimate the binding affinity of zinc containing metalloprotei(wrong string) Cligand complex accurately?
(Fri Mar 30 2012 - 08:00:35 PDT)
Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW
(Mon Mar 19 2012 - 05:51:51 PDT)
[AMBER] The value of Delta G is positive after MMPBSA calculation for metalloprotein
(Tue Mar 13 2012 - 20:02:24 PDT)
Jorge Iulek
Re: [AMBER] charges for ion and surrounding residues at the active site
(Wed Mar 21 2012 - 09:07:08 PDT)
Re: [AMBER] charges for ion and surrounding residues at the active site
(Tue Mar 20 2012 - 17:28:36 PDT)
[AMBER] charges for ion and surrounding residues at the active site
(Mon Mar 19 2012 - 17:33:10 PDT)
[AMBER] charges for ion and surrounding residues at the active site
(Mon Mar 19 2012 - 12:51:05 PDT)
João Ribeiro
[AMBER] Fwd: SASA Plot
(Wed Mar 07 2012 - 02:16:53 PST)
jun kit
[AMBER] esp and resp comparison
(Fri Mar 23 2012 - 01:23:49 PDT)
Junjian Miao
[AMBER] is GB/SA suitable for nonaqueous solvent?
(Sun Mar 18 2012 - 07:21:42 PDT)
kanika sharma
Re: [AMBER] top and crd file error
(Thu Mar 01 2012 - 23:22:07 PST)
[AMBER] top and crd file error
(Thu Mar 01 2012 - 22:59:03 PST)
Karl N. Kirschner
Re: [AMBER] Force Field Parameterization -- Torsion Potentials
(Mon Mar 19 2012 - 05:50:46 PDT)
Re: [AMBER] Force Field Parameterization -- Torsion Potentials
(Wed Mar 14 2012 - 04:53:23 PDT)
Kasprzak, Wojciech (NIH/NCI) [C]
[AMBER] Can I use Amber 10 PRMTOP with Amber 11?
(Thu Mar 08 2012 - 10:40:32 PST)
kirtana S
[AMBER] binding free energy
(Tue Mar 13 2012 - 00:35:19 PDT)
[AMBER] Velocity
(Wed Mar 07 2012 - 11:02:32 PST)
kureeckal ramesh
[AMBER] error in sander_com.1.out
(Thu Mar 01 2012 - 02:30:54 PST)
[AMBER] problem with MMPBSA script
(Thu Mar 01 2012 - 00:52:39 PST)
Kyle Greenway
[AMBER] Extra Bonds For Water
(Tue Mar 13 2012 - 15:37:33 PDT)
Lachele Foley (Lists)
Re: [AMBER] parameters for Lys-sugar
(Sun Mar 25 2012 - 13:10:23 PDT)
Re: [AMBER] parameters for Lys-sugar
(Sat Mar 24 2012 - 08:10:20 PDT)
Re: [AMBER] parameters for Lys-sugar
(Fri Mar 23 2012 - 12:39:04 PDT)
Re: [AMBER] parameters for Lys-sugar
(Fri Mar 23 2012 - 11:01:27 PDT)
Re: [AMBER] parameters for Lys-sugar
(Fri Mar 23 2012 - 08:11:15 PDT)
liu junjun
Re: [AMBER] restrain water in a solvatecap
(Mon Mar 19 2012 - 20:40:22 PDT)
lnedialkova.gmail.com
[AMBER] Question about output files
(Wed Mar 07 2012 - 14:18:42 PST)
Logan Ahlstrom
Re: [AMBER] Replica Exchange
(Wed Mar 14 2012 - 08:34:59 PDT)
Lorenzo Gontrani
Re: [AMBER] Viewing with VMD bonds set by the "bond" command
(Thu Mar 08 2012 - 02:21:57 PST)
Re: [AMBER] Viewing with VMD bonds set by the "bond" command
(Thu Mar 08 2012 - 00:42:00 PST)
M. L. Dodson
Re: [AMBER] No Na molecule type for genion
(Sat Mar 17 2012 - 06:40:06 PDT)
Re: [AMBER] ABMD in pmemd.cuda in AMBER 12
(Thu Mar 01 2012 - 10:43:37 PST)
Mahmoud Ibrahim
[AMBER] Dedication from Ibrahim - Manchester/Minia
(Tue Mar 06 2012 - 14:17:57 PST)
manikanthan bhavaraju
Re: [AMBER] error in nmode calculations
(Wed Mar 28 2012 - 14:18:06 PDT)
[AMBER] error in nmode calculations
(Wed Mar 28 2012 - 11:41:04 PDT)
Re: [AMBER] Comparison of the results
(Thu Mar 08 2012 - 14:19:50 PST)
[AMBER] Fwd: Comparison of the results
(Wed Mar 07 2012 - 22:31:48 PST)
[AMBER] Comparison of the results
(Wed Mar 07 2012 - 14:23:54 PST)
Marc van der Kamp
Re: [AMBER] How to convert multiple mdcrd files to single files with minimium size?
(Thu Mar 08 2012 - 07:53:35 PST)
Martin Peters
Re: [AMBER] Problem with installation of MTKPP
(Thu Mar 29 2012 - 01:41:58 PDT)
Maxier Acosta
[AMBER] Parameters
(Mon Mar 05 2012 - 20:27:45 PST)
mehdi bagherpoor
[AMBER] Free Energy Calculate
(Mon Mar 05 2012 - 04:41:05 PST)
Michael F. Bruist
Re: [AMBER] NAB segmentation fault
(Fri Mar 16 2012 - 09:32:33 PDT)
Re: [AMBER] NAB segmentation fault
(Mon Mar 12 2012 - 11:34:46 PDT)
[AMBER] NAB segmentation fault
(Thu Mar 08 2012 - 08:03:12 PST)
mish
Re: [AMBER] saltconc and string parameters in MM/PB(GB)SA
(Thu Mar 08 2012 - 11:10:10 PST)
[AMBER] saltconc and string parameters in MM/PB(GB)SA
(Thu Mar 08 2012 - 09:34:00 PST)
mjyang
[AMBER] separated thermostat in AMBER
(Fri Mar 09 2012 - 05:25:57 PST)
Nadine.Homeyer.uni-duesseldorf.de
Re: [AMBER] error in sander_com.1.out
(Thu Mar 01 2012 - 03:12:05 PST)
Re: [AMBER] problem with MMPBSA script
(Thu Mar 01 2012 - 01:51:57 PST)
neha sree
[AMBER] control_rmsd_in TMD
(Fri Mar 02 2012 - 11:57:42 PST)
Niel Henriksen
Re: [AMBER] Dihedral analysis
(Thu Mar 08 2012 - 06:10:26 PST)
Olena Dobrovolska
Re: [AMBER] COM
(Wed Mar 28 2012 - 08:40:02 PDT)
[AMBER] COM
(Tue Mar 27 2012 - 08:01:27 PDT)
Qian Wang
[AMBER] rigid body simulation
(Thu Mar 15 2012 - 08:19:06 PDT)
qiao xue
[AMBER] How to get the information of hydrophobic contact?
(Wed Mar 07 2012 - 19:03:48 PST)
Qin Cai
Re: [AMBER] PB with inp=2 doesn't recognize ff10 atom types?
(Mon Mar 19 2012 - 15:15:38 PDT)
Re: [AMBER] PBSA sprob question
(Tue Mar 13 2012 - 16:46:48 PDT)
Re: [AMBER] PBSA sprob question
(Tue Mar 13 2012 - 15:13:42 PDT)
raghav singh
Re: [AMBER] No Na molecule type for genion
(Fri Mar 16 2012 - 22:57:05 PDT)
Rahul Banerjee
[AMBER] Residual Dipolar Coupling
(Tue Mar 06 2012 - 13:32:27 PST)
Rajendra Sharma
Re: [AMBER] Replica Exchange
(Wed Mar 14 2012 - 08:22:38 PDT)
[AMBER] Replica Exchange
(Tue Mar 13 2012 - 08:08:06 PDT)
Rajeswari A.
Re: [AMBER] MMGBSA residue-wise decomposition
(Wed Mar 14 2012 - 23:58:35 PDT)
[AMBER] MMGBSA residue-wise decomposition
(Tue Mar 13 2012 - 04:42:53 PDT)
[AMBER] MMGBSA residue-wise decomposition
(Wed Mar 07 2012 - 21:10:52 PST)
[AMBER] MMGBSA residue-wise decomposition
(Tue Mar 06 2012 - 21:18:28 PST)
Re: [AMBER] SASA Plot
(Tue Mar 06 2012 - 03:31:04 PST)
RAMON
[AMBER] Fwd: V limit
(Mon Mar 26 2012 - 07:21:46 PDT)
Ray Luo, Ph.D.
[AMBER] Fwd: PB with inp=2 doesn't recognize ff10 atom types?
(Sat Mar 17 2012 - 19:33:14 PDT)
Ross Walker
Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi
(Fri Mar 30 2012 - 10:34:17 PDT)
Re: [AMBER] Fwd: V limit
(Thu Mar 29 2012 - 11:47:37 PDT)
Re: [AMBER] GTX680
(Wed Mar 28 2012 - 13:39:14 PDT)
Re: [AMBER] Another question about Amber 12
(Tue Mar 27 2012 - 10:25:43 PDT)
Re: [AMBER] Amber and Short Bonds
(Mon Mar 26 2012 - 09:44:30 PDT)
Re: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues
(Mon Mar 26 2012 - 09:37:02 PDT)
Re: [AMBER] amber12
(Mon Mar 26 2012 - 09:35:22 PDT)
Re: [AMBER] Problems with pmemd.cuda.mpi (again!)
(Sun Mar 25 2012 - 07:03:48 PDT)
Re: [AMBER] GTX680
(Fri Mar 23 2012 - 11:49:15 PDT)
Re: [AMBER] Conflict between AmberTools 1.5 and Cuda
(Fri Mar 23 2012 - 09:19:07 PDT)
Re: [AMBER] Problems compiling pmemd.cuda - undefined reference to ...
(Fri Mar 23 2012 - 09:17:06 PDT)
Re: [AMBER] Fast ibelly?
(Tue Mar 20 2012 - 11:31:10 PDT)
Re: [AMBER] Fast ibelly?
(Tue Mar 20 2012 - 10:09:47 PDT)
[AMBER] Job Opening at Simbios/Stanford University
(Fri Mar 09 2012 - 13:19:54 PST)
Re: [AMBER] ABMD in pmemd.cuda in AMBER 12
(Thu Mar 01 2012 - 13:33:38 PST)
Sangeetha B
Re: [AMBER] cluster configuration help
(Sun Mar 11 2012 - 08:11:30 PDT)
[AMBER] cluster configuration help
(Fri Mar 09 2012 - 09:16:42 PST)
[AMBER] cluster configuration help
(Tue Mar 06 2012 - 19:27:09 PST)
Sangita Kachhap
Re: [AMBER] ATP minimization
(Mon Mar 05 2012 - 21:58:33 PST)
Scott Brozell
Re: [AMBER] compiling failure on ibm
(Mon Mar 26 2012 - 12:20:00 PDT)
Scott Le Grand
Re: [AMBER] GTX680
(Thu Mar 29 2012 - 08:39:21 PDT)
Re: [AMBER] GTX680
(Wed Mar 28 2012 - 10:40:40 PDT)
Re: [AMBER] GTX680
(Wed Mar 28 2012 - 10:07:57 PDT)
Re: [AMBER] GTX680
(Wed Mar 28 2012 - 09:33:39 PDT)
Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs)
(Sat Mar 24 2012 - 09:49:42 PDT)
Re: [AMBER] GTX680
(Fri Mar 23 2012 - 11:57:00 PDT)
setyanto md
[AMBER] Asking About Differences between amber force field ff10 and ff03
(Fri Mar 30 2012 - 02:50:59 PDT)
Re: [AMBER] Problem in Amber installation
(Fri Mar 30 2012 - 02:21:57 PDT)
Re: [AMBER] Problem with installation of MTKPP
(Thu Mar 29 2012 - 03:55:07 PDT)
[AMBER] Problem with installation of MTKPP
(Wed Mar 28 2012 - 19:33:09 PDT)
[AMBER] organics solvent radius
(Mon Mar 19 2012 - 23:04:23 PDT)
Re: [AMBER] asking about mden
(Mon Mar 12 2012 - 03:26:43 PDT)
[AMBER] asking about mden
(Sun Mar 11 2012 - 22:33:57 PDT)
Re: [AMBER] Parameters
(Wed Mar 07 2012 - 21:18:55 PST)
Re: [AMBER] SASA Plot
(Wed Mar 07 2012 - 21:05:23 PST)
Re: [AMBER] SASA Plot
(Wed Mar 07 2012 - 00:51:29 PST)
Shaandar Nyamtulga
Re: [AMBER] Amber10 parallel test example run error
(Fri Mar 30 2012 - 01:04:16 PDT)
[AMBER] Amber10 parallel test example run error
(Thu Mar 29 2012 - 23:25:32 PDT)
[AMBER] Amber10 parallel installation test example
(Fri Mar 23 2012 - 01:08:31 PDT)
[AMBER] Amber10 parallel installation test error
(Wed Mar 14 2012 - 22:48:45 PDT)
[AMBER] Amber10 parallel installation test example run error
(Wed Mar 14 2012 - 20:50:37 PDT)
[AMBER] Amber 10 parallel installation error
(Wed Mar 14 2012 - 00:19:03 PDT)
[AMBER] Amber10 paralel installation
(Fri Mar 09 2012 - 19:06:01 PST)
Soumya Lipsa Rath
Re: [AMBER] About ANAL problem: Amber
(Wed Mar 21 2012 - 23:25:36 PDT)
Souvik Sur
Re: [AMBER] To generate more than one structure using ptraj
(Mon Mar 19 2012 - 22:56:44 PDT)
[AMBER] To generate more than one structure using ptraj
(Mon Mar 19 2012 - 06:36:31 PDT)
Re: [AMBER] Error in amber output files
(Mon Mar 05 2012 - 21:11:01 PST)
[AMBER] Error in amber output files
(Mon Mar 05 2012 - 05:19:40 PST)
steinbrt.rci.rutgers.edu
[AMBER] AmberGS forcefield
(Tue Mar 27 2012 - 07:57:05 PDT)
Re: [AMBER] assignment of partial charge to fullerene2160
(Tue Mar 27 2012 - 01:05:44 PDT)
Re: [AMBER] Best way to implement PBC
(Wed Mar 07 2012 - 13:22:35 PST)
[AMBER] GPU performance and GPU Direct
(Wed Mar 07 2012 - 05:26:53 PST)
Re: [AMBER] performance dependency on OS
(Tue Mar 06 2012 - 02:56:09 PST)
Sushil Mishra
Re: [AMBER] binding free energy
(Tue Mar 13 2012 - 00:55:33 PDT)
Syed Tarique Moin
[AMBER] antechamber error
(Wed Mar 14 2012 - 03:59:45 PDT)
Tan Yaw Sing
[AMBER] Is it possible to just calculate translational and rotational entropy?
(Thu Mar 22 2012 - 03:57:57 PDT)
tdo.chem.ucsb.edu
[AMBER] ptraj: Sort trajectory based on protein-ligand distance
(Tue Mar 13 2012 - 18:27:05 PDT)
[AMBER] Hydrogen bond analysis
(Thu Mar 08 2012 - 23:48:00 PST)
Thomas Cheatham
Re: [AMBER] Amber and Short Bonds
(Mon Mar 26 2012 - 13:21:22 PDT)
Re: [AMBER] ptraj atomicfluct
(Sat Mar 24 2012 - 14:26:16 PDT)
Re: [AMBER] cluster configuration help
(Sat Mar 10 2012 - 10:24:33 PST)
Thomas Cheatham III
Re: [AMBER] saltconc and string parameters in MM/PB(GB)SA
(Thu Mar 08 2012 - 10:00:30 PST)
Thomas Exner
[AMBER] Fast moving system in targeted MD
(Fri Mar 30 2012 - 05:16:18 PDT)
Thomas Gaillard
[AMBER] correct inconsistencies in [DR]NA_CI.lib
(Tue Mar 06 2012 - 08:57:36 PST)
tommaso.casalini.mail.polimi.it
[AMBER] MMPBSA issue: incosistency within internal potential error
(Thu Mar 01 2012 - 07:30:36 PST)
[AMBER] MMPBSA and explicit ions: what should I do?
(Thu Mar 01 2012 - 02:21:51 PST)
Tong Zhu
Re: [AMBER] Another question about Amber 12
(Wed Mar 28 2012 - 18:51:25 PDT)
[AMBER] Another question about Amber 12
(Mon Mar 26 2012 - 18:04:31 PDT)
[AMBER] MP2 for RESP
(Mon Mar 26 2012 - 01:46:36 PDT)
Re: [AMBER] atom type of Sulphur in CYS/CYM (MCPB)
(Fri Mar 23 2012 - 02:12:32 PDT)
[AMBER] covert CHARMM format PDB file to AMBER formart
(Wed Mar 07 2012 - 02:25:05 PST)
Urszula Uciechowska
Re: [AMBER] parameters for Lys-sugar P2N file
(Sun Mar 25 2012 - 23:52:33 PDT)
Re: [AMBER] parameters for Lys-sugar
(Sat Mar 24 2012 - 13:52:42 PDT)
Re: [AMBER] parameters for Lys-sugar
(Sat Mar 24 2012 - 13:41:00 PDT)
Re: [AMBER] parameters for Lys-sugar
(Fri Mar 23 2012 - 08:26:19 PDT)
[AMBER] parameters for Lys-sugar
(Fri Mar 23 2012 - 05:15:38 PDT)
Re: [AMBER] puting restrains
(Fri Mar 16 2012 - 04:01:13 PDT)
[AMBER] puting restrains
(Thu Mar 15 2012 - 06:24:26 PDT)
vishal Nemaysh
Re: [AMBER] Problem in Amber installation
(Wed Mar 28 2012 - 22:01:57 PDT)
[AMBER] Problem in Amber installation
(Thu Mar 22 2012 - 01:06:08 PDT)
Vlad Cojocaru
Re: [AMBER] Converting Gromacs coordinate file to Amber input files formolecular dynamics
(Wed Mar 21 2012 - 10:10:52 PDT)
Re: [AMBER] MD and RAMD
(Tue Mar 20 2012 - 00:59:52 PDT)
Re: [AMBER] Amber8 and RAMD
(Sun Mar 18 2012 - 02:54:15 PDT)
Re: [AMBER] the problem of RAMD
(Fri Mar 16 2012 - 03:52:47 PDT)
wei wang
[AMBER] About ANAL
(Sun Mar 25 2012 - 02:33:33 PDT)
[AMBER] ANAL
(Sat Mar 24 2012 - 20:32:47 PDT)
Wholly Peach
[AMBER] No Na molecule type for genion
(Fri Mar 16 2012 - 22:45:32 PDT)
[AMBER] on the AMBER advanced tutorial 3 MM-PBSA
(Thu Mar 15 2012 - 17:18:01 PDT)
xiaojiong
[AMBER] MD and RAMD
(Tue Mar 20 2012 - 00:12:20 PDT)
[AMBER] Amber8 and RAMD
(Sun Mar 18 2012 - 01:59:00 PDT)
[AMBER] the problem of RAMD
(Fri Mar 16 2012 - 02:02:50 PDT)
[AMBER] different residues use different force to restrict
(Sun Mar 04 2012 - 17:41:16 PST)
Yi An
[AMBER] restrain water in a solvatecap
(Mon Mar 19 2012 - 13:01:44 PDT)
[AMBER] restrain water in a solvatecap
(Thu Mar 15 2012 - 10:05:22 PDT)
Yubo Fan
Re: [AMBER] compiling failure on ibm
(Mon Mar 26 2012 - 13:50:06 PDT)
[AMBER] compiling failure on ibm
(Mon Mar 26 2012 - 11:44:03 PDT)
Yudong Sun
[AMBER] ./nab -c dna3.nab,nab2c failed!
(Mon Mar 05 2012 - 06:40:03 PST)
板垣哲彦
[AMBER] Issue with running sander
(Fri Mar 30 2012 - 05:37:21 PDT)
王伟
[AMBER] ANAL
(Sat Mar 24 2012 - 20:17:43 PDT)
[AMBER] ANAL
(Sat Mar 24 2012 - 00:57:41 PDT)
Re: [AMBER] About ANAL problem: Amber
(Sat Mar 24 2012 - 00:41:00 PDT)
[AMBER] About ANAL problem: Amber
(Fri Mar 23 2012 - 07:37:32 PDT)
Re: [AMBER] About ANAL problem: Amber
(Thu Mar 22 2012 - 06:14:43 PDT)
[AMBER] About ANAL problem: Amber
(Wed Mar 21 2012 - 04:16:23 PDT)
肖立
Re: [AMBER] Announcement: 2012 summer intern position at GSK
(Sun Mar 25 2012 - 16:24:55 PDT)
黄恋琦
[AMBER] Is there some constrains required for the REMD simulation on disaccharide in Amber11?
(Tue Mar 20 2012 - 00:42:05 PDT)
Last message date
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Sat Mar 31 2012 - 23:30:03 PDT
Archived on
: Mon Dec 23 2024 - 05:54:26 PST
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