Amber Archive Apr 2013 by author
494 messages
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Starting
Mon Apr 01 2013 - 00:30:02 PDT,
Ending
Tue Apr 30 2013 - 13:30:03 PDT
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ABEL Stephane 175950
[AMBER] RE : GAFFlipid using custom lipids
(Mon Apr 15 2013 - 13:29:28 PDT)
Abhishek Mukhopadhyay
Re: [AMBER] Using 3D-RISM to compute solvation free energy
(Sat Apr 20 2013 - 15:00:37 PDT)
Re: [AMBER] Using 3D-RISM to compute solvation free energy
(Fri Apr 19 2013 - 15:10:14 PDT)
[AMBER] Using 3D-RISM to compute solvation free energy
(Fri Apr 19 2013 - 13:36:05 PDT)
Acoot Brett
[AMBER] =4/7/2013 3:34:47 PM=
(Sun Apr 07 2013 - 07:35:00 PDT)
Adam Zalewski
[AMBER] Regarding Accelerated Molecular Dynamics
(Fri Apr 05 2013 - 04:33:16 PDT)
Adrian Roitberg
Re: [AMBER] pmemd.cuda.MPI with npt
(Wed Apr 17 2013 - 11:26:00 PDT)
[AMBER] need a box
(Tue Apr 02 2013 - 08:09:27 PDT)
Re: [AMBER] Is SHAKE necessary in running an MD?V
(Tue Apr 02 2013 - 05:48:48 PDT)
Alan
[AMBER] Is SHAKE necessary in running an MD?V
(Mon Apr 01 2013 - 01:29:36 PDT)
Alan
Re: [AMBER] Is SHAKE necessary in running an MD?V
(Tue Apr 02 2013 - 05:23:27 PDT)
Re: [AMBER] Is SHAKE necessary in running an MD?V
(Mon Apr 01 2013 - 23:12:42 PDT)
Albert
Re: [AMBER] MMPBSA failed
(Wed Apr 03 2013 - 07:56:53 PDT)
Re: [AMBER] MMPBSA failed
(Wed Apr 03 2013 - 07:40:25 PDT)
Re: [AMBER] MMPBSA failed
(Wed Apr 03 2013 - 07:08:49 PDT)
Re: [AMBER] MMPBSA failed
(Wed Apr 03 2013 - 06:50:15 PDT)
Re: [AMBER] MMPBSA failed
(Wed Apr 03 2013 - 02:05:47 PDT)
[AMBER] MMPBSA failed
(Wed Apr 03 2013 - 00:12:10 PDT)
[AMBER] ante-MMPBSA.py failed
(Tue Apr 02 2013 - 11:18:14 PDT)
Alexey Zeifman
Re: [AMBER] Palladium complex parametrization in antechamber
(Mon Apr 29 2013 - 04:58:02 PDT)
[AMBER] Palladium complex parametrization in antechamber
(Sun Apr 28 2013 - 23:43:14 PDT)
Amber Amoeba
Re: [AMBER] bug report: tinker_to_amberfailedforsystemscontainingcounter ions
(Wed Apr 10 2013 - 13:52:47 PDT)
Amparo Garcia Lopez
Re: [AMBER] clustering places all frames in one cluster
(Thu Apr 25 2013 - 02:20:04 PDT)
Re: [AMBER] clustering places all frames in one cluster
(Fri Apr 19 2013 - 01:14:55 PDT)
[AMBER] clustering places all frames in one cluster
(Mon Apr 15 2013 - 05:44:15 PDT)
[AMBER] clustering places all frames in one cluster
(Mon Apr 15 2013 - 01:26:00 PDT)
Anna Bauß
Re: [AMBER] sander not installed
(Mon Apr 15 2013 - 01:34:48 PDT)
Anna Marabotti
[AMBER] meaning of values for dihedrals of a chromophore
(Thu Apr 04 2013 - 03:20:15 PDT)
Anselm Horn
[AMBER] Leap: Setting the bounding box manually
(Sun Apr 21 2013 - 09:04:06 PDT)
Re: [AMBER] Constant pH calculation: calcpka
(Thu Apr 11 2013 - 09:17:27 PDT)
[AMBER] Constant pH calculation: calcpka
(Wed Apr 10 2013 - 23:47:18 PDT)
anu chandra
[AMBER] correlation matrix of side-chain dihedral angle in PTRAJ
(Fri Apr 12 2013 - 04:25:42 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
(Tue Apr 09 2013 - 22:55:55 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
(Tue Apr 09 2013 - 22:41:50 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
(Tue Apr 09 2013 - 22:04:27 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
(Mon Apr 08 2013 - 23:40:45 PDT)
[AMBER] Problem with order parameter calculation in PTRAJ
(Mon Apr 08 2013 - 01:56:36 PDT)
[AMBER] Analysis of side-chain conformational changes
(Mon Apr 08 2013 - 01:55:18 PDT)
Re: [AMBER] Analysis of side-chain conformational changes
(Fri Apr 05 2013 - 22:59:44 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
(Fri Apr 05 2013 - 22:48:33 PDT)
[AMBER] Problem with order parameter calculation in PTRAJ
(Fri Apr 05 2013 - 00:16:00 PDT)
[AMBER] Fwd: Analysis of side-chain conformational changes
(Thu Apr 04 2013 - 05:04:53 PDT)
[AMBER] Analysis of side-chain conformational changes
(Thu Apr 04 2013 - 03:10:55 PDT)
[AMBER] clustering based on side-chain conformations
(Mon Apr 01 2013 - 00:40:07 PDT)
arnab bhattacharya
Re: [AMBER] problem in creating circular DNA using NAB
(Tue Apr 16 2013 - 05:30:53 PDT)
[AMBER] problem in creating circular DNA with NAB
(Mon Apr 15 2013 - 05:00:18 PDT)
[AMBER] problem in creating circular DNA using NAB
(Mon Apr 15 2013 - 04:10:33 PDT)
Aron Broom
Re: [AMBER] AMBER12 GPU performance
(Sat Apr 06 2013 - 21:55:47 PDT)
Re: [AMBER] Regarding MD run in vacuum
(Wed Apr 03 2013 - 06:36:33 PDT)
Astrid Maaß
Re: [AMBER] on the usage of Antechamber for the ligand parametrisation
(Wed Apr 10 2013 - 00:06:45 PDT)
Benjamin D Madej
Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein
(Wed Apr 17 2013 - 16:48:09 PDT)
Re: [AMBER] GAFFlipid using custom lipids
(Tue Apr 16 2013 - 12:11:30 PDT)
Re: [AMBER] GAFFlipid using custom lipids
(Mon Apr 15 2013 - 15:00:00 PDT)
Re: [AMBER] GAFFlipid using custom lipids
(Mon Apr 15 2013 - 12:15:30 PDT)
BERGY
[AMBER] DNA basestep stacking energy/interaction energy
(Tue Apr 30 2013 - 03:27:03 PDT)
Bill Miller III
Re: [AMBER] MMPBSA failed
(Wed Apr 03 2013 - 07:26:20 PDT)
Re: [AMBER] MMPBSA failed
(Wed Apr 03 2013 - 07:00:28 PDT)
Re: [AMBER] ante-MMPBSA.py failed
(Tue Apr 02 2013 - 11:45:27 PDT)
Bill Ross
Re: [AMBER] Problem in parameter file generation
(Sat Apr 27 2013 - 14:03:09 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
(Wed Apr 24 2013 - 21:40:14 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
(Tue Apr 23 2013 - 21:26:26 PDT)
Re: [AMBER] Zero vdW parametes for HO in Amber
(Wed Apr 10 2013 - 16:41:27 PDT)
Binwu Zhao
Re: [AMBER] NPT ensemble hydrogen bond calculation (Binwu Zhao)
(Tue Apr 16 2013 - 10:46:00 PDT)
[AMBER] NPT ensemble hydrogen bond calculation
(Fri Apr 12 2013 - 21:20:54 PDT)
Brian Radak
Re: [AMBER] Reducing positional restraint gradually
(Mon Apr 22 2013 - 13:12:56 PDT)
Re: [AMBER] Changing vdW parameters for HO-type atom
(Mon Apr 22 2013 - 06:09:59 PDT)
Re: [AMBER] Input file for NVT simulation
(Mon Apr 22 2013 - 05:51:22 PDT)
Re: [AMBER] Newbie solvent question
(Tue Apr 16 2013 - 12:19:13 PDT)
Carlos Simmerling
Re: [AMBER] Query about checking of convergence in REMD
(Fri Apr 26 2013 - 06:20:01 PDT)
Re: [AMBER] aMD simulations in amber12
(Fri Apr 12 2013 - 06:12:35 PDT)
Re: [AMBER] Problem with folding simulation
(Tue Apr 09 2013 - 19:41:46 PDT)
Re: [AMBER] implicit solvation with periodic boundary
(Mon Apr 08 2013 - 14:39:17 PDT)
Re: [AMBER] implicit solvation with periodic boundary
(Mon Apr 08 2013 - 13:28:20 PDT)
Re: [AMBER] Help with GB-OBC calculations
(Tue Apr 02 2013 - 04:38:56 PDT)
case
Re: [AMBER] minimize problem
(Sun Apr 07 2013 - 06:02:00 PDT)
Re: [AMBER] Error in lmod minimization parallel test
(Sun Apr 07 2013 - 05:57:41 PDT)
Catein Catherine
[AMBER] MMPBSA result interpretation helppppp
(Thu Apr 18 2013 - 23:07:25 PDT)
Chang Woon Jang
Re: [AMBER] dihedral term for furan and thiophene molecules
(Mon Apr 22 2013 - 08:21:29 PDT)
[AMBER] dihedral term for furan and thiophene molecules
(Mon Apr 22 2013 - 07:17:00 PDT)
Changqing Yan
Re: [AMBER] Cyclic peptide problem
(Thu Apr 25 2013 - 00:56:02 PDT)
Re: [AMBER] Cyclic peptide problem
(Thu Apr 25 2013 - 00:55:18 PDT)
[AMBER] Cyclic peptide problem
(Wed Apr 24 2013 - 07:20:59 PDT)
Chinh Su Tran To
Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to Sim failed for K20x using JAC and Cellulose benchmarks
(Thu Apr 25 2013 - 22:46:46 PDT)
Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to Sim failed for K20x using JAC and Cellulose benchmarks
(Thu Apr 25 2013 - 21:00:30 PDT)
Chris Chris
Re: [AMBER] ante-MMPBSA.py problem
(Fri Apr 19 2013 - 23:18:59 PDT)
[AMBER] ante-MMPBSA.py problem
(Fri Apr 19 2013 - 09:56:37 PDT)
Covington, Cody Lance
[AMBER] improper Dihedral Specification
(Tue Apr 30 2013 - 13:06:35 PDT)
[AMBER] paramfit question
(Fri Apr 26 2013 - 15:20:08 PDT)
[AMBER] paramfit questions
(Thu Apr 18 2013 - 10:42:24 PDT)
[AMBER] GAFFLipid parameters
(Wed Apr 17 2013 - 11:45:14 PDT)
Re: [AMBER] GAFFlipid using custom lipids
(Mon Apr 15 2013 - 18:02:12 PDT)
Re: [AMBER] Solute concentration
(Mon Apr 15 2013 - 17:10:39 PDT)
Re: [AMBER] GAFFlipid using custom lipids
(Mon Apr 15 2013 - 12:52:03 PDT)
[AMBER] GAFFlipid using custom lipids
(Mon Apr 15 2013 - 11:23:27 PDT)
crazylyf
[AMBER] Gradually reduce the restraint within one step
(Thu Apr 25 2013 - 20:28:45 PDT)
crazylyf.126.com
Re: [AMBER] Gradually reduce the restraint within one step
(Sat Apr 27 2013 - 17:27:07 PDT)
Re: [AMBER] Gradually reduce the restraint within one step
(Fri Apr 26 2013 - 21:29:53 PDT)
Re: [AMBER] Gradually reduce the restraint within one step
(Fri Apr 26 2013 - 20:40:51 PDT)
Re: [AMBER] Gradually reduce the restraint within one step
(Fri Apr 26 2013 - 17:51:32 PDT)
Daniel Roe
Re: [AMBER] hbond print option equivalent in cpptraj from AmberTools13?
(Sat Apr 27 2013 - 10:01:42 PDT)
Re: [AMBER] Query about checking of convergence in REMD
(Fri Apr 26 2013 - 09:47:38 PDT)
Re: [AMBER] list of (dihedral and angle) parameters (GAFF)
(Fri Apr 26 2013 - 09:42:30 PDT)
Re: [AMBER] Question for AMBER input files
(Thu Apr 25 2013 - 07:33:55 PDT)
Re: [AMBER] clustering places all frames in one cluster
(Thu Apr 25 2013 - 07:32:52 PDT)
Re: [AMBER] Problem with cluster analysis in ptraj
(Tue Apr 23 2013 - 07:18:22 PDT)
Re: [AMBER] VMD shows an atom stretched waaaay out
(Mon Apr 22 2013 - 14:20:24 PDT)
Re: [AMBER] NPT ensemble hydrogen bond calculation (Binwu Zhao)
(Tue Apr 16 2013 - 10:52:46 PDT)
Re: [AMBER] Plotting heat maps in AMBER aMD simualtions
(Tue Apr 16 2013 - 08:38:34 PDT)
Re: [AMBER] NPT ensemble hydrogen bond calculation
(Mon Apr 15 2013 - 07:21:25 PDT)
Re: [AMBER] correlation matrix of side-chain dihedral angle in PTRAJ
(Mon Apr 15 2013 - 07:12:09 PDT)
Re: [AMBER] clustering places all frames in one cluster
(Mon Apr 15 2013 - 07:09:51 PDT)
Re: [AMBER] Amber installation problems
(Wed Apr 10 2013 - 07:04:11 PDT)
Re: [AMBER] xleap error - Created a new atom named: P within residue: .R<DG5 478>
(Tue Apr 09 2013 - 08:00:42 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
(Tue Apr 09 2013 - 07:58:45 PDT)
Re: [AMBER] The latest topology file format.
(Tue Apr 09 2013 - 07:54:25 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
(Mon Apr 08 2013 - 10:25:45 PDT)
Re: [AMBER] Analysis of side-chain conformational changes
(Fri Apr 05 2013 - 09:27:38 PDT)
Re: [AMBER] Out of Box in PMEMD
(Fri Apr 05 2013 - 09:15:07 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
(Fri Apr 05 2013 - 08:38:36 PDT)
Re: [AMBER] clustering based on side-chain conformations
(Tue Apr 02 2013 - 07:28:19 PDT)
David A Case
Re: [AMBER] DNA basestep stacking energy/interaction energy
(Tue Apr 30 2013 - 06:20:49 PDT)
Re: [AMBER] bug in impose command in amber tleap
(Mon Apr 29 2013 - 11:42:11 PDT)
Re: [AMBER] Palladium complex parametrization in antechamber
(Mon Apr 29 2013 - 04:53:16 PDT)
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
(Sun Apr 28 2013 - 13:34:08 PDT)
Re: [AMBER-Developers] [AMBER] Compilation errors for AmberTools 13 with OpenMP
(Sun Apr 28 2013 - 04:10:11 PDT)
Re: [AMBER] Compiling problems with -openmp
(Sun Apr 28 2013 - 03:57:37 PDT)
Re: [AMBER] how to get force information through MD run
(Sat Apr 27 2013 - 04:02:38 PDT)
Re: [AMBER] Gradually reduce the restraint within one step
(Sat Apr 27 2013 - 03:57:13 PDT)
Re: [AMBER] the role of surface charge
(Fri Apr 26 2013 - 17:28:28 PDT)
Re: [AMBER] RMD with selected NMR restraints
(Fri Apr 26 2013 - 17:24:49 PDT)
Re: [AMBER] distance restraint
(Fri Apr 26 2013 - 17:22:29 PDT)
[AMBER] Compiling problems with -openmp
(Fri Apr 26 2013 - 12:51:28 PDT)
Re: [AMBER] Gradually reduce the restraint within one step
(Fri Apr 26 2013 - 12:08:33 PDT)
Re: [AMBER] amber tutorial13 :constructing and simulating crystals with amber12
(Thu Apr 25 2013 - 16:48:03 PDT)
Re: [AMBER] Cyclic peptide problem
(Thu Apr 25 2013 - 04:30:23 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
(Wed Apr 24 2013 - 11:20:21 PDT)
Re: [AMBER] Reducing positional restraint gradually
(Tue Apr 23 2013 - 09:02:30 PDT)
Re: [AMBER] carbohydrate-GLYCAM 06-cellulose Iβ
(Mon Apr 22 2013 - 17:56:33 PDT)
[AMBER] Release of AmberTools13
(Mon Apr 22 2013 - 13:33:11 PDT)
Re: [AMBER] dihedral term for furan and thiophene molecules
(Mon Apr 22 2013 - 08:04:18 PDT)
Re: [AMBER] parameters for single amino acid MD
(Mon Apr 22 2013 - 08:03:04 PDT)
Re: [AMBER] protein-ligand docking
(Sat Apr 20 2013 - 05:48:27 PDT)
Re: [AMBER] Using MTKPP to turn a nonstandard organometallic compound in pdb format into AMBER inpcrd and prmtop files
(Sat Apr 20 2013 - 05:43:39 PDT)
Re: [AMBER] gaff support for iron?
(Thu Apr 18 2013 - 06:14:25 PDT)
Re: [AMBER] tleap cannot create topology and coordinate files
(Wed Apr 17 2013 - 06:44:11 PDT)
Re: [AMBER] Fortran error while runnig
(Wed Apr 17 2013 - 00:34:14 PDT)
Re: [AMBER] problem in creating circular DNA using NAB
(Wed Apr 17 2013 - 00:19:30 PDT)
Re: [AMBER] on the ussage of mopac with Antechamber
(Tue Apr 16 2013 - 04:51:32 PDT)
Re: [AMBER] Whirling ssDNA like a helicopter (Movie attached)
(Tue Apr 16 2013 - 04:47:35 PDT)
Re: [AMBER] problem in creating circular DNA using NAB
(Mon Apr 15 2013 - 10:58:48 PDT)
Re: [AMBER] on the ussage of mopac with Antechamber
(Mon Apr 15 2013 - 10:29:59 PDT)
Re: [AMBER] Amber installation problems
(Fri Apr 12 2013 - 17:37:54 PDT)
Re: [AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program
(Fri Apr 12 2013 - 04:49:01 PDT)
Re: [AMBER] Amber installation problems
(Fri Apr 12 2013 - 04:44:47 PDT)
Re: [AMBER] LINMIN FAILURE in amber12
(Mon Apr 08 2013 - 04:48:50 PDT)
Re: [AMBER] Out of Box in PMEMD
(Sat Apr 06 2013 - 06:10:20 PDT)
Re: [AMBER] parameter problem for NVE/NPE or NPV ensemble
(Thu Apr 04 2013 - 07:00:27 PDT)
Re: [AMBER] parameter problem for NVE/NPE or NPV ensemble
(Thu Apr 04 2013 - 04:49:38 PDT)
Re: [AMBER] vecs file
(Wed Apr 03 2013 - 08:20:05 PDT)
Re: [AMBER] Different binding energy order between ATP (GTP) and protein in Amber ff10 FF and CHARMM27 FF using MMPBSA.py script
(Tue Apr 02 2013 - 04:46:36 PDT)
dbaogen
Re: [AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program
(Sat Apr 13 2013 - 23:17:09 PDT)
Re: [AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program
(Fri Apr 12 2013 - 03:23:44 PDT)
[AMBER] large Standard Deviation of binding free energy using QM/MM-GBSA method in Amber 11 with AmberTools 12
(Thu Apr 11 2013 - 05:15:31 PDT)
[AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program
(Wed Apr 10 2013 - 20:37:00 PDT)
Re: [AMBER] large difference of nonpolar solvation free energy using MMPBSA.py in AmberTools1.5 or AmberTools12
(Tue Apr 09 2013 - 18:29:23 PDT)
[AMBER] large difference of nonpolar solvation free energy using MMPBSA.py in AmberTools1.5 or AmberTools12
(Tue Apr 09 2013 - 00:24:58 PDT)
[AMBER] CalcError: sander.APBS failed with prmtop using MMPBSA.py by Amber 11 and AmberTools 12
(Thu Apr 04 2013 - 19:14:43 PDT)
[AMBER] Different binding energy order between ATP (GTP) and protein in Amber ff10 FF and CHARMM27 FF using MMPBSA.py script
(Mon Apr 01 2013 - 19:05:30 PDT)
Deák Robert
Re: [AMBER] vecs file
(Thu Apr 04 2013 - 05:38:30 PDT)
Re: [AMBER] vecs file
(Wed Apr 03 2013 - 06:11:25 PDT)
Re: [AMBER] vecs file
(Wed Apr 03 2013 - 05:44:43 PDT)
Dickson, Callum
Re: [AMBER] GAFFlipid forcefield
(Mon Apr 08 2013 - 05:02:30 PDT)
diego alonso
Re: [AMBER] aMD question: How to read the amd.log file
(Tue Apr 16 2013 - 16:00:12 PDT)
Diego Javier Alonso de Armiño
Re: [AMBER] aMD reweighting and amd.log file.
(Wed Apr 17 2013 - 07:54:04 PDT)
[AMBER] aMD reweighting and amd.log file.
(Tue Apr 16 2013 - 16:05:56 PDT)
[AMBER] aMD question: How to read the amd.log file
(Tue Apr 16 2013 - 14:56:54 PDT)
Re: [AMBER] Measure (and print to file) distances on the fly in pmemd.cuda
(Sun Apr 07 2013 - 09:33:11 PDT)
[AMBER] Fwd: Accelerated Molecular Dynamics
(Sat Apr 06 2013 - 13:40:18 PDT)
[AMBER] Measure (and print to file) distances on the fly in pmemd.cuda
(Sat Apr 06 2013 - 13:38:11 PDT)
[AMBER] Accelerated Molecular Dynamics
(Fri Apr 05 2013 - 08:44:33 PDT)
Donato Pera
[AMBER] Amber MPI CPU number problem
(Mon Apr 22 2013 - 02:34:43 PDT)
Re: [AMBER] Amber installation problems
(Mon Apr 15 2013 - 03:16:31 PDT)
Re: [AMBER] Amber installation problems
(Fri Apr 12 2013 - 01:49:01 PDT)
Re: [AMBER] Amber installation problems
(Thu Apr 11 2013 - 23:57:20 PDT)
Re: [AMBER] Amber installation problems
(Wed Apr 10 2013 - 07:32:19 PDT)
[AMBER] Amber installation problems
(Wed Apr 10 2013 - 06:48:39 PDT)
ET
[AMBER] Paper detailing GPU Simulations Compared to CPU code
(Mon Apr 29 2013 - 08:15:02 PDT)
Eugene Yedvabny
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
(Sat Apr 27 2013 - 15:26:15 PDT)
Re: [AMBER] Compiling problems with -openmp
(Fri Apr 26 2013 - 17:22:00 PDT)
[AMBER] Compilation errors for AmberTools 13 with OpenMP
(Thu Apr 25 2013 - 18:32:34 PDT)
Fabrício Bracht
Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein
(Thu Apr 18 2013 - 11:19:56 PDT)
Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein
(Wed Apr 17 2013 - 10:40:54 PDT)
[AMBER] Fwd: Problems with tleap and popc membrane with protein
(Tue Apr 16 2013 - 19:16:01 PDT)
[AMBER] Problems with tleap and popc membrane with protein
(Tue Apr 16 2013 - 14:17:14 PDT)
filip fratev
Re: [AMBER] aMD question: How to read the amd.log file
(Tue Apr 16 2013 - 18:15:50 PDT)
FyD
Re: [AMBER] Using MTKPP to turn a nonstandard organometallic compound in pdb format into AMBER inpcrd and prmtop files
(Sun Apr 21 2013 - 07:42:29 PDT)
Re: [AMBER] problem in loading 5'terminal phosphate group of tRNA
(Fri Apr 12 2013 - 07:03:34 PDT)
Re: [AMBER] ff atom types
(Fri Apr 12 2013 - 06:46:00 PDT)
Re: [AMBER] on the usage of Antechamber for the ligand parametrisation
(Tue Apr 09 2013 - 23:13:42 PDT)
Re: [AMBER] on the usage of Antechamber for the ligand parametrisation
(Tue Apr 09 2013 - 03:12:23 PDT)
Re: [AMBER] problem in loading 5'terminal phosphate group of tRNA
(Mon Apr 08 2013 - 05:33:23 PDT)
Re: [AMBER] problem in loading 5'terminal phosphate group of tRNA
(Mon Apr 08 2013 - 00:48:41 PDT)
Re: [AMBER] problem in loading 5'terminal phosphate group of tRNA
(Sat Apr 06 2013 - 05:51:08 PDT)
Re: [AMBER] chromium in leap
(Thu Apr 04 2013 - 23:25:55 PDT)
Re: [AMBER] MD Simulation of Heavy Metal(Bi or Sb) compound molecule
(Thu Apr 04 2013 - 02:36:15 PDT)
Ganesh Kamath
Re: [AMBER] GAFFlipid using custom lipids
(Mon Apr 15 2013 - 11:32:21 PDT)
gargi borgohai
Re: [AMBER] Query about checking of convergence in REMD
(Fri Apr 26 2013 - 06:14:58 PDT)
Gaurao Dhoke
Re: [AMBER] Regarding MD run in vacuum
(Wed Apr 03 2013 - 03:26:57 PDT)
[AMBER] Regarding MD run in vacuum
(Wed Apr 03 2013 - 01:56:21 PDT)
George M Giambasu
Re: [AMBER] calculating diffusion constants - multiplying factor (10/6)?
(Mon Apr 01 2013 - 07:19:15 PDT)
George Tzotzos
Re: [AMBER] Clarification on sander
(Tue Apr 16 2013 - 13:02:31 PDT)
[AMBER] Clarification on sander
(Tue Apr 16 2013 - 11:24:08 PDT)
Gerald Monard
Re: [AMBER] Time step of 5 fs??
(Wed Apr 03 2013 - 01:07:18 PDT)
Re: [AMBER] Is SHAKE necessary in running an MD?V
(Tue Apr 02 2013 - 00:30:34 PDT)
Re: [AMBER] Is SHAKE necessary in running an MD?V
(Mon Apr 01 2013 - 03:08:06 PDT)
Gustavo Seabra
Re: [AMBER] pmemd.cuda.MPI with npt
(Wed Apr 17 2013 - 11:30:40 PDT)
Re: [AMBER] pmemd.cuda.MPI with npt
(Wed Apr 17 2013 - 11:10:43 PDT)
Hai Nguyen
Re: [AMBER] VMD shows an atom stretched waaaay out
(Mon Apr 22 2013 - 12:15:02 PDT)
HIMANSHU JOSHI
Re: [AMBER] pmemd.cuda.MPI with npt
(Thu Apr 18 2013 - 23:01:05 PDT)
Re: [AMBER] pmemd.cuda.MPI with npt
(Wed Apr 17 2013 - 22:33:11 PDT)
Re: [AMBER] pmemd.cuda.MPI with npt
(Wed Apr 17 2013 - 22:24:07 PDT)
Re: [AMBER] pmemd.cuda.MPI with npt
(Wed Apr 17 2013 - 11:24:37 PDT)
[AMBER] pmemd.cuda.MPI with npt
(Wed Apr 17 2013 - 11:03:07 PDT)
HM
[AMBER] Time step of 5 fs??
(Tue Apr 02 2013 - 23:59:55 PDT)
Hoshin Kim
[AMBER] Whirling ssDNA like a helicopter (Movie attached)
(Mon Apr 15 2013 - 15:23:05 PDT)
Igor Marques
Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein
(Thu Apr 18 2013 - 06:36:43 PDT)
Re: [AMBER] Amber installation problems
(Mon Apr 15 2013 - 08:58:01 PDT)
Re: [AMBER] Amber installation problems
(Sat Apr 13 2013 - 03:31:28 PDT)
Re: [AMBER] Amber installation problems
(Fri Apr 12 2013 - 10:40:34 PDT)
Ilyas Yildirim
Re: [AMBER] list of (dihedral and angle) parameters (GAFF)
(Fri Apr 26 2013 - 09:41:48 PDT)
Jagur Lambix
Re: [AMBER] Tool to parameterize the ligand molecules
(Fri Apr 12 2013 - 08:05:53 PDT)
[AMBER] Tool to parameterize the ligand molecules
(Thu Apr 11 2013 - 16:18:14 PDT)
James Starlight
[AMBER] protein-ligand docking
(Fri Apr 19 2013 - 23:57:37 PDT)
Re: [AMBER] on the ussage of mopac with Antechamber
(Tue Apr 16 2013 - 08:00:53 PDT)
Re: [AMBER] on the ussage of mopac with Antechamber
(Mon Apr 15 2013 - 21:44:20 PDT)
[AMBER] on the ussage of mopac with Antechamber
(Fri Apr 12 2013 - 22:58:56 PDT)
Re: [AMBER] on the usage of Antechamber for the ligand parametrisation
(Wed Apr 10 2013 - 00:18:26 PDT)
Re: [AMBER] on the usage of Antechamber for the ligand parametrisation
(Tue Apr 09 2013 - 22:33:39 PDT)
Re: [AMBER] on the usage of Antechamber for the ligand parametrisation
(Mon Apr 08 2013 - 04:52:31 PDT)
[AMBER] on the usage of Antechamber for the ligand parametrisation
(Mon Apr 08 2013 - 04:48:40 PDT)
Re: [AMBER] Problem with the amber12 compilation
(Mon Apr 08 2013 - 03:50:04 PDT)
[AMBER] Problem with the amber12 compilation
(Mon Apr 08 2013 - 02:36:23 PDT)
Jan-Philip Gehrcke
Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
(Tue Apr 30 2013 - 06:37:27 PDT)
[AMBER] pb_read.F90: minor issue // AmberTools . GitHub?
(Tue Apr 30 2013 - 06:27:51 PDT)
Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
(Tue Apr 30 2013 - 06:05:09 PDT)
Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
(Tue Apr 30 2013 - 03:51:27 PDT)
[AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
(Tue Apr 30 2013 - 03:06:56 PDT)
Re: [AMBER] pmemd: time-dependent distance restraint (as with jar=1) + torsional restraints
(Thu Apr 25 2013 - 07:35:12 PDT)
Re: [AMBER] pmemd: time-dependent distance restraint (as with jar=1) + torsional restraints
(Thu Apr 25 2013 - 05:22:58 PDT)
[AMBER] pmemd: time-dependent distance restraint (as with jar=1) + torsional restraints
(Thu Apr 25 2013 - 05:08:06 PDT)
Re: [AMBER] Reducing positional restraint gradually
(Wed Apr 24 2013 - 01:46:24 PDT)
Re: [AMBER] Reducing positional restraint gradually
(Tue Apr 23 2013 - 07:17:44 PDT)
Re: [AMBER] Reducing positional restraint gradually
(Mon Apr 22 2013 - 14:11:07 PDT)
Re: [AMBER] Problem with the amber12 compilation
(Mon Apr 08 2013 - 03:34:05 PDT)
Re: [AMBER] GPU job scheduling: looking for recommendations and experiences
(Fri Apr 05 2013 - 07:35:41 PDT)
Re: [AMBER] MMPBSA failed
(Wed Apr 03 2013 - 05:22:53 PDT)
Re: [AMBER] MMPBSA failed
(Wed Apr 03 2013 - 01:30:59 PDT)
Jason Swails
Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
(Tue Apr 30 2013 - 06:32:20 PDT)
Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
(Tue Apr 30 2013 - 05:07:27 PDT)
Re: [AMBER] Sander/PMEMD doesn't understand line - corrupted RST output?
(Sun Apr 28 2013 - 17:59:48 PDT)
Re: [AMBER] Problem in parameter file generation
(Sat Apr 27 2013 - 21:58:54 PDT)
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
(Sat Apr 27 2013 - 14:43:14 PDT)
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
(Sat Apr 27 2013 - 06:53:51 PDT)
Re: [AMBER] Cyclic peptide problem
(Wed Apr 24 2013 - 08:34:50 PDT)
Re: [AMBER] About modelling the separation of the "DNA" strands
(Tue Apr 23 2013 - 19:02:21 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
(Tue Apr 23 2013 - 18:01:54 PDT)
Re: [AMBER] Reducing positional restraint gradually
(Tue Apr 23 2013 - 07:05:06 PDT)
Re: [AMBER] MMPBSA result interpretation helppppp
(Tue Apr 23 2013 - 05:12:43 PDT)
Re: [AMBER] Amber MPI CPU number problem
(Mon Apr 22 2013 - 19:15:37 PDT)
Re: [AMBER] ambertools13 fails to update
(Mon Apr 22 2013 - 15:59:40 PDT)
Re: [AMBER] ambertools13 fails to update
(Mon Apr 22 2013 - 15:39:04 PDT)
Re: [AMBER] Leap: Setting the bounding box manually
(Sun Apr 21 2013 - 20:05:19 PDT)
Re: [AMBER] ante-MMPBSA.py problem
(Fri Apr 19 2013 - 11:07:25 PDT)
Re: [AMBER] problems with explicit solvent MD
(Fri Apr 19 2013 - 03:50:11 PDT)
Re: [AMBER] Plotting heat maps in AMBER aMD simualtions
(Thu Apr 18 2013 - 05:04:15 PDT)
Re: [AMBER] AmberTools12 re-installation test log file
(Tue Apr 16 2013 - 18:27:50 PDT)
Re: [AMBER] Newbie solvent question
(Tue Apr 16 2013 - 12:31:09 PDT)
Re: [AMBER] Clarification on sander
(Tue Apr 16 2013 - 12:07:03 PDT)
Re: [AMBER] Plotting heat maps in AMBER aMD simualtions
(Tue Apr 16 2013 - 08:10:05 PDT)
Re: [AMBER] on the ussage of mopac with Antechamber
(Tue Apr 16 2013 - 04:51:59 PDT)
Re: [AMBER] Amber installation problems
(Mon Apr 15 2013 - 04:29:10 PDT)
Re: [AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program
(Thu Apr 11 2013 - 23:07:52 PDT)
Re: [AMBER] mopac.sh file missing in amber12/bin directory
(Thu Apr 11 2013 - 22:59:44 PDT)
Re: [AMBER] Tool to parameterize the ligand molecules
(Thu Apr 11 2013 - 16:45:52 PDT)
Re: [AMBER] Constant pH calculation: calcpka
(Thu Apr 11 2013 - 07:36:39 PDT)
Re: [AMBER] large Standard Deviation of binding free energy using QM/MM-GBSA method in Amber 11 with AmberTools 12
(Thu Apr 11 2013 - 07:28:11 PDT)
Re: [AMBER] Problem compiling AMBER12 sander.MPI with gnu
(Thu Apr 11 2013 - 07:15:15 PDT)
Re: [AMBER] Zero vdW parametes for HO in Amber
(Wed Apr 10 2013 - 21:12:24 PDT)
Re: [AMBER] Amber installation problems
(Wed Apr 10 2013 - 07:55:36 PDT)
Re: [AMBER] Extra Points support in pmemd.cuda.MPI
(Wed Apr 10 2013 - 06:27:41 PDT)
Re: [AMBER] Extra Points support in pmemd.cuda.MPI
(Wed Apr 10 2013 - 05:30:18 PDT)
Re: [AMBER] Problem with folding simulation
(Tue Apr 09 2013 - 19:51:28 PDT)
Re: [AMBER] large difference of nonpolar solvation free energy using MMPBSA.py in AmberTools1.5 or AmberTools12
(Tue Apr 09 2013 - 18:45:45 PDT)
Re: [AMBER] large difference of nonpolar solvation free energy using MMPBSA.py in AmberTools1.5 or AmberTools12
(Tue Apr 09 2013 - 14:56:17 PDT)
Re: [AMBER] implicit solvation with periodic boundary
(Mon Apr 08 2013 - 13:10:55 PDT)
Re: [AMBER] Measure (and print to file) distances on the fly in pmemd.cuda
(Sun Apr 07 2013 - 05:56:39 PDT)
Re: [AMBER] where does sander open the output files?
(Sun Apr 07 2013 - 05:43:29 PDT)
Re: [AMBER] How to modifie "runmd.f" to calculate force from obtained MD trajectory?
(Fri Apr 05 2013 - 20:33:54 PDT)
Re: [AMBER] parameter problem for NVE/NPE or NPV ensemble
(Thu Apr 04 2013 - 04:34:50 PDT)
Re: [AMBER] MMPBSA failed
(Wed Apr 03 2013 - 07:30:19 PDT)
Re: [AMBER] Regarding MD run in vacuum
(Wed Apr 03 2013 - 06:53:28 PDT)
Re: [AMBER] MMPBSA failed
(Wed Apr 03 2013 - 04:53:18 PDT)
Re: [AMBER] error in perl script (mm_pbsa.pl) for binding energy
(Mon Apr 01 2013 - 05:09:25 PDT)
Re: [AMBER] Problems with MMPBSA: mmphsa_py_energy could not be found
(Mon Apr 01 2013 - 05:07:22 PDT)
javier alejandro rendon carrillo
[AMBER] Fortran error while runnig
(Tue Apr 16 2013 - 22:00:03 PDT)
[AMBER] tleap cannot create topology and coordinate files
(Mon Apr 15 2013 - 14:22:52 PDT)
Jesper Sørensen
Re: [AMBER] PBSA focusing
(Tue Apr 16 2013 - 10:33:13 PDT)
Re: [AMBER] PBSA focusing
(Mon Apr 15 2013 - 16:03:50 PDT)
[AMBER] PBSA focusing
(Mon Apr 15 2013 - 14:06:09 PDT)
Jian Yin
Re: [AMBER] Gradually reduce the restraint within one step
(Fri Apr 26 2013 - 21:08:50 PDT)
[AMBER] Gradually reduce the restraint within one step
(Fri Apr 26 2013 - 20:24:56 PDT)
Re: [AMBER] aMD simulations in amber12
(Fri Apr 12 2013 - 10:21:20 PDT)
Jonathan Gough
Re: [AMBER] Is there a trick to fix a poor structural feature?
(Sat Apr 27 2013 - 17:39:08 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
(Wed Apr 24 2013 - 14:13:00 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
(Wed Apr 24 2013 - 13:32:21 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
(Wed Apr 24 2013 - 10:54:18 PDT)
[AMBER] Is there a trick to fix a poor structural feature?
(Tue Apr 23 2013 - 11:47:19 PDT)
Re: [AMBER] ambertools13 fails to update
(Mon Apr 22 2013 - 17:09:08 PDT)
Re: [AMBER] ambertools13 fails to update
(Mon Apr 22 2013 - 15:45:18 PDT)
[AMBER] ambertools13 fails to update
(Mon Apr 22 2013 - 15:32:22 PDT)
Re: [AMBER] VMD shows an atom stretched waaaay out
(Mon Apr 22 2013 - 14:27:57 PDT)
Re: [AMBER] VMD shows an atom stretched waaaay out
(Mon Apr 22 2013 - 12:50:05 PDT)
[AMBER] VMD shows an atom stretched waaaay out
(Mon Apr 22 2013 - 08:50:10 PDT)
Re: [AMBER] segmentation fault in tleap
(Sun Apr 21 2013 - 21:39:32 PDT)
[AMBER] segmentation fault in tleap
(Sun Apr 21 2013 - 20:09:37 PDT)
Re: [AMBER] Newbie solvent question
(Tue Apr 16 2013 - 12:34:48 PDT)
[AMBER] Newbie solvent question
(Tue Apr 16 2013 - 10:57:55 PDT)
[AMBER] Anyone (else) at the ACS meeting in NOLA?
(Sun Apr 07 2013 - 19:26:03 PDT)
Jonathan Saboury
[AMBER] Using MTKPP to turn a nonstandard organometallic compound in pdb format into AMBER inpcrd and prmtop files
(Fri Apr 19 2013 - 13:50:37 PDT)
[AMBER] gaff support for iron?
(Thu Apr 18 2013 - 00:51:17 PDT)
[AMBER] sander not installed
(Mon Apr 15 2013 - 00:50:04 PDT)
journal.update
Re: [AMBER] Out of Box in PMEMD
(Fri Apr 05 2013 - 22:03:21 PDT)
[AMBER] Out of Box in PMEMD
(Thu Apr 04 2013 - 23:38:41 PDT)
Julio Dominguez
[AMBER] RRe: Ligand-Receptor complex MD - ligand doesn't > appear?
(Wed Apr 10 2013 - 13:39:18 PDT)
Re: [AMBER] Ligand-Receptor complex MD - ligand doesn't appear?
(Tue Apr 09 2013 - 13:13:58 PDT)
Kamakshi
[AMBER] Help with GB-OBC calculations
(Tue Apr 02 2013 - 04:34:06 PDT)
Kanin Wichapong
[AMBER] AMBER CUDA Installation
(Tue Apr 30 2013 - 09:17:59 PDT)
Karl N. Kirschner
Re: [AMBER] dihedral term for furan and thiophene molecules
(Tue Apr 23 2013 - 04:31:29 PDT)
Re: [AMBER] paramfit questions
(Fri Apr 19 2013 - 00:26:09 PDT)
[AMBER] Wolf2Pack Parameterization Tool
(Tue Apr 16 2013 - 02:27:11 PDT)
Kepa K. Burusco
Re: [AMBER] Hydration Free Energy by TI
(Tue Apr 23 2013 - 09:33:54 PDT)
[AMBER] Hydration Free Energy by TI
(Mon Apr 15 2013 - 05:09:45 PDT)
Krisztina Feher
[AMBER] RMD with selected NMR restraints
(Fri Apr 26 2013 - 06:32:40 PDT)
Kshatresh Dutta Dubey
Re: [AMBER] Problem in parameter file generation
(Sun Apr 28 2013 - 00:23:31 PDT)
Re: [AMBER] Problem in parameter file generation
(Sat Apr 27 2013 - 14:28:23 PDT)
[AMBER] Problem in parameter file generation
(Sat Apr 27 2013 - 13:41:34 PDT)
kureeckal ramesh
[AMBER] error in perl script (mm_pbsa.pl) for binding energy
(Mon Apr 01 2013 - 02:42:09 PDT)
kurisaki
Re: [AMBER] Prepare PRMTOP file for off-SHAKE simulation
(Sun Apr 28 2013 - 21:14:20 PDT)
[AMBER] Prepare PRMTOP file for off-SHAKE simulation
(Sun Apr 28 2013 - 20:18:56 PDT)
[AMBER] how to get force information through MD run
(Sat Apr 27 2013 - 01:06:54 PDT)
Re: [AMBER] Fwd: Input file for NVT simulation
(Mon Apr 22 2013 - 00:59:49 PDT)
Re: [AMBER] # of snapshots for force does not match that of mdcrd
(Sun Apr 14 2013 - 01:58:13 PDT)
[AMBER] # of snapshots for force does not match that of mdcrd
(Sat Apr 13 2013 - 23:20:21 PDT)
Re: [AMBER] where does sander open the output files?
(Sun Apr 07 2013 - 06:00:49 PDT)
Re: [AMBER] where does sander open the output files?
(Sun Apr 07 2013 - 05:59:23 PDT)
Re: [AMBER] How to modifie "runmd.f" to calculate force from obtained MD trajectory?
(Sun Apr 07 2013 - 03:39:03 PDT)
Re: [AMBER] How to modifie "runmd.f" to calculate force from obtained MD trajectory?
(Sun Apr 07 2013 - 01:22:59 PDT)
[AMBER] where does sander open the output files?
(Sun Apr 07 2013 - 01:20:48 PDT)
Re: [AMBER] How to modifie "runmd.f" to calculate force from obtained MD trajectory?
(Sat Apr 06 2013 - 20:46:01 PDT)
[AMBER] How to modifie "runmd.f" to calculate force from obtained MD trajectory?
(Fri Apr 05 2013 - 18:50:40 PDT)
Lachele Foley
Re: [AMBER] carbohydrate-GLYCAM 06-cellulose Iβ
(Mon Apr 22 2013 - 09:59:58 PDT)
Re: [AMBER] Zero vdW parametes for HO in Amber
(Wed Apr 10 2013 - 17:22:03 PDT)
Levi Pierce
Re: [AMBER] Plotting heat maps in AMBER aMD simualtions
(Thu Apr 18 2013 - 07:36:12 PDT)
Re: [AMBER] Plotting heat maps in AMBER aMD simualtions
(Wed Apr 17 2013 - 07:52:38 PDT)
M. L. Dodson
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
(Sun Apr 28 2013 - 15:38:45 PDT)
Re: [AMBER] [AMBER-Developers] Compilation errors for AmberTools 13 with OpenMP
(Sun Apr 28 2013 - 14:07:32 PDT)
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
(Sun Apr 28 2013 - 05:55:56 PDT)
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
(Sat Apr 27 2013 - 17:05:15 PDT)
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
(Sat Apr 27 2013 - 07:21:34 PDT)
Re: [AMBER] ambertools13 fails to update
(Mon Apr 22 2013 - 17:25:21 PDT)
manikanthan bhavaraju
Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein
(Tue Apr 16 2013 - 20:26:32 PDT)
Re: [AMBER] Problems with tleap and popc membrane with protein
(Tue Apr 16 2013 - 14:35:39 PDT)
marawan hussain
[AMBER] GAFFlipid forcefield
(Sun Apr 07 2013 - 20:49:44 PDT)
Marc van der Kamp
Re: [AMBER] Problem compiling AMBER12 sander.MPI with gnu
(Thu Apr 11 2013 - 13:39:14 PDT)
[AMBER] Problem compiling AMBER12 sander.MPI with gnu
(Thu Apr 11 2013 - 03:19:44 PDT)
marta wisniewska.
[AMBER] chromium in leap
(Thu Apr 04 2013 - 15:02:44 PDT)
Massimiliano Porrini
Re: [AMBER] Regarding MD run in vacuum
(Wed Apr 03 2013 - 09:54:50 PDT)
miguel
Re: [AMBER] hbond print option equivalent in cpptraj from AmberTools13?
(Sun Apr 28 2013 - 00:48:07 PDT)
[AMBER] hbond print option equivalent in cpptraj from AmberTools13?
(Sat Apr 27 2013 - 08:01:54 PDT)
Miguel Ortiz Lombardía
Re: [AMBER] clustering places all frames in one cluster
(Mon Apr 22 2013 - 06:11:46 PDT)
Re: [AMBER] Error in lmod minimization parallel test
(Mon Apr 08 2013 - 01:10:12 PDT)
[AMBER] Error in lmod minimization parallel test
(Sat Apr 06 2013 - 06:31:21 PDT)
moitrayee.mbu.iisc.ernet.in
[AMBER] Problem with folding simulation
(Tue Apr 09 2013 - 19:07:43 PDT)
Morteza Chehel Amirani
[AMBER] Changing vdW parameters for HO-type atom
(Fri Apr 19 2013 - 15:17:25 PDT)
[AMBER] Zero vdW parametes for HO in Amber
(Wed Apr 10 2013 - 15:55:40 PDT)
Mu Xia
[AMBER] About modelling the separation of the "DNA" strands
(Thu Apr 11 2013 - 01:36:50 PDT)
[AMBER] About modelling the separation of the "DNA" strands
(Mon Apr 08 2013 - 19:09:33 PDT)
N Nandi
[AMBER] problem in loading 5'terminal phosphate group of tRNA
(Thu Apr 11 2013 - 22:57:07 PDT)
[AMBER] problem in loading 5'terminal phosphate group of tRNA
(Mon Apr 08 2013 - 04:14:58 PDT)
[AMBER] problem in loading 5'terminal phosphate group of tRNA
(Sun Apr 07 2013 - 22:18:29 PDT)
[AMBER] problem in loading 5'terminal phosphate group of tRNA
(Fri Apr 05 2013 - 09:49:22 PDT)
Neha Gandhi
Re: [AMBER] Plotting heat maps in AMBER aMD simualtions
(Tue Apr 16 2013 - 22:28:43 PDT)
[AMBER] Plotting heat maps in AMBER aMD simualtions
(Tue Apr 16 2013 - 00:19:22 PDT)
Re: [AMBER] aMD simulations in amber12
(Fri Apr 12 2013 - 09:20:08 PDT)
[AMBER] aMD simulations in amber12
(Fri Apr 12 2013 - 05:59:07 PDT)
[AMBER] AMBER12 GPU performance
(Sat Apr 06 2013 - 21:17:09 PDT)
nguyentb.bii.a-star.edu.sg
Re: [AMBER] parameter problem for NVE/NPE or NPV ensemble
(Thu Apr 04 2013 - 05:51:51 PDT)
[AMBER] parameter problem for NVE/NPE or NPV ensemble
(Thu Apr 04 2013 - 01:36:14 PDT)
Nhai
Re: [AMBER] implicit solvation with periodic boundary
(Mon Apr 08 2013 - 08:50:42 PDT)
nicolai petelski
[AMBER] Problem with cluster analysis in ptraj
(Mon Apr 22 2013 - 18:12:41 PDT)
Niels Geudens
[AMBER] problems with explicit solvent MD
(Fri Apr 19 2013 - 01:09:45 PDT)
Odin Zeus
[AMBER] tleap problem
(Mon Apr 08 2013 - 07:54:46 PDT)
parul sharma
[AMBER] mopac.sh file missing in amber12/bin directory
(Thu Apr 11 2013 - 22:20:12 PDT)
Rahul Banerjee
Re: [AMBER] Reducing positional restraint gradually
(Tue Apr 23 2013 - 06:32:14 PDT)
[AMBER] Reducing positional restraint gradually
(Mon Apr 22 2013 - 12:11:44 PDT)
Rasha Alqus
Re: [AMBER] carbohydrate-GLYCAM 06-cellulose Iβ
(Fri Apr 26 2013 - 06:19:53 PDT)
[AMBER] carbohydrate-GLYCAM 06-cellulose Iβ
(Mon Apr 22 2013 - 09:14:49 PDT)
Re: [AMBER] vecs file
(Wed Apr 03 2013 - 07:51:22 PDT)
Re: [AMBER] vecs file
(Wed Apr 03 2013 - 05:58:22 PDT)
[AMBER] vecs file
(Wed Apr 03 2013 - 05:26:12 PDT)
Ray Luo
Re: [AMBER] implicit solvation with periodic boundary
(Mon Apr 08 2013 - 09:57:43 PDT)
Ray Luo, Ph.D.
Re: [AMBER] About halogen in MMPBSA calculation in AMBER9
(Fri Apr 19 2013 - 14:52:09 PDT)
Re: [AMBER] PBSA focusing
(Tue Apr 16 2013 - 11:27:51 PDT)
Re: [AMBER] PBSA focusing
(Mon Apr 15 2013 - 16:54:43 PDT)
Re: [AMBER] PBSA focusing
(Mon Apr 15 2013 - 14:38:48 PDT)
Rilei Yu
[AMBER] parameters for single amino acid MD
(Mon Apr 22 2013 - 05:49:47 PDT)
Robin Betz
Re: [AMBER] paramfit question
(Fri Apr 26 2013 - 17:16:29 PDT)
Re: [AMBER] segmentation fault in tleap
(Sun Apr 21 2013 - 21:05:33 PDT)
Re: [AMBER] paramfit questions
(Thu Apr 18 2013 - 16:53:02 PDT)
Ross Walker
Re: [AMBER] Paper detailing GPU Simulations Compared to CPU code
(Mon Apr 29 2013 - 09:19:46 PDT)
Re: [AMBER-Developers] [AMBER] Compilation errors for AmberTools 13 with OpenMP
(Sun Apr 28 2013 - 13:18:21 PDT)
Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to Sim failed for K20x using JAC and Cellulose benchmarks
(Thu Apr 25 2013 - 21:10:22 PDT)
Re: [AMBER] ig=-1 in NVE simulation
(Tue Apr 23 2013 - 23:33:10 PDT)
[AMBER] AMBER Training Workshop - Recife, Brazil - Save the Date
(Mon Apr 22 2013 - 12:53:01 PDT)
Re: [AMBER] pmemd.cuda.MPI with npt
(Thu Apr 18 2013 - 23:35:00 PDT)
Re: [AMBER] Print pressure tensor components of NVT ensemble by running pmemd.cuda.MPI
(Wed Apr 17 2013 - 16:48:57 PDT)
Re: [AMBER] Clarification on sander
(Tue Apr 16 2013 - 13:13:08 PDT)
Re: [AMBER] aMD simulations in amber12
(Fri Apr 12 2013 - 08:10:43 PDT)
Re: [AMBER] Amber installation problems
(Fri Apr 12 2013 - 08:05:58 PDT)
Re: [AMBER] Extra Points support in pmemd.cuda.MPI
(Wed Apr 10 2013 - 06:39:58 PDT)
sandeep singh
[AMBER] bug in impose command in amber tleap
(Mon Apr 29 2013 - 11:21:19 PDT)
Sangita Kachhap
[AMBER] distance restraint
(Fri Apr 26 2013 - 10:54:38 PDT)
Saugata Hazra
Re: [AMBER] AmberTools12 re-installation test log file
(Tue Apr 16 2013 - 20:23:30 PDT)
[AMBER] AmberTools12 re-installation test log file
(Tue Apr 16 2013 - 14:46:11 PDT)
Scott Brozell
Re: [AMBER-Developers] [AMBER] Compilation errors for AmberTools 13 with OpenMP
(Sun Apr 28 2013 - 15:29:57 PDT)
Scott Le Grand
Re: [AMBER] AMBER CUDA Installation
(Tue Apr 30 2013 - 11:13:26 PDT)
Re: [AMBER] pmemd.cuda.MPI with npt
(Wed Apr 17 2013 - 17:56:42 PDT)
Sebastian Petrik
Re: [AMBER] Sander/PMEMD doesn't understand line - corrupted RST output?
(Sun Apr 28 2013 - 18:49:56 PDT)
[AMBER] Sander/PMEMD doesn't understand line - corrupted RST output?
(Sun Apr 28 2013 - 17:17:26 PDT)
Re: [AMBER] RRe: Ligand-Receptor complex MD - ligand doesn't > appear?
(Wed Apr 10 2013 - 20:14:24 PDT)
Re: [AMBER] Ligand-Receptor complex MD - ligand doesn't appear?
(Wed Apr 10 2013 - 18:39:20 PDT)
Re: [AMBER] Ligand-Receptor complex MD - ligand doesn't appear?
(Tue Apr 09 2013 - 16:43:24 PDT)
[AMBER] Ligand-Receptor complex MD - ligand doesn't appear?
(Mon Apr 08 2013 - 18:26:30 PDT)
Sergio R Aragon
Re: [AMBER] antechamber espgen error for molybdenum complex:fitting values are missing
(Mon Apr 29 2013 - 19:52:56 PDT)
[AMBER] antechamber espgen error for molybdenum complex:fitting values are missing
(Mon Apr 29 2013 - 17:57:49 PDT)
Soumya Lipsa Rath
Re: [AMBER] aMD simulations in amber12
(Fri Apr 12 2013 - 09:28:18 PDT)
Re: [AMBER] LINMIN FAILURE in amber12
(Mon Apr 08 2013 - 05:16:30 PDT)
[AMBER] LINMIN FAILURE in amber12
(Sun Apr 07 2013 - 23:00:57 PDT)
steinbrt.rci.rutgers.edu
Re: [AMBER] Hydration Free Energy by TI
(Tue Apr 23 2013 - 04:45:40 PDT)
Re: [AMBER] RRe: Ligand-Receptor complex MD - ligand doesn't > appear?
(Thu Apr 11 2013 - 02:01:52 PDT)
Re: [AMBER] Ligand-Receptor complex MD - ligand doesn't appear?
(Wed Apr 10 2013 - 00:53:34 PDT)
Re: [AMBER] Ligand-Receptor complex MD - ligand doesn't appear?
(Tue Apr 09 2013 - 00:45:38 PDT)
Re: [AMBER] tleap problem
(Mon Apr 08 2013 - 08:07:06 PDT)
Re: [AMBER] Regarding MD run in vacuum
(Wed Apr 03 2013 - 03:17:13 PDT)
Re: [AMBER] Time step of 5 fs??
(Wed Apr 03 2013 - 00:43:17 PDT)
Subrata Paul
[AMBER] ig=-1 in NVE simulation
(Tue Apr 23 2013 - 23:02:11 PDT)
Sun
[AMBER] the role of surface charge
(Fri Apr 26 2013 - 01:13:53 PDT)
suresh satpati
[AMBER] xleap error - Created a new atom named: P within residue: .R<DG5 478>
(Tue Apr 09 2013 - 01:37:39 PDT)
[AMBER] Fwd: xleap problem
(Sun Apr 07 2013 - 22:52:40 PDT)
Syed Tarique Moin
Re: [AMBER] implicit solvation with periodic boundary
(Mon Apr 08 2013 - 16:32:59 PDT)
Re: [AMBER] implicit solvation with periodic boundary
(Mon Apr 08 2013 - 14:27:35 PDT)
Re: [AMBER] implicit solvation with periodic boundary
(Mon Apr 08 2013 - 09:17:32 PDT)
[AMBER] implicit solvation with periodic boundary
(Mon Apr 08 2013 - 08:39:37 PDT)
Symon Gathiaka
Re: [AMBER] Is there a trick to fix a poor structural feature?
(Thu Apr 25 2013 - 08:04:22 PDT)
Takeshi Baba
Re: [AMBER] The latest topology file format.
(Wed Apr 10 2013 - 16:38:49 PDT)
[AMBER] The latest topology file format.
(Tue Apr 09 2013 - 05:56:58 PDT)
tec3.utah.edu
Re: [AMBER] Is there a trick to fix a poor structural feature?
(Wed Apr 24 2013 - 19:51:23 PDT)
Thomas Evangelidis
Re: [AMBER] Is there a trick to fix a poor structural feature?
(Wed Apr 24 2013 - 23:02:23 PDT)
Re: [AMBER] Extra Points support in pmemd.cuda.MPI
(Wed Apr 10 2013 - 13:47:52 PDT)
Re: [AMBER] Extra Points support in pmemd.cuda.MPI
(Wed Apr 10 2013 - 06:09:56 PDT)
[AMBER] Extra Points support in pmemd.cuda.MPI
(Wed Apr 10 2013 - 03:10:51 PDT)
tluchko
Re: [AMBER] Using 3D-RISM to compute solvation free energy
(Fri Apr 19 2013 - 15:34:19 PDT)
Re: [AMBER] Using 3D-RISM to compute solvation free energy
(Fri Apr 19 2013 - 14:02:06 PDT)
Tommy Yap
[AMBER] Problems with MMPBSA: mmphsa_py_energy could not be found
(Mon Apr 01 2013 - 00:18:54 PDT)
Tru Huynh
Re: [AMBER] Amber installation problems
(Mon Apr 15 2013 - 07:40:00 PDT)
Tyler Luchko
Re: [AMBER] Using 3D-RISM to compute solvation free energy
(Sat Apr 20 2013 - 15:23:57 PDT)
Urszula Uciechowska
[AMBER] ff atom types
(Fri Apr 12 2013 - 06:12:36 PDT)
Vaibhav Dixit
[AMBER] Fwd: Input file for NVT simulation
(Mon Apr 22 2013 - 00:46:53 PDT)
[AMBER] Input file for NVT simulation
(Mon Apr 22 2013 - 00:43:16 PDT)
Re: [AMBER] clustering places all frames in one cluster
(Sun Apr 21 2013 - 22:20:38 PDT)
Vedat Durmaz
[AMBER] list of (dihedral and angle) parameters (GAFF)
(Fri Apr 26 2013 - 09:14:24 PDT)
Vijay Manickam Achari
[AMBER] calculating diffusion constants - multiplying factor (10/6)?
(Mon Apr 01 2013 - 02:21:09 PDT)
waleed zalloum
[AMBER] Solute concentration
(Mon Apr 15 2013 - 12:45:33 PDT)
Wang Bo
[AMBER] About halogen in MMPBSA calculation in AMBER9
(Fri Apr 19 2013 - 14:43:50 PDT)
[AMBER] About halogen in MMPBSA calculation in AMBER9
(Fri Apr 19 2013 - 12:17:11 PDT)
Wei Lin
[AMBER] Print pressure tensor components of NVT ensemble by running pmemd.cuda.MPI
(Wed Apr 17 2013 - 16:42:18 PDT)
[AMBER] Print pressure tensor components of NVT ensemble by running pmemd.cuda.MPI
(Wed Apr 17 2013 - 16:31:02 PDT)
Wholly Peach
[AMBER] FW: No subject
(Wed Apr 03 2013 - 06:39:22 PDT)
Yasuo Kurita
[AMBER] MD Simulation of Heavy Metal(Bi or Sb) compound molecule
(Thu Apr 04 2013 - 02:12:34 PDT)
Yong Duan
Re: [AMBER] Zero vdW parametes for HO in Amber
(Wed Apr 10 2013 - 19:27:19 PDT)
Yongxiu Li
[AMBER] amber tutorial13 :constructing and simulating crystals with amber12
(Mon Apr 22 2013 - 05:16:14 PDT)
涂志萍
[AMBER] minimize problem
(Sat Apr 06 2013 - 20:12:45 PDT)
陶晓芳
[AMBER] Question for AMBER input files (inpcrd file)
(Wed Apr 24 2013 - 19:00:07 PDT)
[AMBER] Question for AMBER input files
(Wed Apr 24 2013 - 18:19:01 PDT)
Last message date
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Tue Apr 30 2013 - 13:30:03 PDT
Archived on
: Fri Dec 20 2024 - 05:54:47 PST
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