Amber Archive May 2012 by author
873 messages
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Starting
Mon Apr 30 2012 - 19:00:03 PDT,
Ending
Thu May 31 2012 - 22:00:02 PDT
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. mirage
[AMBER] mmpbsa problem
(Fri May 04 2012 - 03:01:47 PDT)
21119012
Re: [AMBER] high value in MMPBSA
(Tue May 08 2012 - 08:56:12 PDT)
aa aa
[AMBER] conformational entropy of a peptide - how to calculate with AMBER?
(Mon May 28 2012 - 01:37:19 PDT)
[AMBER] How to get a reliable RMSF value?
(Sun May 27 2012 - 23:31:03 PDT)
Acoot Brett
[AMBER] How AMBER process the energy of hydrogen bond
(Wed May 30 2012 - 23:40:41 PDT)
[AMBER] charge and ionization state at pH 6.5
(Wed May 16 2012 - 04:11:30 PDT)
Aditya Padhi
[AMBER] Hydrogen bond energy calculation
(Wed May 23 2012 - 20:55:35 PDT)
Agostino Bruno
[AMBER] Max Pairlist Cutoff issue
(Wed May 02 2012 - 23:50:35 PDT)
Alan
Re: [AMBER] where's http://ambermd.org/bugfixes/11.0/bugfix.all?
(Wed May 23 2012 - 01:41:02 PDT)
[AMBER] where's http://ambermd.org/bugfixes/11.0/bugfix.all?
(Tue May 22 2012 - 04:03:11 PDT)
Re: [AMBER] setting gcc compiler
(Tue May 22 2012 - 01:44:01 PDT)
[AMBER] setting gcc compiler
(Mon May 21 2012 - 05:49:03 PDT)
[AMBER] How does radial work?
(Mon May 14 2012 - 09:27:22 PDT)
Re: [AMBER] ACPYPE error
(Mon May 14 2012 - 06:45:04 PDT)
Re: [AMBER] Why not AmberTools12 bugfix.all
(Fri May 04 2012 - 04:25:01 PDT)
[AMBER] Why not AmberTools12 bugfix.all
(Fri May 04 2012 - 04:15:37 PDT)
Albert
[AMBER] convert error
(Wed May 23 2012 - 00:38:57 PDT)
Re: [AMBER] was the bug fixed for tleap?
(Wed May 23 2012 - 00:23:59 PDT)
[AMBER] was the bug fixed for tleap?
(Fri May 18 2012 - 11:43:17 PDT)
Re: [AMBER] how to calculate the volume of our system?
(Thu May 17 2012 - 08:17:33 PDT)
[AMBER] how to calculate the volume of our system?
(Thu May 17 2012 - 00:13:06 PDT)
[AMBER] ACPYPE error
(Mon May 14 2012 - 06:01:07 PDT)
Re: [AMBER] bi-layer membrane system shrink with NPgamaT
(Mon May 14 2012 - 00:46:03 PDT)
[AMBER] bi-layer membrane system shrink with NPgamaT
(Sun May 13 2012 - 23:49:44 PDT)
Re: [AMBER] how can we add ACE and NME to to the cap protein terminal?
(Fri May 11 2012 - 11:03:32 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 10:58:31 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 10:20:11 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 08:52:42 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 07:20:30 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 06:58:39 PDT)
Re: [AMBER] how can we add ACE and NME to to the cap protein terminal?
(Fri May 11 2012 - 06:40:06 PDT)
Re: [AMBER] how can we add ACE and NME to to the cap protein terminal?
(Thu May 10 2012 - 21:48:58 PDT)
[AMBER] how can we add ACE and NME to to the cap protein terminal?
(Thu May 10 2012 - 13:12:44 PDT)
Re: [AMBER] job error
(Thu May 10 2012 - 00:40:15 PDT)
Re: [AMBER] job error
(Thu May 10 2012 - 00:33:02 PDT)
Re: [AMBER] how to assign SS bond?
(Thu May 10 2012 - 00:13:03 PDT)
[AMBER] how to assign SS bond?
(Thu May 10 2012 - 00:05:00 PDT)
Re: [AMBER] job error
(Wed May 09 2012 - 23:27:49 PDT)
Re: [AMBER] job error
(Wed May 09 2012 - 12:48:36 PDT)
Re: [AMBER] job error
(Wed May 09 2012 - 12:36:26 PDT)
[AMBER] job error
(Wed May 09 2012 - 12:07:58 PDT)
[AMBER] is NPAT available in Amber 12?
(Wed May 09 2012 - 10:57:56 PDT)
[AMBER] how much dyne/cm should we use for lipids?
(Wed May 09 2012 - 08:54:49 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Wed May 09 2012 - 05:55:20 PDT)
[AMBER] how to specify CUDA devices?
(Wed May 09 2012 - 05:47:44 PDT)
Re: [AMBER] bug.7 for Amber 12 has some problem
(Wed May 09 2012 - 05:42:53 PDT)
[AMBER] bug.7 for Amber 12 has some problem
(Wed May 09 2012 - 02:52:06 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Wed May 09 2012 - 02:23:22 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Wed May 09 2012 - 02:01:37 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Wed May 09 2012 - 02:00:46 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Tue May 08 2012 - 12:25:06 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Tue May 08 2012 - 11:58:31 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Tue May 08 2012 - 11:47:17 PDT)
Re: [AMBER] CUDA running error
(Tue May 08 2012 - 10:50:56 PDT)
Re: [AMBER] CUDA running error
(Tue May 08 2012 - 10:41:44 PDT)
Re: [AMBER] strange CUDA benchmark
(Tue May 08 2012 - 10:14:44 PDT)
Re: [AMBER] CUDA running error
(Tue May 08 2012 - 10:11:31 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Tue May 08 2012 - 10:06:00 PDT)
Re: [AMBER] strange CUDA benchmark
(Tue May 08 2012 - 10:01:43 PDT)
Re: [AMBER] job terminate abnormally
(Tue May 08 2012 - 08:03:48 PDT)
[AMBER] job terminate abnormally
(Tue May 08 2012 - 07:16:25 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Tue May 08 2012 - 06:47:47 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Tue May 08 2012 - 05:32:52 PDT)
[AMBER] charmmlipid2amber.x error
(Tue May 08 2012 - 02:39:37 PDT)
[AMBER] strange CUDA benchmark
(Tue May 08 2012 - 01:36:01 PDT)
[AMBER] CUDA test failed
(Mon May 07 2012 - 23:44:15 PDT)
[AMBER] CUDA running error
(Mon May 07 2012 - 22:19:07 PDT)
[AMBER] CUDA running error
(Mon May 07 2012 - 13:31:15 PDT)
Re: [AMBER] intel compiler still doesn't work for MPI
(Mon May 07 2012 - 13:07:21 PDT)
[AMBER] intel compiler still doesn't work for MPI
(Mon May 07 2012 - 12:09:37 PDT)
Re: [AMBER] strange CUDA MD output in VMD
(Mon May 07 2012 - 06:52:57 PDT)
[AMBER] strange CUDA MD output in VMD
(Sun May 06 2012 - 23:22:41 PDT)
[AMBER] a question about ensemble
(Wed May 02 2012 - 22:33:10 PDT)
[AMBER] what's the difference between sandar.MPI and sander.LES.MPI ?
(Wed May 02 2012 - 05:26:45 PDT)
Alejandro Blanco
[AMBER] MM-PBSA ATP binding
(Tue May 22 2012 - 15:54:15 PDT)
amin.imtech.res.in
[AMBER] Difference in PB results of mmpbsa and mmpbsa.mpi
(Fri May 11 2012 - 02:52:17 PDT)
Andre Serobian
Re: [AMBER] ptraj closest water script problem
(Sun May 06 2012 - 20:59:26 PDT)
[AMBER] ptraj closest water script problem
(Fri May 04 2012 - 02:32:21 PDT)
Andreas Goetz
Re: [AMBER] The QMMM_MD err calculation of amber12+ gamessUS
(Wed May 23 2012 - 13:22:53 PDT)
Re: [AMBER] qmmm_EXTERN/ tests failing
(Mon May 14 2012 - 12:52:59 PDT)
Re: [AMBER] am1d problem
(Sat May 12 2012 - 03:15:37 PDT)
Re: [AMBER] AM1-DH+
(Thu May 10 2012 - 12:08:09 PDT)
Re: [AMBER] am1d problem
(Mon May 07 2012 - 13:40:35 PDT)
anyiphysics.gmail.com
[AMBER] antechamber problem
(Mon May 21 2012 - 20:11:10 PDT)
Aron Broom
Re: [AMBER] Max Pairlist Cutoff issue
(Thu May 03 2012 - 09:06:30 PDT)
Arthur Roberts
Re: [AMBER] Problem Installing Amber on Mac OSX Lion
(Sun May 20 2012 - 19:28:28 PDT)
Re: [AMBER] Problem Installing Amber on Mac OSX Lion
(Sun May 20 2012 - 16:12:33 PDT)
[AMBER] Problem Installing Amber on Mac OSX Lion
(Sat May 19 2012 - 17:45:53 PDT)
ashley chen
Re: [AMBER] Help! Assigned Bond types may be wrong
(Mon May 28 2012 - 21:07:45 PDT)
Re: [AMBER] Help! Assigned Bond types are wrong
(Sun May 27 2012 - 23:58:47 PDT)
Asma Abro 28-FBAS/MSBI/F09
Re: [AMBER] Problem regarding antechamber
(Thu May 31 2012 - 02:22:32 PDT)
Re: [AMBER] Problem regarding antechamber
(Wed May 16 2012 - 00:44:35 PDT)
Re: [AMBER] Problem regarding antechamber
(Tue May 15 2012 - 23:17:34 PDT)
Re: [AMBER] Problem regarding antechamber
(Tue May 15 2012 - 22:32:49 PDT)
Re: [AMBER] Problem regarding antechamber
(Tue May 15 2012 - 22:09:28 PDT)
Re: [AMBER] Problem regarding antechamber
(Tue May 15 2012 - 21:05:27 PDT)
Re: [AMBER] Problem regarding antechamber
(Tue May 15 2012 - 03:25:14 PDT)
Re: [AMBER] Problem regarding antechamber
(Fri May 11 2012 - 23:25:36 PDT)
Re: [AMBER] Problem regarding antechamber
(Fri May 11 2012 - 08:10:43 PDT)
[AMBER] Problem regarding antechamber
(Fri May 11 2012 - 01:13:48 PDT)
[AMBER] My email
(Wed May 09 2012 - 00:32:21 PDT)
Asmita Gupta
Re: [AMBER] new Mg parameters
(Fri May 18 2012 - 11:35:27 PDT)
Re: [AMBER] new Mg parameters
(Fri May 18 2012 - 04:26:01 PDT)
[AMBER] new Mg parameters
(Wed May 16 2012 - 11:01:50 PDT)
Re: [AMBER] problem in reading pdb file
(Tue May 15 2012 - 01:37:47 PDT)
[AMBER] problem in reading pdb file
(Tue May 15 2012 - 00:18:42 PDT)
[AMBER] different files for protein-protein complex?
(Wed May 09 2012 - 10:09:12 PDT)
Audrius Laurynėnas
[AMBER] manual prmtop file editing for free energy calculation
(Fri May 25 2012 - 04:16:42 PDT)
Bala subramanian
[AMBER] input card for relative permittivity
(Fri May 25 2012 - 05:39:53 PDT)
[AMBER] adding/deleting water molecules in leap
(Thu May 03 2012 - 04:33:13 PDT)
Ben Ahmady
Re: [AMBER] Visualisation of periodic boundary conditions within VMD
(Wed May 23 2012 - 09:45:54 PDT)
Ben Roberts
Re: [AMBER] parameters for Zinc ion with five coordination bonds.
(Thu May 10 2012 - 15:50:48 PDT)
Re: [AMBER] Sander Error
(Tue May 08 2012 - 16:47:58 PDT)
Re: [AMBER] qmmmmask
(Tue May 08 2012 - 14:20:07 PDT)
Re: [AMBER] MCPB espgen error
(Mon May 07 2012 - 13:28:56 PDT)
Re: [AMBER] Max Pairlist Cutoff issue
(Sat May 05 2012 - 23:16:48 PDT)
Benjamin D Madej
Re: [AMBER] was the bug fixed for tleap?
(Fri May 18 2012 - 17:03:27 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 12:21:47 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Tue May 08 2012 - 12:44:40 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Tue May 08 2012 - 12:10:39 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Tue May 08 2012 - 11:36:14 PDT)
Re: [AMBER] a question about ensemble
(Thu May 03 2012 - 12:40:14 PDT)
Re: [AMBER] anisotropic pressure in bilayer simulation
(Wed May 02 2012 - 09:11:21 PDT)
Bill Miller III
Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0
(Thu May 31 2012 - 18:43:47 PDT)
Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0
(Thu May 31 2012 - 10:20:26 PDT)
Re: [AMBER] High standard deviation in entropy and decomping calculation
(Tue May 29 2012 - 05:58:02 PDT)
Re: [AMBER] Can I use “-rewrite-output” option in redoing the free energy calculation
(Tue May 29 2012 - 04:55:03 PDT)
Re: [AMBER] large deviation on entropy value using ambertools1.5
(Mon May 28 2012 - 06:55:41 PDT)
Re: [AMBER] why is internal energy not taken into account for G gas?
(Mon May 28 2012 - 04:53:02 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Tue May 22 2012 - 18:40:01 PDT)
Re: [AMBER] MM-PBSA ATP binding
(Tue May 22 2012 - 18:16:42 PDT)
Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI)
(Mon May 21 2012 - 15:33:06 PDT)
Re: [AMBER] MMPBSA-CalcError
(Sun May 20 2012 - 19:32:43 PDT)
Re: [AMBER] MMPBSA-CalcError
(Sun May 20 2012 - 19:14:50 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Sat May 19 2012 - 06:55:47 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Fri May 18 2012 - 17:20:53 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Fri May 18 2012 - 14:06:50 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Fri May 18 2012 - 12:46:13 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Fri May 18 2012 - 12:02:15 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Fri May 18 2012 - 11:49:47 PDT)
Re: [AMBER] Periodicity errors in pymdsapb
(Fri May 18 2012 - 11:38:41 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Fri May 18 2012 - 11:35:56 PDT)
Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI)
(Fri May 18 2012 - 11:02:56 PDT)
Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI)
(Fri May 18 2012 - 08:36:07 PDT)
Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI)
(Fri May 18 2012 - 06:11:30 PDT)
Re: [AMBER] MMPBSA.py problem
(Tue May 15 2012 - 17:39:56 PDT)
Re: [AMBER] Energy Differences between mmpbsa_py_energy and sander outputs (reposting)
(Fri May 11 2012 - 08:19:43 PDT)
Re: [AMBER] Difference in PB results of mmpbsa and mmpbsa.mpi
(Fri May 11 2012 - 05:14:47 PDT)
Re: [AMBER] SA Bomb in sa_arc(): Allocation aborted
(Wed May 09 2012 - 06:08:50 PDT)
Re: [AMBER] MMPBSA calculation of large proteins
(Wed May 09 2012 - 06:07:18 PDT)
Re: [AMBER] inconsistent results in MMPBSA w/o energy decomposition
(Tue May 08 2012 - 11:56:52 PDT)
Re: [AMBER] inconsistent results in MMPBSA w/o energy decomposition
(Tue May 08 2012 - 11:35:48 PDT)
Re: [AMBER] high value in MMPBSA
(Tue May 08 2012 - 04:51:08 PDT)
Bill Ross
Re: [AMBER] antechamber problem
(Mon May 21 2012 - 20:23:42 PDT)
Re: [AMBER] job error
(Wed May 09 2012 - 13:36:27 PDT)
Re: [AMBER] job error
(Wed May 09 2012 - 13:29:33 PDT)
bin wang
Re: [AMBER] How to resume production phase simulation from power failure?
(Tue May 29 2012 - 06:40:22 PDT)
[AMBER] How to resume production phase simulation from power failure?
(Mon May 28 2012 - 08:54:59 PDT)
bmartini
[AMBER] Trouble calculating free energy
(Thu May 31 2012 - 20:14:57 PDT)
[AMBER] mm_pbsa.pl analysis
(Thu May 31 2012 - 08:52:27 PDT)
Brian Radak
Re: [AMBER] How AMBER process the energy of hydrogen bond
(Thu May 31 2012 - 04:33:21 PDT)
Re: [AMBER] am1d problem
(Wed May 30 2012 - 19:15:48 PDT)
Re: [AMBER] manual prmtop file editing for free energy calculation
(Fri May 25 2012 - 06:17:33 PDT)
Re: [AMBER] AM1/D - ATP+PROTEIN
(Fri May 25 2012 - 06:02:46 PDT)
Re: [AMBER] qmmmmask
(Wed May 09 2012 - 11:21:04 PDT)
Re: [AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 )
(Tue May 08 2012 - 11:10:50 PDT)
Re: [AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 )
(Tue May 08 2012 - 05:32:07 PDT)
C.M. Baker
Re: [AMBER] sleap/tleap differences for parmbsc0 DNA
(Wed May 16 2012 - 04:38:03 PDT)
[AMBER] sleap/tleap differences for parmbsc0 DNA
(Tue May 15 2012 - 02:46:22 PDT)
c00jsw00.nchc.narl.org.tw
Re: [AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 )
(Tue May 08 2012 - 10:35:41 PDT)
[AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 )
(Mon May 07 2012 - 10:20:07 PDT)
Cao Yang
Re: [AMBER] large deviation on entropy value using ambertools1.5
(Wed May 30 2012 - 05:11:43 PDT)
Re: [AMBER] large deviation on entropy value using ambertools1.5
(Tue May 29 2012 - 21:49:45 PDT)
Re: [AMBER] large deviation on entropy value using ambertools1.5
(Tue May 29 2012 - 19:45:47 PDT)
Re: [AMBER] large deviation on entropy value using ambertools1.5
(Tue May 29 2012 - 19:07:13 PDT)
[AMBER] High standard deviation in entropy and decomping calculation
(Tue May 29 2012 - 05:53:53 PDT)
[AMBER] Can I use “-rewrite-output” option in redoing the free energy calculation
(Tue May 29 2012 - 02:59:16 PDT)
Re: [AMBER] large deviation on entropy value using ambertools1.5
(Mon May 28 2012 - 23:52:46 PDT)
[AMBER] slow AMBER on my machine
(Fri May 11 2012 - 01:42:17 PDT)
Carlos Simmerling
Re: [AMBER] regarding REMD
(Fri May 11 2012 - 10:59:08 PDT)
Re: [AMBER] regarding REMD
(Fri May 11 2012 - 07:38:38 PDT)
Re: [AMBER] remd simulation
(Wed May 09 2012 - 04:56:40 PDT)
Re: [AMBER] Homotrimeric structure not holding together during equilibration steps an MD simulations.
(Mon May 07 2012 - 04:13:54 PDT)
case
Re: [AMBER] Cuda-enabled amber 11 installation error
(Thu May 31 2012 - 04:33:57 PDT)
Re: [AMBER] Loading charged Peptide in tleap
(Thu May 31 2012 - 04:28:02 PDT)
Re: [AMBER] Trouble compiling cuda, need help.
(Wed May 30 2012 - 20:38:45 PDT)
Re: [AMBER] How to resume production phase simulation from power failure?
(Mon May 28 2012 - 13:49:06 PDT)
Re: [AMBER] Compile Amber 12 with IBM compilers
(Mon May 28 2012 - 13:45:35 PDT)
Re: [AMBER] Help! Assigned Bond types are wrong
(Mon May 28 2012 - 06:11:46 PDT)
Re: [AMBER] Saving the original position of atoms on using LEaP
(Sun May 27 2012 - 06:25:50 PDT)
Re: [AMBER] Problem Installing Amber on Mac OSX Lion
(Sun May 20 2012 - 04:52:49 PDT)
Re: [AMBER] pmemd.cuda for JAC benchmark
(Sat May 19 2012 - 10:45:48 PDT)
Re: [AMBER] (no subject)
(Sat May 19 2012 - 06:18:51 PDT)
Re: [AMBER] (no subject)
(Sat May 19 2012 - 06:12:40 PDT)
Re: [AMBER] (no subject)
(Wed May 16 2012 - 18:23:59 PDT)
Re: [AMBER] charge and ionization state at pH 6.5
(Wed May 16 2012 - 15:07:14 PDT)
Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large
(Wed May 16 2012 - 15:05:27 PDT)
Re: [AMBER] Problem regarding antechamber
(Tue May 15 2012 - 22:52:39 PDT)
Re: [AMBER] MMPBSA.py problem
(Tue May 15 2012 - 22:45:25 PDT)
Re: [AMBER] problems with added hydrogens to non standard residue
(Tue May 15 2012 - 06:07:55 PDT)
Re: [AMBER] Problem regarding antechamber
(Tue May 15 2012 - 05:59:34 PDT)
Re: [AMBER] sleap/tleap differences for parmbsc0 DNA
(Tue May 15 2012 - 03:53:03 PDT)
Re: [AMBER] problem in reading pdb file
(Tue May 15 2012 - 03:26:15 PDT)
Re: [AMBER] problem in reading pdb file
(Tue May 15 2012 - 01:18:03 PDT)
Re: [AMBER] Antechamber Error
(Mon May 14 2012 - 15:41:31 PDT)
Re: [AMBER] Periodicity errors in pymdsapb
(Mon May 14 2012 - 14:54:04 PDT)
Re: [AMBER] How to generate single mismatch DNA duplex using NAB
(Sat May 12 2012 - 10:48:45 PDT)
Re: [AMBER] apply an external force
(Sat May 12 2012 - 10:46:24 PDT)
Re: [AMBER] how can we add ACE and NME to to the cap protein terminal?
(Thu May 10 2012 - 15:05:53 PDT)
Re: [AMBER] error with torus in ffgbsa
(Mon May 07 2012 - 18:26:16 PDT)
Re: [AMBER] A1. Conversion of Gaussian output into mol 2 file
(Sun May 06 2012 - 08:17:23 PDT)
Re: [AMBER] 答复: 答复: add H-atoms automatic in tleap
(Sun May 06 2012 - 04:48:39 PDT)
Re: [AMBER] 答复: add H-atoms automatic in tleap
(Sat May 05 2012 - 18:41:53 PDT)
Re: [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration
(Sat May 05 2012 - 06:45:09 PDT)
Re: [AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug
(Sat May 05 2012 - 06:28:02 PDT)
Re: [AMBER] mbondi3
(Thu May 03 2012 - 19:14:00 PDT)
Re: [AMBER] Building Amber 12 & python
(Thu May 03 2012 - 13:57:58 PDT)
Re: [AMBER] a question about ensemble
(Thu May 03 2012 - 12:40:57 PDT)
Catein Catherine
[AMBER] Can AMBER do Go model?
(Sat May 26 2012 - 08:14:09 PDT)
[AMBER] How to calculate entropy lost upon binding?
(Fri May 25 2012 - 19:16:10 PDT)
[AMBER] How can we make sure we have the extent of conformational sampling is enough?
(Fri May 25 2012 - 19:10:32 PDT)
Charles Johnson
Re: [AMBER] How to generate single mismatch DNA duplex using NAB
(Mon May 14 2012 - 05:41:19 PDT)
Re: [AMBER] RNA xleap
(Fri May 11 2012 - 11:07:54 PDT)
[AMBER] RNA xleap
(Fri May 11 2012 - 09:18:53 PDT)
Charlotte Siska
[AMBER] error with torus in ffgbsa
(Mon May 07 2012 - 15:31:29 PDT)
Chris Chris
[AMBER] problem with mol2 to pdb conversion
(Mon May 21 2012 - 20:46:04 PDT)
Re: [AMBER] Problems doing MD on protein complex
(Wed May 09 2012 - 14:58:45 PDT)
[AMBER] Problems doing MD on protein complex
(Wed May 09 2012 - 08:29:22 PDT)
Re: [AMBER] help with pmemd .in file
(Tue May 08 2012 - 21:49:28 PDT)
Re: [AMBER] help with pmemd .in file
(Tue May 08 2012 - 09:23:17 PDT)
Re: [AMBER] help with pmemd .in file
(Mon May 07 2012 - 18:43:13 PDT)
Re: [AMBER] help with pmemd .in file
(Mon May 07 2012 - 18:30:43 PDT)
[AMBER] help with pmemd .in file
(Mon May 07 2012 - 18:15:58 PDT)
[AMBER] error when using PMEMD
(Mon May 07 2012 - 12:22:06 PDT)
Claire Shoemake
Re: [AMBER] problem in reading pdb file
(Tue May 15 2012 - 14:53:06 PDT)
colvin
Re: [AMBER] cpptraj-secstruct
(Wed May 23 2012 - 02:00:50 PDT)
Re: [AMBER] cpptraj-secstruct
(Wed May 23 2012 - 01:06:01 PDT)
[AMBER] prmtop generated from chamber
(Thu May 17 2012 - 20:38:54 PDT)
[AMBER] cpptraj-secstruct
(Thu May 17 2012 - 01:06:30 PDT)
Damodaran, Komath
[AMBER] Energy Differences between mmpbsa_py_energy and sander outputs (reposting)
(Wed May 09 2012 - 16:01:16 PDT)
[AMBER] Energy Differences between mmpbsa_py_energy and sander outputs
(Wed May 02 2012 - 13:45:36 PDT)
Daniel Roe
Re: [AMBER] base pairs missing from nastruct analysis of canonical B-DNA dodecamer
(Thu May 31 2012 - 13:55:25 PDT)
Re: [AMBER] cpptraj-secstruct
(Tue May 22 2012 - 11:41:29 PDT)
Re: [AMBER] lipid11 force filed question
(Mon May 21 2012 - 16:26:45 PDT)
Re: [AMBER] lipid11 force filed question
(Mon May 21 2012 - 04:09:00 PDT)
Re: [AMBER] cpptraj-secstruct
(Thu May 17 2012 - 04:17:02 PDT)
Re: [AMBER] NetCDF Restart Files - Amber 12
(Mon May 14 2012 - 08:30:36 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 09:17:40 PDT)
Re: [AMBER] question about cpptraj surf command
(Thu May 10 2012 - 06:44:01 PDT)
Re: [AMBER] question about cpptraj surf command
(Wed May 09 2012 - 17:41:29 PDT)
Re: [AMBER] remd simulation
(Wed May 09 2012 - 05:26:34 PDT)
Re: [AMBER] strange CUDA MD output in VMD
(Mon May 07 2012 - 04:52:52 PDT)
Re: [AMBER] ptraj closest water script problem
(Fri May 04 2012 - 03:39:28 PDT)
Daniel Sindhikara
Re: [AMBER] FW: getting metal ions coordinates of nmr structures of a protein
(Thu May 10 2012 - 18:45:25 PDT)
Re: [AMBER] getting metal ions coordinates of nmr structures of a protein
(Mon Apr 30 2012 - 18:48:44 PDT)
David Cowburn
[AMBER] Purchasing -challenged researcher seeks help on GPU purchase
(Tue May 08 2012 - 11:50:12 PDT)
David A Case
Re: [AMBER] Trouble compiling cuda, need help.
(Wed May 30 2012 - 11:09:08 PDT)
Re: [AMBER] problem with solute that breaks up
(Wed May 30 2012 - 07:45:36 PDT)
Re: [AMBER] Problem regarding simulation of bio-molecules using AMBER 9
(Wed May 30 2012 - 04:51:08 PDT)
Re: [AMBER] Looping over a trajectory
(Tue May 29 2012 - 05:00:39 PDT)
Re: [AMBER] Help! Assigned Bond types may be wrong
(Tue May 29 2012 - 04:53:01 PDT)
Re: [AMBER] Compile Amber 12 with IBM compilers
(Tue May 29 2012 - 04:48:50 PDT)
Re: [AMBER] DNA capping
(Fri May 25 2012 - 04:46:58 PDT)
Re: [AMBER] Problem in Amber11 Compilation
(Thu May 24 2012 - 05:06:10 PDT)
Re: [AMBER] problem installing AMBER12 on MacOSX
(Thu May 24 2012 - 04:57:48 PDT)
Re: [AMBER] Electrostatic potential calculation
(Fri May 18 2012 - 13:02:17 PDT)
Re: [AMBER] how to calculate the volume of our system?
(Thu May 17 2012 - 05:11:31 PDT)
Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined
(Fri May 11 2012 - 13:07:17 PDT)
Re: [AMBER] RNA xleap
(Fri May 11 2012 - 11:30:13 PDT)
Re: [AMBER] RNA xleap
(Fri May 11 2012 - 10:49:35 PDT)
Re: [AMBER] Problem regarding antechamber
(Fri May 11 2012 - 10:45:45 PDT)
Re: [AMBER] regarding REMD
(Fri May 11 2012 - 10:40:02 PDT)
Re: [AMBER] slow AMBER on my machine
(Fri May 11 2012 - 05:06:45 PDT)
Re: [AMBER] Problem regarding antechamber
(Fri May 11 2012 - 05:03:12 PDT)
Re: [AMBER] how can we add ACE and NME to to the cap protein terminal?
(Fri May 11 2012 - 04:52:14 PDT)
Re: [AMBER] Amber11 using openmpi (parallel install problem)
(Thu May 10 2012 - 04:41:21 PDT)
Re: [AMBER] job error
(Wed May 09 2012 - 13:31:01 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Wed May 09 2012 - 04:43:52 PDT)
Re: [AMBER] error in SMD
(Tue May 08 2012 - 10:01:14 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Tue May 08 2012 - 05:28:11 PDT)
Re: [AMBER] Sander Error
(Tue May 08 2012 - 05:25:04 PDT)
Re: [AMBER] PLEASE GIVE SOME SUGGESTION
(Tue May 08 2012 - 05:19:32 PDT)
Re: [AMBER] help with pmemd .in file
(Tue May 08 2012 - 05:15:36 PDT)
Re: [AMBER] PLEASE GIVE SOME SUGGESTION
(Mon May 07 2012 - 10:40:14 PDT)
Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined
(Mon May 07 2012 - 05:10:00 PDT)
Re: [AMBER] add H-atoms automatic in tleap
(Fri May 04 2012 - 11:39:45 PDT)
Re: [AMBER] Amber10 parallel test
(Fri May 04 2012 - 05:14:13 PDT)
Re: [AMBER] Fwd: question
(Fri May 04 2012 - 05:09:06 PDT)
David A. Case
Re: [AMBER] mbondi3
(Wed May 23 2012 - 18:44:28 PDT)
Re: [AMBER] Antechamber Atom Types
(Wed May 23 2012 - 18:42:59 PDT)
Re: [AMBER] periodic box blow up
(Wed May 23 2012 - 04:17:38 PDT)
Re: [AMBER] how can i introduce Zn2+ in amber
(Wed May 23 2012 - 04:10:30 PDT)
Re: [AMBER] simulation with special amino acid
(Wed May 23 2012 - 04:09:07 PDT)
Re: [AMBER] MMPBSA.py issues
(Wed May 23 2012 - 04:04:24 PDT)
Re: [AMBER] refc error with PMEMD.MPI
(Tue May 22 2012 - 18:10:59 PDT)
Re: [AMBER] where's http://ambermd.org/bugfixes/11.0/bugfix.all?
(Tue May 22 2012 - 18:04:47 PDT)
Re: [AMBER] antechamber problem
(Tue May 22 2012 - 03:54:28 PDT)
Re: [AMBER] add new functions into Amber10
(Mon May 21 2012 - 18:29:14 PDT)
Re: [AMBER] setting gcc compiler
(Mon May 21 2012 - 18:02:35 PDT)
David Case
Re: [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration
(Sun May 06 2012 - 14:13:53 PDT)
David Condon
Re: [AMBER] amber99tor and amber99ez force field
(Mon May 21 2012 - 16:48:49 PDT)
Re: [AMBER] amber99tor and amber99ez force field
(Mon May 21 2012 - 15:04:09 PDT)
Re: [AMBER] amber99tor and amber99ez force field
(Mon May 21 2012 - 14:21:00 PDT)
David Watson
Re: [AMBER] problem installing AMBER12 on MacOSX
(Fri May 25 2012 - 20:35:34 PDT)
Dean Cuebas
[AMBER] base pairs missing from nastruct analysis of canonical B-DNA dodecamer
(Thu May 31 2012 - 12:00:09 PDT)
Re: [AMBER] Problems doing MD on protein complex
(Wed May 09 2012 - 11:40:26 PDT)
Re: [AMBER] RESP structure optimization for larger ligand
(Thu May 03 2012 - 09:19:42 PDT)
Debolina Mitra
[AMBER] Reallocation of memory space
(Mon May 28 2012 - 23:23:17 PDT)
[AMBER] Reallocation of memory space
(Fri May 25 2012 - 02:39:09 PDT)
[AMBER] Generate Gaussian file in antechamber
(Thu May 24 2012 - 01:33:08 PDT)
[AMBER] Solvation of surfactant molecules
(Thu May 24 2012 - 01:19:44 PDT)
[AMBER] A1. Conversion of Gaussian output into mol 2 file
(Sun May 06 2012 - 06:23:51 PDT)
DEBOSTUTI GHOSHDASTIDAR
Re: [AMBER] (no subject)
(Sat May 19 2012 - 11:14:34 PDT)
Re: [AMBER] (no subject)
(Sat May 19 2012 - 11:13:26 PDT)
Re: [AMBER] (no subject)
(Sat May 19 2012 - 02:16:36 PDT)
Re: [AMBER] (no subject)
(Wed May 16 2012 - 10:31:44 PDT)
Dickson, Callum
Re: [AMBER] Placing molecules randomly in a simulation box
(Mon May 14 2012 - 03:14:13 PDT)
Dilraj LAMA
[AMBER] regarding REMD
(Fri May 11 2012 - 00:17:55 PDT)
Dwight McGee
Re: [AMBER] MM-RISM and per residue energy decomposition
(Wed May 09 2012 - 13:40:00 PDT)
Emilio Lence
[AMBER] Homotrimeric structure not holding together during equilibration steps an MD simulations.
(Mon May 07 2012 - 03:38:47 PDT)
Fabrício Bracht
Re: [AMBER] MCPB espgen error
(Thu May 31 2012 - 09:42:14 PDT)
Re: [AMBER] MCPB espgen error
(Tue May 29 2012 - 19:54:48 PDT)
Re: [AMBER] MCPB espgen error
(Sat May 19 2012 - 07:18:02 PDT)
Re: [AMBER] MCPB espgen error
(Tue May 15 2012 - 10:27:05 PDT)
Re: [AMBER] MCPB espgen error
(Thu May 10 2012 - 05:40:56 PDT)
Re: [AMBER] MCPB espgen error
(Wed May 09 2012 - 05:40:14 PDT)
Re: [AMBER] MCPB espgen error
(Mon May 07 2012 - 21:12:44 PDT)
Re: [AMBER] MCPB espgen error
(Mon May 07 2012 - 13:36:52 PDT)
[AMBER] MCPB espgen error
(Mon May 07 2012 - 07:19:36 PDT)
[AMBER] MCPB espgen error
(Thu May 03 2012 - 14:00:58 PDT)
Fernando Martín García
Re: [AMBER] AM1/D - ATP+PROTEIN
(Fri May 25 2012 - 07:07:11 PDT)
[AMBER] AM1/D - ATP+PROTEIN
(Fri May 25 2012 - 03:22:47 PDT)
Re: [AMBER] Amber 12 cuda test failed
(Wed May 16 2012 - 23:55:12 PDT)
[AMBER] Amber 12 cuda test failed
(Wed May 16 2012 - 00:32:39 PDT)
Re: [AMBER] Amber 12 parallel compilation error
(Mon May 14 2012 - 03:53:56 PDT)
[AMBER] Amber 12 parallel compilation error
(Mon May 14 2012 - 03:46:18 PDT)
filip fratev
Re: [AMBER] Is the performance issue of CUDA 4.1 compilers resolved in CUDA 4.2 compilers?
(Wed May 16 2012 - 04:54:29 PDT)
Fluder, Eugene
[AMBER] openf90 seg-faults during compilation
(Wed May 23 2012 - 06:04:57 PDT)
francesco oteri
Re: [AMBER] Iron-Sulfur Cluster
(Fri May 25 2012 - 09:45:48 PDT)
Re: [AMBER] Iron-Sulfur Cluster
(Thu May 17 2012 - 15:51:22 PDT)
Francesco Pietra
[AMBER] Saving the original position of atoms on using LEaP
(Sat May 26 2012 - 07:13:12 PDT)
FyD
Re: [AMBER] MCPB espgen error
(Thu May 31 2012 - 12:37:52 PDT)
Re: [AMBER] Problem regarding antechamber
(Thu May 31 2012 - 02:51:27 PDT)
Re: [AMBER] MCPB espgen error
(Tue May 29 2012 - 22:42:39 PDT)
Re: [AMBER] Solvation of surfactant molecules
(Thu May 24 2012 - 23:33:49 PDT)
Re: [AMBER] DNA capping
(Thu May 24 2012 - 23:31:25 PDT)
Re: [AMBER] SIMMULATION OF CARBON NANOTUBE
(Thu May 24 2012 - 23:18:32 PDT)
Re: [AMBER] MCPB espgen error
(Sat May 19 2012 - 08:52:14 PDT)
Re: [AMBER] 1-4 scale factors
(Fri May 18 2012 - 23:30:29 PDT)
Re: [AMBER] 1-4 scale factors
(Wed May 16 2012 - 22:58:27 PDT)
Re: [AMBER] 1-4 scale factors
(Wed May 16 2012 - 12:30:50 PDT)
Re: [AMBER] problems with added hydrogens to non standard residue
(Wed May 16 2012 - 06:19:52 PDT)
Re: [AMBER] Problem regarding antechamber
(Wed May 16 2012 - 01:29:11 PDT)
Re: [AMBER] problems with added hydrogens to non standard residue
(Tue May 15 2012 - 06:42:45 PDT)
Re: [AMBER] problems with added hydrogens to non standard residue
(Tue May 15 2012 - 00:07:44 PDT)
Re: [AMBER] problems with added hydrogens to non standard residue
(Mon May 14 2012 - 03:40:03 PDT)
Re: [AMBER] Zinc ion with five coordination bonds
(Wed May 09 2012 - 04:31:25 PDT)
Re: [AMBER] MCPB espgen error
(Mon May 07 2012 - 13:56:55 PDT)
Re: [AMBER] A1. Conversion of Gaussian output into mol 2 file
(Sun May 06 2012 - 23:49:50 PDT)
Re: [AMBER] : add H-atoms automatic in tleap
(Sun May 06 2012 - 01:40:00 PDT)
Re: [AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug
(Sat May 05 2012 - 01:15:31 PDT)
Re: [AMBER] Some problem with building Non-standard residue
(Fri May 04 2012 - 06:14:49 PDT)
Re: [AMBER] RESP structure optimization for larger ligand
(Fri May 04 2012 - 01:33:40 PDT)
Re: [AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug
(Fri May 04 2012 - 01:04:13 PDT)
Re: [AMBER] Some problem with building Non-standard residue
(Wed May 02 2012 - 02:25:32 PDT)
g t
Re: [AMBER] problem with mol2 to pdb conversion
(Thu May 24 2012 - 01:24:44 PDT)
Re: [AMBER] refc error with PMEMD.MPI
(Wed May 23 2012 - 09:56:57 PDT)
[AMBER] creating a primitive object such as a cylinder in amber
(Tue May 22 2012 - 10:58:58 PDT)
[AMBER] refc error with PMEMD.MPI
(Tue May 22 2012 - 10:55:41 PDT)
Gabriel Jara
Re: [AMBER] am1d problem
(Wed May 16 2012 - 18:02:25 PDT)
Re: [AMBER] am1d problem
(Fri May 11 2012 - 17:36:47 PDT)
[AMBER] am1d problem
(Thu May 03 2012 - 15:10:38 PDT)
Genzo Tanaka
[AMBER] Failure in mol surf in pymdpbsa
(Tue May 22 2012 - 12:25:19 PDT)
Re: [AMBER] Periodicity errors in pymdsapb
(Tue May 22 2012 - 09:19:05 PDT)
[AMBER] Failure in mol surf in pymdpbsa
(Thu May 17 2012 - 09:08:10 PDT)
Re: [AMBER] Periodicity errors in pymdsapb
(Thu May 17 2012 - 09:02:31 PDT)
Re: [AMBER] Periodicity errors in pymdsapb
(Tue May 15 2012 - 08:36:43 PDT)
Re: [AMBER] Periodicity errors in pymdsapb
(Mon May 14 2012 - 10:07:44 PDT)
[AMBER] Periodicity errors in pymdsapb
(Mon May 14 2012 - 09:57:46 PDT)
George Tzotzos
Re: [AMBER] problem with mol2 to pdb conversion
(Thu May 24 2012 - 06:06:25 PDT)
Re: [AMBER] sander.MPI error
(Fri May 11 2012 - 06:26:22 PDT)
Re: [AMBER] sander.MPI error
(Fri May 11 2012 - 06:02:35 PDT)
Re: [AMBER] sander.MPI error
(Fri May 11 2012 - 05:32:47 PDT)
[AMBER] sander.MPI error
(Fri May 11 2012 - 02:30:12 PDT)
Gould, Ian R
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 10:14:16 PDT)
Hai Nguyen
Re: [AMBER] Build B form RNA by NAB?
(Sun May 20 2012 - 08:09:56 PDT)
Re: [AMBER] Build B form RNA by NAB?
(Sat May 19 2012 - 09:01:30 PDT)
Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large
(Wed May 16 2012 - 16:04:48 PDT)
[AMBER] Build B form RNA by NAB?
(Mon May 14 2012 - 22:36:19 PDT)
Re: [AMBER] mbondi3
(Tue May 01 2012 - 21:44:46 PDT)
Hector A. Baldoni
Re: [AMBER] parameters for Zinc ion with five coordination bonds.
(Thu May 10 2012 - 17:04:39 PDT)
HIMANSHU JOSHI
[AMBER] Problem in Amber11 Compilation
(Wed May 23 2012 - 22:07:00 PDT)
Re: [AMBER] Not able to apply bugfix on Amber 11
(Mon May 14 2012 - 07:15:33 PDT)
[AMBER] Not able to apply bugfix on Amber 11
(Mon May 14 2012 - 03:48:22 PDT)
hwchem chem
[AMBER] Heme force field
(Wed May 30 2012 - 17:48:51 PDT)
Indrajit Deb
Re: [AMBER] amber99tor and amber99ez force field
(Mon May 21 2012 - 23:35:21 PDT)
Re: [AMBER] amber99tor and amber99ez force field
(Mon May 21 2012 - 15:17:01 PDT)
Re: [AMBER] amber99tor and amber99ez force field
(Mon May 21 2012 - 15:06:06 PDT)
Re: [AMBER] amber99tor and amber99ez force field
(Mon May 21 2012 - 14:43:10 PDT)
[AMBER] amber99tor and amber99ez force field
(Mon May 21 2012 - 13:21:43 PDT)
Jacopo Sgrignani
Re: [AMBER] qmmmmask
(Wed May 09 2012 - 11:49:59 PDT)
[AMBER] qmmmmask
(Tue May 08 2012 - 13:45:16 PDT)
Jagur Lambix
[AMBER] parameters for Zinc ion with five coordination bonds.
(Thu May 10 2012 - 13:12:56 PDT)
[AMBER] Zinc ion with five coordination bonds
(Wed May 09 2012 - 09:58:21 PDT)
[AMBER] Zinc ion with five coordination bonds
(Tue May 08 2012 - 13:15:10 PDT)
[AMBER] Zinc ion with five coordination bonds
(Tue May 08 2012 - 10:53:19 PDT)
Jan-Philip Gehrcke
Re: [AMBER] Amber tools 12 and esp visualization in VMD and PyMol
(Wed May 23 2012 - 09:20:52 PDT)
Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster
(Tue May 22 2012 - 10:11:28 PDT)
Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster
(Tue May 22 2012 - 09:25:39 PDT)
Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster
(Tue May 22 2012 - 08:21:14 PDT)
Re: [AMBER] Electrostatic potential calculation
(Mon May 21 2012 - 04:43:41 PDT)
Re: [AMBER] Electrostatic potential calculation
(Sat May 19 2012 - 03:48:48 PDT)
[AMBER] Is the performance issue of CUDA 4.1 compilers resolved in CUDA 4.2 compilers?
(Wed May 16 2012 - 04:45:27 PDT)
Jason Swails
Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0
(Thu May 31 2012 - 20:36:26 PDT)
Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0
(Thu May 31 2012 - 19:02:00 PDT)
Re: [AMBER] Problem Installing Amber on Mac OSX Lion
(Thu May 31 2012 - 13:02:45 PDT)
Re: [AMBER] Problem Installing Amber on Mac OSX Lion
(Thu May 31 2012 - 13:01:43 PDT)
Re: [AMBER] Ptraj and new netcdf Restart files
(Thu May 31 2012 - 12:16:29 PDT)
Re: [AMBER] problem with solute that breaks up
(Wed May 30 2012 - 15:03:06 PDT)
Re: [AMBER] how long does cuda test usually take?
(Wed May 30 2012 - 13:49:19 PDT)
Re: [AMBER] Amber 12 on x86_64 CentOS 5
(Wed May 30 2012 - 08:01:51 PDT)
Re: [AMBER] Trouble compiling cuda, need help.
(Wed May 30 2012 - 06:06:55 PDT)
Re: [AMBER] Amber 12 on x86_64 CentOS 5
(Wed May 30 2012 - 06:04:45 PDT)
Re: [AMBER] large deviation on entropy value using ambertools1.5
(Wed May 30 2012 - 05:44:48 PDT)
Re: [AMBER] large deviation on entropy value using ambertools1.5
(Tue May 29 2012 - 22:06:23 PDT)
Re: [AMBER] large deviation on entropy value using ambertools1.5
(Tue May 29 2012 - 20:30:01 PDT)
Re: [AMBER] large deviation on entropy value using ambertools1.5
(Tue May 29 2012 - 19:34:23 PDT)
Re: [AMBER] multi-threading cpu's or no multi-threading
(Tue May 29 2012 - 19:33:07 PDT)
Re: [AMBER] multi-threading cpu's or no multi-threading
(Tue May 29 2012 - 18:25:01 PDT)
Re: [AMBER] Looping over a trajectory
(Tue May 29 2012 - 11:41:00 PDT)
Re: [AMBER] Looping over a trajectory
(Tue May 29 2012 - 11:06:37 PDT)
Re: [AMBER] High standard deviation in entropy and decomping calculation
(Tue May 29 2012 - 10:50:38 PDT)
Re: [AMBER] Looping over a trajectory
(Tue May 29 2012 - 10:33:22 PDT)
Re: [AMBER] large deviation on entropy value using ambertools1.5
(Tue May 29 2012 - 10:28:39 PDT)
Re: [AMBER] Can I use “-rewrite-output” option in redoing the free energy calculation
(Tue May 29 2012 - 10:16:53 PDT)
Re: [AMBER] Visualisation of periodic boundary conditions within VMD
(Tue May 29 2012 - 09:59:38 PDT)
Re: [AMBER] How to get a reliable RMSF value?
(Tue May 29 2012 - 09:45:20 PDT)
Re: [AMBER] large deviation on entropy value using ambertools1.5
(Tue May 29 2012 - 06:42:48 PDT)
Re: [AMBER] AMBER Digest, Vol 162, Issue 3
(Mon May 28 2012 - 15:41:54 PDT)
Re: [AMBER] why is internal energy not taken into account for G gas?
(Mon May 28 2012 - 15:31:43 PDT)
Re: [AMBER] relaxation time
(Sun May 27 2012 - 16:57:03 PDT)
Re: [AMBER] manual prmtop file editing for free energy calculation
(Sat May 26 2012 - 16:14:55 PDT)
Re: [AMBER] pnetcdf.h missing in compiling of ptraj.MPI
(Fri May 25 2012 - 19:26:52 PDT)
Re: [AMBER] problem installing AMBER12 on MacOSX
(Fri May 25 2012 - 19:22:42 PDT)
Re: [AMBER] mbondi3
(Wed May 23 2012 - 17:25:42 PDT)
Re: [AMBER] MMPBSA.py issues
(Wed May 23 2012 - 03:02:56 PDT)
Re: [AMBER] 1-4 scale factors
(Wed May 23 2012 - 02:49:36 PDT)
Re: [AMBER] Problem Installing Amber on Mac OSX Lion
(Sun May 20 2012 - 18:50:54 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Sun May 20 2012 - 18:35:26 PDT)
Re: [AMBER] mbondi3
(Sun May 20 2012 - 15:59:09 PDT)
Re: [AMBER] sleap/tleap differences for parmbsc0 DNA
(Sun May 20 2012 - 15:56:24 PDT)
Re: [AMBER] Several types of extra point charges in sander?
(Sun May 20 2012 - 15:50:06 PDT)
Re: [AMBER] MMPBSA.py problem
(Tue May 15 2012 - 19:02:47 PDT)
Re: [AMBER] Periodicity errors in pymdsapb
(Tue May 15 2012 - 08:57:58 PDT)
Re: [AMBER] mpi problem
(Tue May 15 2012 - 07:42:02 PDT)
Re: [AMBER] mpi problem
(Tue May 15 2012 - 00:53:09 PDT)
Re: [AMBER] How to implement a new energy function in AMBER
(Mon May 14 2012 - 19:22:58 PDT)
Re: [AMBER] How to implement a new energy function in AMBER
(Mon May 14 2012 - 17:10:10 PDT)
Re: [AMBER] qmmm_EXTERN/ tests failing
(Mon May 14 2012 - 12:41:14 PDT)
Re: [AMBER] problem installing AMBER12 on MacOSX
(Mon May 14 2012 - 08:38:25 PDT)
Re: [AMBER] Not able to apply bugfix on Amber 11
(Mon May 14 2012 - 08:13:05 PDT)
Re: [AMBER] problem installing AMBER12 on MacOSX
(Mon May 14 2012 - 08:11:59 PDT)
Re: [AMBER] NetCDF Restart Files - Amber 12
(Mon May 14 2012 - 06:35:59 PDT)
Re: [AMBER] qmmm_EXTERN/ tests failing
(Mon May 14 2012 - 06:12:23 PDT)
Re: [AMBER] printing out total energy in sander with high precision (more digits)
(Mon May 14 2012 - 05:52:32 PDT)
Re: [AMBER] Not able to apply bugfix on Amber 11
(Mon May 14 2012 - 05:47:22 PDT)
Re: [AMBER] Large standard deviation of entropy obtained from NMODE
(Mon May 14 2012 - 01:11:19 PDT)
Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined
(Sun May 13 2012 - 19:21:32 PDT)
Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined
(Fri May 11 2012 - 16:22:44 PDT)
Re: [AMBER] regarding REMD
(Fri May 11 2012 - 12:28:57 PDT)
Re: [AMBER] sander.MPI error
(Fri May 11 2012 - 12:23:50 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 05:53:46 PDT)
Re: [AMBER] regarding REMD
(Fri May 11 2012 - 05:51:54 PDT)
Re: [AMBER] sander.MPI error
(Fri May 11 2012 - 05:40:38 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 05:34:26 PDT)
Re: [AMBER] sander.MPI error
(Fri May 11 2012 - 05:29:23 PDT)
Re: [AMBER] job error
(Wed May 09 2012 - 12:41:17 PDT)
Re: [AMBER] job error
(Wed May 09 2012 - 12:26:44 PDT)
Re: [AMBER] Question on Entropy and MMPBSA calculation
(Wed May 09 2012 - 12:18:58 PDT)
Re: [AMBER] how to specify CUDA devices?
(Wed May 09 2012 - 06:36:10 PDT)
Re: [AMBER] bug.7 for Amber 12 has some problem
(Wed May 09 2012 - 04:13:17 PDT)
Re: [AMBER] non-polar solvation energies decomposed in PB
(Tue May 08 2012 - 12:26:27 PDT)
Re: [AMBER] inconsistent results in MMPBSA w/o energy decomposition
(Tue May 08 2012 - 11:42:04 PDT)
Re: [AMBER] strange CUDA benchmark
(Tue May 08 2012 - 10:10:35 PDT)
Re: [AMBER] job terminate abnormally
(Tue May 08 2012 - 07:37:51 PDT)
Re: [AMBER] job terminate abnormally
(Tue May 08 2012 - 07:30:24 PDT)
Re: [AMBER] help with pmemd .in file
(Mon May 07 2012 - 18:27:58 PDT)
Re: [AMBER] error when using PMEMD
(Mon May 07 2012 - 12:44:00 PDT)
Re: [AMBER] intel compiler still doesn't work for MPI
(Mon May 07 2012 - 12:43:06 PDT)
Re: [AMBER] MMPBSA calculation of large proteins
(Mon May 07 2012 - 07:14:04 PDT)
Re: [AMBER] Why not AmberTools12 bugfix.all
(Fri May 04 2012 - 06:21:02 PDT)
Re: [AMBER] adding/deleting water molecules in leap
(Thu May 03 2012 - 18:15:23 PDT)
Re: [AMBER] adding/deleting water molecules in leap
(Thu May 03 2012 - 15:59:55 PDT)
Re: [AMBER] mbondi3
(Wed May 02 2012 - 17:00:14 PDT)
Re: [AMBER] error in decomposition analysis using ambertools 1.5
(Wed May 02 2012 - 16:42:23 PDT)
Re: [AMBER] mbondi3
(Wed May 02 2012 - 13:07:09 PDT)
Re: [AMBER] error in decomposition analysis using ambertools 1.5
(Wed May 02 2012 - 12:57:39 PDT)
Re: [AMBER] error in decomposition analysis using ambertools 1.5
(Tue May 01 2012 - 08:41:05 PDT)
Re: [AMBER] input format for qms
(Tue May 01 2012 - 03:26:27 PDT)
javacfish
[AMBER] The QMMM_MD err calculation of amber12+ gamessUS
(Fri May 18 2012 - 02:52:12 PDT)
Jesper Soerensen
Re: [AMBER] mbondi3
(Wed May 02 2012 - 16:21:08 PDT)
Jesper Sørensen
Re: [AMBER] mbondi3
(Wed May 23 2012 - 15:21:21 PDT)
Re: [AMBER] new Mg parameters
(Fri May 18 2012 - 09:49:21 PDT)
Re: [AMBER] new Mg parameters
(Thu May 17 2012 - 12:39:22 PDT)
Re: [AMBER] mbondi3
(Wed May 16 2012 - 15:26:49 PDT)
Re: [AMBER] new Mg parameters
(Wed May 16 2012 - 12:16:06 PDT)
Re: [AMBER] new Mg parameters
(Wed May 16 2012 - 11:51:13 PDT)
Re: [AMBER] vdW parameters for cations
(Wed May 09 2012 - 10:58:37 PDT)
[AMBER] vdW parameters for cations
(Tue May 08 2012 - 22:20:57 PDT)
Re: [AMBER] mbondi3
(Thu May 03 2012 - 14:08:09 PDT)
Re: [AMBER] mbondi3
(Thu May 03 2012 - 08:56:02 PDT)
Re: [AMBER] mbondi3
(Wed May 02 2012 - 08:05:41 PDT)
Re: [AMBER] Radii in prmtop
(Wed May 02 2012 - 07:59:56 PDT)
Jiri Sponer
Re: [AMBER] new Mg parameters
(Fri May 18 2012 - 04:59:31 PDT)
Re: [AMBER] new Mg parameters
(Thu May 17 2012 - 12:54:44 PDT)
Re: [AMBER] new Mg parameters
(Thu May 17 2012 - 12:19:46 PDT)
jit mukherjee
[AMBER] simmulation of carbon nanotube
(Mon May 28 2012 - 21:18:20 PDT)
Re: [AMBER] SIMMULATION OF CARBON NANOTUBE
(Fri May 25 2012 - 12:35:11 PDT)
[AMBER] SIMMULATION OF CARBON NANOTUBE
(Wed May 23 2012 - 21:52:50 PDT)
Re: [AMBER] AMBER Digest, Vol 162, Issue 3
(Wed May 23 2012 - 21:37:56 PDT)
Re: [AMBER] PLEASE GIVE SOME SUGGESTION
(Tue May 08 2012 - 20:40:48 PDT)
Re: [AMBER] PLEASE GIVE SOME SUGGESTION
(Mon May 07 2012 - 19:18:18 PDT)
Re: [AMBER] PLEASE GIVE SOME SUGGESTION
(Mon May 07 2012 - 13:10:04 PDT)
Re: [AMBER] PLEASE GIVE SOME SUGGESTION
(Mon May 07 2012 - 10:08:21 PDT)
[AMBER] PLEASE GIVE SOME SUGGESTION
(Mon May 07 2012 - 05:14:44 PDT)
John S
[AMBER] Volume fraction
(Mon May 28 2012 - 12:36:43 PDT)
Jonathan Gough
Re: [AMBER] how long does cuda test usually take?
(Wed May 30 2012 - 17:48:46 PDT)
Re: [AMBER] how long does cuda test usually take?
(Wed May 30 2012 - 13:52:15 PDT)
[AMBER] how long does cuda test usually take?
(Wed May 30 2012 - 13:23:09 PDT)
Re: [AMBER] Trouble compiling cuda, need help.
(Wed May 30 2012 - 12:20:12 PDT)
Re: [AMBER] Trouble compiling cuda, need help.
(Wed May 30 2012 - 11:44:19 PDT)
Re: [AMBER] Trouble compiling cuda, need help.
(Wed May 30 2012 - 11:27:08 PDT)
Re: [AMBER] Trouble compiling cuda, need help.
(Wed May 30 2012 - 09:54:23 PDT)
Re: [AMBER] Trouble compiling cuda, need help.
(Wed May 30 2012 - 09:29:44 PDT)
Re: [AMBER] Trouble compiling cuda, need help.
(Wed May 30 2012 - 06:08:06 PDT)
[AMBER] Trouble compiling cuda, need help.
(Wed May 30 2012 - 05:25:39 PDT)
Re: [AMBER] multi-threading cpu's or no multi-threading
(Tue May 29 2012 - 19:25:33 PDT)
[AMBER] multi-threading cpu's or no multi-threading
(Tue May 29 2012 - 15:40:05 PDT)
Joshua Adelman
[AMBER] Ptraj and new netcdf Restart files
(Thu May 31 2012 - 10:55:05 PDT)
Julio Dominguez
Re: [AMBER] AMBER Digest, Vol 162, Issue 3
(Thu May 24 2012 - 08:48:15 PDT)
Re: [AMBER] Problem Installing Amber on Mac OSX Lion (lenin)
(Sun May 20 2012 - 16:08:53 PDT)
jyoti alyan
[AMBER] SA Bomb in sa_arc(): Allocation aborted
(Tue May 08 2012 - 23:53:50 PDT)
Jyotsna Bhat
Re: [AMBER] MMPBSA calculation of large proteins
(Wed May 09 2012 - 07:57:49 PDT)
Re: [AMBER] MMPBSA calculation of large proteins
(Tue May 08 2012 - 22:05:21 PDT)
Re: [AMBER] MMPBSA calculation of large proteins
(Tue May 08 2012 - 03:02:40 PDT)
Re: [AMBER] PLEASE GIVE SOME SUGGESTION
(Mon May 07 2012 - 21:25:48 PDT)
Re: [AMBER] MMPBSA calculation of large proteins
(Mon May 07 2012 - 09:31:30 PDT)
[AMBER] MMPBSA calculation of large proteins
(Sun May 06 2012 - 23:58:16 PDT)
kamlesh sahu
Re: [AMBER] periodic box blow up
(Wed May 23 2012 - 23:55:14 PDT)
[AMBER] periodic box blow up
(Wed May 23 2012 - 02:23:48 PDT)
Karl N. Kirschner
Re: [AMBER] 1-4 scale factors
(Mon May 21 2012 - 00:31:40 PDT)
Kevin Parkes
Re: [AMBER] Amber 12 on x86_64 CentOS 5
(Thu May 31 2012 - 06:21:55 PDT)
Re: [AMBER] Amber 12 on x86_64 CentOS 5
(Wed May 30 2012 - 06:25:54 PDT)
[AMBER] Amber 12 on x86_64 CentOS 5
(Wed May 30 2012 - 05:48:40 PDT)
Khaled Barakat
[AMBER] High Electrostatic Energy in MMPBSA analysis
(Tue May 22 2012 - 19:41:29 PDT)
[AMBER] High Electrostatic interaction
(Tue May 22 2012 - 07:41:25 PDT)
[AMBER] High Electrostatic Interaction
(Fri May 18 2012 - 07:54:39 PDT)
kirtana S
[AMBER] relaxation time
(Sat May 26 2012 - 23:59:50 PDT)
[AMBER] Error while loading file in VMD
(Tue May 08 2012 - 07:26:42 PDT)
Kumar, Sonu
[AMBER] Question on Entropy and MMPBSA calculation
(Wed May 09 2012 - 09:09:57 PDT)
Re: [AMBER] error in decomposition analysis using ambertools 1.5
(Wed May 02 2012 - 14:13:10 PDT)
Re: [AMBER] error in decomposition analysis using ambertools 1.5
(Wed May 02 2012 - 03:46:08 PDT)
Lachele Foley (Lists)
[AMBER] OT -- Have a Model Setup Wish List?
(Mon May 21 2012 - 18:03:48 PDT)
Re: [AMBER] 1-4 scale factors
(Thu May 17 2012 - 12:21:01 PDT)
Re: [AMBER] 1-4 scale factors
(Wed May 16 2012 - 15:12:32 PDT)
Re: [AMBER] 1-4 scale factors
(Wed May 16 2012 - 10:19:25 PDT)
Re: [AMBER] Placing molecules randomly in a simulation box
(Sat May 12 2012 - 18:48:58 PDT)
Lee-Ping Wang
Re: [AMBER] Looping over a trajectory
(Tue May 29 2012 - 11:18:15 PDT)
Re: [AMBER] Looping over a trajectory
(Tue May 29 2012 - 10:53:23 PDT)
Re: [AMBER] Looping over a trajectory
(Tue May 29 2012 - 10:29:48 PDT)
[AMBER] Looping over a trajectory
(Tue May 29 2012 - 00:27:22 PDT)
Lucas A. Defelipe
[AMBER] NetCDF Restart Files - Amber 12
(Mon May 14 2012 - 06:26:05 PDT)
[AMBER] MM-RISM and per residue energy decomposition
(Wed May 09 2012 - 13:30:16 PDT)
M. L. Dodson
Re: [AMBER] How to generate single mismatch DNA duplex using NAB
(Sat May 12 2012 - 12:40:13 PDT)
Mahendra B Thapa
Re: [AMBER] FW: getting metal ions coordinates of nmr structures of a protein
(Thu May 10 2012 - 15:22:46 PDT)
manikanthan bhavaraju
[AMBER] large deviation on entropy value using ambertools1.5
(Sat May 26 2012 - 08:20:08 PDT)
[AMBER] large deviation on entropy value using ambertools1.5
(Thu May 24 2012 - 21:30:34 PDT)
marawan hussain
[AMBER] MMPBSA.py issues
(Tue May 22 2012 - 18:24:39 PDT)
Re: [AMBER] MMPBSA-CalcError
(Sun May 20 2012 - 19:30:14 PDT)
[AMBER] MMPBSA-CalcError
(Sun May 20 2012 - 19:00:46 PDT)
Re: [AMBER] MMPBSA.py problem
(Tue May 15 2012 - 21:05:38 PDT)
Re: [AMBER] MMPBSA.py problem
(Tue May 15 2012 - 20:22:06 PDT)
[AMBER] MMPBSA.py problem
(Tue May 15 2012 - 17:13:13 PDT)
[AMBER] AM1-DH+
(Thu May 10 2012 - 01:03:13 PDT)
Marc van der Kamp
Re: [AMBER] Help! Assigned Bond types are wrong
(Mon May 28 2012 - 00:59:14 PDT)
Re: [AMBER] Problem regarding CaDA
(Fri May 25 2012 - 03:36:18 PDT)
Re: [AMBER] problem with mol2 to pdb conversion
(Thu May 24 2012 - 04:40:48 PDT)
Re: [AMBER] how to introduce Zn2+ in amber
(Wed May 23 2012 - 02:01:10 PDT)
Re: [AMBER] cpptraj-secstruct
(Wed May 23 2012 - 01:10:50 PDT)
Re: [AMBER] prmtop generated from chamber
(Fri May 18 2012 - 00:43:29 PDT)
Re: [AMBER] qmmm_EXTERN/ tests failing
(Tue May 15 2012 - 02:03:53 PDT)
Re: [AMBER] qmmm_EXTERN/ tests failing
(Tue May 15 2012 - 01:36:14 PDT)
Re: [AMBER] qmmm_EXTERN/ tests failing
(Mon May 14 2012 - 09:39:34 PDT)
Re: [AMBER] printing out total energy in sander with high precision (more digits)
(Mon May 14 2012 - 05:56:15 PDT)
Re: [AMBER] printing out total energy in sander with high precision (more digits)
(Mon May 14 2012 - 02:56:21 PDT)
[AMBER] printing out total energy in sander with high precision (more digits)
(Mon May 14 2012 - 01:53:52 PDT)
[AMBER] qmmm_EXTERN/ tests failing
(Mon May 14 2012 - 00:58:52 PDT)
Re: [AMBER] sander.MPI error
(Fri May 11 2012 - 06:13:39 PDT)
Re: [AMBER] job error
(Thu May 10 2012 - 01:19:35 PDT)
Re: [AMBER] job error
(Thu May 10 2012 - 00:30:16 PDT)
Re: [AMBER] job terminate abnormally
(Tue May 08 2012 - 07:27:54 PDT)
Marek Maly
Re: [AMBER] charge and ionization state at pH 6.5
(Wed May 16 2012 - 16:15:49 PDT)
Re: [AMBER] Placing molecules randomly in a simulation box
(Mon May 14 2012 - 04:36:17 PDT)
Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ?
(Thu May 10 2012 - 15:32:02 PDT)
Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ?
(Wed May 09 2012 - 08:43:13 PDT)
Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ?
(Wed May 09 2012 - 07:38:11 PDT)
Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ?
(Mon May 07 2012 - 08:05:03 PDT)
[AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ?
(Sun May 06 2012 - 18:26:46 PDT)
Re: [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration
(Sun May 06 2012 - 14:16:29 PDT)
Re: [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration
(Sun May 06 2012 - 09:15:01 PDT)
Re: [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration
(Tue May 01 2012 - 20:12:18 PDT)
Mark Rance
[AMBER] cuda.a(kNLRadixSort. o): undefined reference to symbol '__cxa_pure_virtual
(Tue May 22 2012 - 10:18:36 PDT)
Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined
(Mon May 14 2012 - 12:07:59 PDT)
Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined
(Sun May 13 2012 - 15:56:07 PDT)
Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined
(Fri May 11 2012 - 14:52:52 PDT)
Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined
(Fri May 11 2012 - 12:51:48 PDT)
[AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined
(Sun May 06 2012 - 20:56:45 PDT)
Mark Williamson
Re: [AMBER] Heme force field
(Thu May 31 2012 - 03:16:46 PDT)
Re: [AMBER] printing out total energy in sander with high precision (more digits)
(Mon May 14 2012 - 03:21:56 PDT)
Re: [AMBER] printing out total energy in sander with high precision (more digits)
(Mon May 14 2012 - 02:40:03 PDT)
Re: [AMBER] CHAMBER with RNA
(Tue May 08 2012 - 04:11:15 PDT)
Marko Wehle
Re: [AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug
(Fri May 04 2012 - 08:38:18 PDT)
[AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug
(Thu May 03 2012 - 09:58:07 PDT)
Markus Kaukonen
Re: [AMBER] SIMMULATION OF CARBON NANOTUBE
(Thu May 24 2012 - 23:44:49 PDT)
Massimiliano Porrini
Re: [AMBER] problem with solute that breaks up
(Thu May 31 2012 - 04:55:15 PDT)
Re: [AMBER] problem with solute that breaks up
(Wed May 30 2012 - 11:05:03 PDT)
[AMBER] problem with solute that breaks up
(Wed May 30 2012 - 05:46:16 PDT)
Re: [AMBER] Placing molecules randomly in a simulation box
(Mon May 14 2012 - 04:58:18 PDT)
[AMBER] Placing molecules randomly in a simulation box
(Sat May 12 2012 - 11:09:25 PDT)
[AMBER] Umbrella sampling using GPU acceleration
(Wed May 02 2012 - 06:22:41 PDT)
mehdi bagherpoor
[AMBER] apply an external force
(Sat May 12 2012 - 07:18:11 PDT)
[AMBER] Umbrella sampling
(Thu May 10 2012 - 00:58:48 PDT)
Re: [AMBER] error in SMD
(Tue May 08 2012 - 23:15:22 PDT)
[AMBER] error in SMD
(Tue May 08 2012 - 08:41:56 PDT)
[AMBER] apply an external force between two residue
(Tue May 08 2012 - 02:08:04 PDT)
Melissa Buskes
[AMBER] Sander Error
(Tue May 08 2012 - 16:19:03 PDT)
[AMBER] Sander Error
(Mon May 07 2012 - 22:27:40 PDT)
mish
Re: [AMBER] question
(Thu May 03 2012 - 22:49:22 PDT)
Mithun Biswas
[AMBER] DNA capping
(Wed May 23 2012 - 07:54:03 PDT)
Mohammad Ashraf Bhuiyan
[AMBER] pmemd.cuda for JAC benchmark
(Fri May 18 2012 - 13:26:31 PDT)
Nadeem Ahmad Vellore
[AMBER] remd simulation
(Tue May 08 2012 - 15:43:15 PDT)
Nadine Homeyer
Re: [AMBER] A1. Conversion of Gaussian output into mol 2 file
(Sun May 06 2012 - 23:23:55 PDT)
natty yoshisawa
Re: [AMBER] How to generate single mismatch DNA duplex using NAB
(Sun May 13 2012 - 20:30:05 PDT)
[AMBER] How to generate single mismatch DNA duplex using NAB
(Thu May 10 2012 - 20:43:30 PDT)
Nicholus Bhattacharjee
Re: [AMBER] Some problem with building Non-standard residue
(Thu May 03 2012 - 23:04:29 PDT)
[AMBER] Some problem with building Non-standard residue
(Tue May 01 2012 - 04:43:49 PDT)
Niel Henriksen
Re: [AMBER] help with pmemd .in file
(Mon May 07 2012 - 18:52:49 PDT)
Re: [AMBER] help with pmemd .in file
(Mon May 07 2012 - 18:24:09 PDT)
Pedro Swagger
[AMBER] Antechamber Error
(Mon May 14 2012 - 15:01:50 PDT)
Philip Winter
Re: [AMBER] problem installing AMBER12 on MacOSX
(Wed May 23 2012 - 13:05:27 PDT)
pooja chahal
[AMBER] question
(Thu May 03 2012 - 22:16:58 PDT)
[AMBER] Fwd: question
(Thu May 03 2012 - 22:15:23 PDT)
Qin Cai
Re: [AMBER] Electrostatic potential and forces computation
(Sat May 26 2012 - 22:25:17 PDT)
Re: [AMBER] Electrostatic potential and forces computation
(Thu May 24 2012 - 14:36:18 PDT)
Re: [AMBER] Electrostatic potential calculation
(Mon May 21 2012 - 13:44:36 PDT)
Re: [AMBER] Fwd: Bug? Zero decomposed vdw and ele energies for explicit water molecules in the decomposed PB calculation.
(Wed May 16 2012 - 10:46:07 PDT)
Re: [AMBER] Electrostatic potential calculation
(Wed May 02 2012 - 13:06:21 PDT)
Qiong Zhang
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Tue May 22 2012 - 19:04:27 PDT)
Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster
(Tue May 22 2012 - 10:15:59 PDT)
Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster
(Tue May 22 2012 - 10:05:07 PDT)
Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster
(Tue May 22 2012 - 08:52:41 PDT)
[AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster
(Tue May 22 2012 - 07:59:40 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Tue May 22 2012 - 07:28:53 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Mon May 21 2012 - 17:43:27 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Sun May 20 2012 - 19:49:01 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Sat May 19 2012 - 08:01:59 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Sat May 19 2012 - 07:55:37 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Sat May 19 2012 - 07:45:58 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Fri May 18 2012 - 20:00:09 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Fri May 18 2012 - 14:37:01 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Fri May 18 2012 - 12:57:15 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Fri May 18 2012 - 12:52:17 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Fri May 18 2012 - 12:14:37 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Fri May 18 2012 - 11:56:54 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Fri May 18 2012 - 11:43:11 PDT)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Fri May 18 2012 - 11:38:44 PDT)
[AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11
(Fri May 18 2012 - 11:29:30 PDT)
Re: [AMBER] Bug? Zero decomposed vdw and ele energies for explicit water molecules in the decomposed PB calculation.
(Mon May 14 2012 - 19:48:44 PDT)
[AMBER] Bug? Zero decomposed vdw and ele energies for explicit water molecules in the decomposed PB calculation.
(Mon May 14 2012 - 11:45:40 PDT)
Re: [AMBER] Problem with the binding free energy from MMPBSA decomposed energies
(Fri May 11 2012 - 07:54:37 PDT)
[AMBER] Problem with the binding free energy from MMPBSA decomposed energies
(Thu May 10 2012 - 13:17:09 PDT)
Re: [AMBER] non-polar solvation energies decomposed in PB
(Tue May 08 2012 - 13:16:10 PDT)
[AMBER] non-polar solvation energies decomposed in PB
(Tue May 08 2012 - 09:19:22 PDT)
Rajeswari A.
Re: [AMBER] Cuda-enabled amber 11 installation error
(Thu May 31 2012 - 06:36:44 PDT)
[AMBER] Cuda-enabled amber 11 installation error
(Thu May 31 2012 - 00:33:04 PDT)
Ray Luo
Re: [AMBER] MMPBSA calculation of large proteins
(Wed May 09 2012 - 09:51:04 PDT)
Ray Luo, Ph.D.
Re: [AMBER] Electrostatic potential and forces computation
(Sun May 27 2012 - 06:25:55 PDT)
[AMBER] Fwd: Electrostatic potential and forces computation
(Fri May 25 2012 - 10:11:39 PDT)
Re: [AMBER] Electrostatic potential and forces computation
(Thu May 24 2012 - 09:35:38 PDT)
Re: [AMBER] Amber tools 12 and esp visualization in VMD and PyMol
(Wed May 23 2012 - 11:14:33 PDT)
Re: [AMBER] Amber tools 12 and esp visualization in VMD and PyMol
(Wed May 23 2012 - 10:09:27 PDT)
Re: [AMBER] High Electrostatic Energy in MMPBSA analysis
(Wed May 23 2012 - 10:03:34 PDT)
Re: [AMBER] Amber tools 12 and esp visualization in VMD and PyMol
(Mon May 21 2012 - 17:55:59 PDT)
Re: [AMBER] Electrostatic potential calculation
(Fri May 18 2012 - 09:41:02 PDT)
Re: [AMBER] Electrostatic potential calculation
(Thu May 17 2012 - 09:57:05 PDT)
Re: [AMBER] Electrostatic potential calculation
(Thu May 17 2012 - 09:52:46 PDT)
[AMBER] Fwd: Bug? Zero decomposed vdw and ele energies for explicit water molecules in the decomposed PB calculation.
(Mon May 14 2012 - 15:00:37 PDT)
Re: [AMBER] Errrors in mm_pbsa.pl
(Mon May 14 2012 - 11:05:14 PDT)
Re: [AMBER] Electrostatic potential calculation
(Thu May 10 2012 - 10:37:52 PDT)
Re: [AMBER] SA Bomb in sa_arc(): Allocation aborted
(Wed May 09 2012 - 09:29:31 PDT)
Re: [AMBER] high value in MMPBSA
(Tue May 08 2012 - 09:43:49 PDT)
Re: [AMBER] MMPBSA calculation of large proteins
(Tue May 08 2012 - 09:39:13 PDT)
Re: [AMBER] MMPBSA calculation of large proteins
(Mon May 07 2012 - 10:15:32 PDT)
Re: [AMBER] mmpbsa problem
(Fri May 04 2012 - 06:27:03 PDT)
[AMBER] Fwd: Electrostatic potential calculation
(Wed May 02 2012 - 10:13:00 PDT)
Renata KWIECIEN
Re: [AMBER] problems with added hydrogens to non standard residue
(Mon May 14 2012 - 05:26:41 PDT)
Robert Crovella
Re: [AMBER] using two GPUs
(Tue May 01 2012 - 12:15:05 PDT)
Robert Oswald
Re: [AMBER] problem installing AMBER12 on MacOSX
(Mon May 14 2012 - 08:23:31 PDT)
[AMBER] problem installing AMBER12 on MacOSX
(Mon May 14 2012 - 08:06:38 PDT)
Robin Betz
Re: [AMBER] MCPB espgen error
(Mon May 14 2012 - 17:14:35 PDT)
Re: [AMBER] MCPB espgen error
(Tue May 08 2012 - 11:23:36 PDT)
[AMBER] RESP structure optimization for larger ligand
(Wed May 02 2012 - 15:44:09 PDT)
ros
Re: [AMBER] apply an external force
(Sat May 12 2012 - 07:57:43 PDT)
Re: [AMBER] Umbrella sampling
(Thu May 10 2012 - 07:43:17 PDT)
Ross Walker
Re: [AMBER] cuda errors
(Thu May 31 2012 - 21:35:26 PDT)
Re: [AMBER] Trouble compiling cuda, need help.
(Wed May 30 2012 - 11:59:20 PDT)
Re: [AMBER] Trouble compiling cuda, need help.
(Wed May 30 2012 - 09:39:14 PDT)
Re: [AMBER] Trouble compiling cuda, need help.
(Wed May 30 2012 - 09:23:53 PDT)
Re: [AMBER] lipid11 force filed question
(Mon May 21 2012 - 12:23:49 PDT)
Re: [AMBER] prmtop generated from chamber
(Fri May 18 2012 - 10:14:26 PDT)
Re: [AMBER] Amber 12 cuda test failed
(Wed May 16 2012 - 08:19:10 PDT)
Re: [AMBER] Is the performance issue of CUDA 4.1 compilers resolved in CUDA 4.2 compilers?
(Wed May 16 2012 - 08:19:04 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 10:15:59 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 10:10:49 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 10:08:47 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 10:07:47 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 08:12:52 PDT)
Re: [AMBER] Purchasing -challenged researcher seeks help on GPU purchase
(Tue May 08 2012 - 11:58:11 PDT)
Re: [AMBER] CUDA running error
(Tue May 08 2012 - 10:48:52 PDT)
Re: [AMBER] CUDA running error
(Tue May 08 2012 - 10:24:30 PDT)
Re: [AMBER] CUDA running error
(Tue May 08 2012 - 09:57:24 PDT)
Re: [AMBER] strange CUDA benchmark
(Tue May 08 2012 - 09:50:51 PDT)
Re: [AMBER] charmmlipid2amber.x error
(Tue May 08 2012 - 09:46:18 PDT)
Re: [AMBER] help with pmemd .in file
(Tue May 08 2012 - 09:42:36 PDT)
Re: [AMBER] using two GPUs
(Thu May 03 2012 - 01:41:45 PDT)
Re: [AMBER] anisotropic pressure in bilayer simulation
(Wed May 02 2012 - 06:31:18 PDT)
Re: [AMBER] Umbrella sampling using GPU acceleration
(Wed May 02 2012 - 06:28:35 PDT)
Re: [AMBER] what's the difference between sandar.MPI and sander.LES.MPI ?
(Wed May 02 2012 - 05:40:08 PDT)
Re: [AMBER] using two GPUs
(Wed May 02 2012 - 05:38:20 PDT)
Sajeewa Pemasinghe
[AMBER] Fwd: problem with running equilibration MD in an LES system
(Thu May 31 2012 - 13:58:06 PDT)
[AMBER] problem with running equilibration MD in an LES system
(Thu May 31 2012 - 13:39:02 PDT)
[AMBER] ammonia parameters
(Tue May 22 2012 - 16:00:56 PDT)
Re: [AMBER] how can we add ACE and NME to to the cap protein terminal?
(Fri May 11 2012 - 08:18:28 PDT)
Sanjib Paul
[AMBER] Problem regarding CaDA
(Sun May 27 2012 - 03:27:56 PDT)
[AMBER] Problem regarding CaDA
(Fri May 25 2012 - 03:30:05 PDT)
Re: [AMBER] how to introduce Zn2+ in amber
(Wed May 23 2012 - 21:45:11 PDT)
[AMBER] how to introduce Zn2+ in amber
(Wed May 23 2012 - 01:50:28 PDT)
[AMBER] how can i introduce Zn2+ in amber
(Wed May 23 2012 - 00:17:45 PDT)
Sarah Edwards
[AMBER] Antechamber Atom Types
(Wed May 23 2012 - 14:43:07 PDT)
Scott Le Grand
Re: [AMBER] Trouble compiling cuda, need help.
(Wed May 30 2012 - 15:43:31 PDT)
Re: [AMBER] how long does cuda test usually take?
(Wed May 30 2012 - 14:55:47 PDT)
Re: [AMBER] Is the performance issue of CUDA 4.1 compilers resolved in CUDA 4.2 compilers?
(Wed May 16 2012 - 09:19:48 PDT)
Re: [AMBER] using two GPUs
(Tue May 01 2012 - 14:57:40 PDT)
Sean Law
[AMBER] CHAMBER with RNA
(Thu May 03 2012 - 08:16:22 PDT)
Shaandar Nyamtulga
[AMBER] Amber10 parallel test
(Thu May 03 2012 - 22:34:11 PDT)
Shaw, Sharon
Re: [AMBER] Building Amber 12 & python
(Fri May 04 2012 - 11:59:30 PDT)
[AMBER] Building Amber 12 & python
(Thu May 03 2012 - 12:58:17 PDT)
Re: [AMBER] using two GPUs
(Tue May 01 2012 - 12:21:25 PDT)
shradhey gupta
[AMBER] ptraj Hbond analysis
(Thu May 31 2012 - 06:55:04 PDT)
[AMBER] ptraj Hbond analysis
(Thu May 31 2012 - 06:53:26 PDT)
[AMBER] ptraj Hbond analysis
(Thu May 31 2012 - 06:51:00 PDT)
[AMBER] ptraj Hbond analysis
(Thu May 31 2012 - 04:51:14 PDT)
Shulin Zhuang
Re: [AMBER] Amber 12 Installation errors relevant to fftw3
(Tue May 01 2012 - 18:53:32 PDT)
Sidney Elmer
Re: [AMBER] question about cpptraj surf command
(Wed May 09 2012 - 17:56:37 PDT)
[AMBER] question about cpptraj surf command
(Wed May 09 2012 - 17:33:25 PDT)
Simon Becker
Re: [AMBER] adding/deleting water molecules in leap
(Thu May 03 2012 - 04:56:05 PDT)
somedatta pal
[AMBER] Problem regarding simulation of bio-molecules using AMBER 9
(Wed May 30 2012 - 03:41:59 PDT)
Soumya Lipsa Rath
[AMBER] Quantification of forces
(Fri May 11 2012 - 03:56:54 PDT)
Souvik Sur
[AMBER] Errrors in mm_pbsa.pl
(Mon May 14 2012 - 09:05:32 PDT)
steinbrt.rci.rutgers.edu
Re: [AMBER] Visualizing ptraj eigenvectors
(Tue May 22 2012 - 02:57:28 PDT)
Re: [AMBER] Quantification of forces
(Fri May 11 2012 - 04:32:30 PDT)
Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ?
(Thu May 10 2012 - 00:33:34 PDT)
Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ?
(Wed May 09 2012 - 08:08:52 PDT)
Re: [AMBER] PLEASE GIVE SOME SUGGESTION
(Wed May 09 2012 - 00:55:07 PDT)
Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ?
(Tue May 08 2012 - 09:40:14 PDT)
Re: [AMBER] PLEASE GIVE SOME SUGGESTION
(Mon May 07 2012 - 06:02:06 PDT)
Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ?
(Mon May 07 2012 - 00:49:31 PDT)
Re: [AMBER] question
(Fri May 04 2012 - 00:24:38 PDT)
Sudarshan Debnath
[AMBER] Amber tools 12 and esp visualization in VMD and PyMol
(Thu May 24 2012 - 02:30:10 PDT)
[AMBER] Amber tools 12 and esp visualization in VMD and PyMol
(Thu May 24 2012 - 04:00:09 PDT)
[AMBER] Amber tools 12 and esp visualization in VMD and PyMol
(Wed May 23 2012 - 22:24:34 PDT)
[AMBER] Amber tools 12 and esp visualization in VMD and PyMol
(Wed May 23 2012 - 06:10:18 PDT)
[AMBER] Amber tools 12 and esp visualization in VMD and PyMol
(Wed May 23 2012 - 05:30:31 PDT)
[AMBER] Amber tools 12 and esp visualization in VMD and PyMol
(Tue May 22 2012 - 21:23:45 PDT)
[AMBER] Amber tools 12 and esp visualization in VMD and PyMol
(Mon May 21 2012 - 12:11:04 PDT)
[AMBER] Electrostatic potential calculation
(Mon May 21 2012 - 01:20:52 PDT)
[AMBER] Electrostatic potential calculation
(Sun May 20 2012 - 02:27:58 PDT)
[AMBER] Electrostatic potential calculation
(Fri May 18 2012 - 21:50:10 PDT)
[AMBER] Electrostatic potential calculation
(Fri May 18 2012 - 21:33:18 PDT)
[AMBER] Electrostatic potential calculation
(Fri May 18 2012 - 12:29:45 PDT)
[AMBER] Electrostatic potential calculation
(Fri May 18 2012 - 05:59:00 PDT)
[AMBER] Electrostatic potential calculation
(Thu May 17 2012 - 22:11:00 PDT)
[AMBER] Electrostatic potential calculation
(Thu May 17 2012 - 08:45:49 PDT)
[AMBER] Electrostatic potential calculation
(Wed May 16 2012 - 20:09:50 PDT)
[AMBER] Electrostatic potential calculation.
(Wed May 16 2012 - 02:54:59 PDT)
[AMBER] Electrostatic potential calculation
(Thu May 10 2012 - 10:34:33 PDT)
[AMBER] Electrostatic potential calculation
(Wed May 02 2012 - 05:54:08 PDT)
Syed Tarique Moin
Re: [AMBER] mpi problem
(Fri May 18 2012 - 00:30:15 PDT)
Re: [AMBER] mpi problem
(Tue May 15 2012 - 22:29:07 PDT)
Re: [AMBER] mpi problem
(Tue May 15 2012 - 03:29:23 PDT)
[AMBER] mpi problem
(Mon May 14 2012 - 23:04:29 PDT)
Tales Yuan
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 10:36:18 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 09:24:37 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 09:11:01 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 05:43:53 PDT)
[AMBER] lipid11 force filed question
(Fri May 11 2012 - 03:19:58 PDT)
[AMBER] lipid11 force filed problem with tleap
(Fri May 11 2012 - 02:00:57 PDT)
[AMBER] lipid11 problem with leap
(Fri May 11 2012 - 00:39:14 PDT)
[AMBER] lipid11 problem with leap
(Fri May 11 2012 - 00:32:49 PDT)
tdo.chem.ucsb.edu
Re: [AMBER] how can we add ACE and NME to to the cap protein terminal?
(Thu May 10 2012 - 22:40:42 PDT)
Thomas Cheatham
Re: [AMBER] problem with solute that breaks up
(Wed May 30 2012 - 15:09:22 PDT)
Re: [AMBER] ptraj closest water script problem
(Fri May 04 2012 - 02:39:28 PDT)
Thomas Cheatham III
Re: [AMBER] new Mg parameters
(Wed May 16 2012 - 12:03:42 PDT)
Thorsten Pisternick
[AMBER] Loading charged Peptide in tleap
(Thu May 31 2012 - 01:52:31 PDT)
tluchko
Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined
(Mon May 14 2012 - 13:36:12 PDT)
Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined
(Fri May 11 2012 - 08:13:31 PDT)
tommaso.casalini.mail.polimi.it
Re: [AMBER] Electrostatic potential and forces computation
(Tue May 29 2012 - 01:56:49 PDT)
Re: [AMBER] Electrostatic potential and forces computation
(Fri May 25 2012 - 08:20:18 PDT)
[AMBER] Electrostatic potential and forces computation
(Thu May 24 2012 - 06:52:14 PDT)
[AMBER] Force.dat file from pbsa calculation
(Thu May 17 2012 - 05:04:26 PDT)
Urszula Uciechowska
Re: [AMBER] how to introduce Zn2+ in amber
(Wed May 23 2012 - 02:17:02 PDT)
Re: [AMBER] 1-4 scale factors
(Thu May 17 2012 - 04:56:50 PDT)
Re: [AMBER] 1-4 scale factors
(Wed May 16 2012 - 22:27:25 PDT)
Re: [AMBER] 1-4 scale factors
(Wed May 16 2012 - 14:49:48 PDT)
[AMBER] 1-4 scale factors
(Wed May 16 2012 - 04:01:39 PDT)
[AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large
(Wed May 16 2012 - 03:26:36 PDT)
Re: [AMBER] problems with added hydrogens to non standard residue
(Tue May 15 2012 - 07:28:41 PDT)
Re: [AMBER] problems with added hydrogens to non standard residue
(Tue May 15 2012 - 06:27:14 PDT)
Re: [AMBER] problems with added hydrogens to non standard residue
(Tue May 15 2012 - 04:47:53 PDT)
Re: [AMBER] problems with added hydrogens to non standard residue
(Mon May 14 2012 - 04:43:30 PDT)
[AMBER] problems with added hydrogens to non standard residue
(Mon May 14 2012 - 01:26:00 PDT)
Victor Ma
Re: [AMBER] inconsistent results in MMPBSA w/o energy decomposition
(Tue May 08 2012 - 11:52:19 PDT)
Re: [AMBER] inconsistent results in MMPBSA w/o energy decomposition
(Tue May 08 2012 - 11:50:12 PDT)
[AMBER] inconsistent results in MMPBSA w/o energy decomposition
(Tue May 08 2012 - 11:29:53 PDT)
Vijay Manickam Achari
[AMBER] using two GPUs
(Wed May 02 2012 - 20:55:34 PDT)
Re: [AMBER] using two GPUs
(Wed May 02 2012 - 16:37:46 PDT)
[AMBER] anisotropic pressure in bilayer simulation
(Wed May 02 2012 - 04:26:22 PDT)
Vlad Cojocaru
Re: [AMBER] Build B form RNA by NAB?
(Sat May 19 2012 - 09:48:19 PDT)
Re: [AMBER] lipid11 force filed question
(Fri May 11 2012 - 07:14:24 PDT)
[AMBER] does LIPID11 require surface tension ?
(Fri May 11 2012 - 03:03:00 PDT)
Wilson, Katie
Re: [AMBER] Iron-Sulfur Cluster
(Fri May 25 2012 - 08:06:29 PDT)
[AMBER] Iron-Sulfur Cluster
(Thu May 17 2012 - 12:14:41 PDT)
xiaojiong
[AMBER] high value in MMPBSA
(Tue May 08 2012 - 02:34:20 PDT)
Xin Geng
[AMBER] add new functions into Amber10
(Mon May 21 2012 - 12:59:51 PDT)
Re: [AMBER] How to implement a new energy function in AMBER
(Thu May 17 2012 - 16:41:27 PDT)
Re: [AMBER] How to implement a new energy function in AMBER
(Wed May 16 2012 - 10:04:12 PDT)
Re: [AMBER] How to implement a new energy function in AMBER
(Mon May 14 2012 - 18:01:40 PDT)
[AMBER] How to implement a new energy function in AMBER
(Mon May 14 2012 - 15:55:10 PDT)
Xioling Chuang
Re: [AMBER] why is internal energy not taken into account for G gas?
(Tue May 29 2012 - 19:03:45 PDT)
[AMBER] why is internal energy not taken into account for G gas?
(Sun May 27 2012 - 23:02:13 PDT)
Re: [AMBER] Large standard deviation of entropy obtained from NMODE
(Tue May 15 2012 - 18:33:38 PDT)
[AMBER] Large standard deviation of entropy obtained from NMODE
(Sat May 12 2012 - 21:40:36 PDT)
Yeng-Tseng Wang
Re: [AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 )
(Wed May 16 2012 - 01:59:15 PDT)
[AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 )
(Mon May 07 2012 - 18:05:55 PDT)
yjzhao.wh.gmail.com
[AMBER] simulation with special amino acid
(Tue May 22 2012 - 19:38:00 PDT)
[AMBER] Amber11 using openmpi (parallel install problem)
(Thu May 10 2012 - 02:45:39 PDT)
Yubo Fan
Re: [AMBER] Compile Amber 12 with IBM compilers
(Mon May 28 2012 - 18:48:56 PDT)
[AMBER] Compile Amber 12 with IBM compilers
(Mon May 28 2012 - 08:33:28 PDT)
[AMBER] pnetcdf.h missing in compiling of ptraj.MPI
(Fri May 25 2012 - 13:47:06 PDT)
Yue
Re: [AMBER] Heme force field
(Thu May 31 2012 - 18:40:10 PDT)
Yunjie Zhao
Re: [AMBER] simulation with special amino acid
(Wed May 23 2012 - 04:47:29 PDT)
Zhou Gong
[AMBER] 答复: 答复: 答复: add H-atoms automatic in tleap
(Sun May 06 2012 - 07:47:16 PDT)
[AMBER] 答复: 答复: add H-atoms automatic in tleap
(Sat May 05 2012 - 19:06:01 PDT)
[AMBER] 答复: add H-atoms automatic in tleap
(Sat May 05 2012 - 07:59:16 PDT)
[AMBER] add H-atoms automatic in tleap
(Fri May 04 2012 - 07:52:34 PDT)
Zubin Kuvadia
[AMBER] Two Dimensional Periodic Boundary Conditions
(Fri May 25 2012 - 14:10:01 PDT)
Åge Skjevik
Re: [AMBER] was the bug fixed for tleap?
(Wed May 23 2012 - 04:37:21 PDT)
Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI)
(Mon May 21 2012 - 14:56:46 PDT)
Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI)
(Fri May 18 2012 - 10:53:09 PDT)
Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI)
(Fri May 18 2012 - 07:07:17 PDT)
[AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI)
(Fri May 18 2012 - 06:01:26 PDT)
Re: [AMBER] bi-layer membrane system shrink with NPgamaT
(Mon May 14 2012 - 00:40:56 PDT)
Олег Титов
[AMBER] Several types of extra point charges in sander?
(Wed May 16 2012 - 03:10:25 PDT)
Last message date
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Thu May 31 2012 - 22:00:02 PDT
Archived on
: Sun Dec 22 2024 - 05:54:35 PST
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