Amber Archive Jun 2014 by author
574 messages
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Starting
Sun Jun 01 2014 - 03:00:02 PDT,
Ending
Mon Jun 30 2014 - 14:30:02 PDT
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#YIP YEW MUN#
[AMBER] Is it possible to tleap a protein molecule without adding terminal atoms?
(Mon Jun 09 2014 - 05:12:30 PDT)
adm
Re: [AMBER] Contributing new water models
(Mon Jun 02 2014 - 00:35:57 PDT)
Ahmed Ayoub
[AMBER] WaterBox Dimensions
(Mon Jun 02 2014 - 14:53:00 PDT)
Ahmet yıldırım
[AMBER] active site water cluster analysis
(Tue Jun 03 2014 - 02:41:47 PDT)
Aldo Segura
Re: [AMBER] GAFFlipid parameters
(Wed Jun 04 2014 - 05:56:48 PDT)
Re: [AMBER] Ligand movement in protein cavatiy
(Mon Jun 02 2014 - 06:12:26 PDT)
Re: [AMBER] Ligand movement in protein cavatiy
(Sun Jun 01 2014 - 20:34:56 PDT)
Alexandra Antipina
Re: [AMBER] GAFFlipid parameters
(Wed Jun 11 2014 - 02:35:02 PDT)
Andrew.Warden.csiro.au
[AMBER] Issues in .out trying to simulat a polymer in AMBER
(Wed Jun 25 2014 - 13:28:30 PDT)
[AMBER] Issues in .out trying to simulat a polymer in AMBER
(Tue Jun 24 2014 - 22:23:34 PDT)
Re: [AMBER] MMPBSA - calculating energy decomposition by residue in a trajectory without a ligand
(Mon Jun 23 2014 - 14:11:40 PDT)
[AMBER] MMPBSA - calculating energy decomposition by residue in a trajectory without a ligand
(Wed Jun 18 2014 - 14:53:57 PDT)
Anna Bauß
Re: [AMBER] Early termination of parallel MD
(Mon Jun 30 2014 - 01:32:04 PDT)
Anselm Horn
Re: [AMBER] Early termination of parallel MD
(Mon Jun 30 2014 - 03:20:17 PDT)
[AMBER] Isopeptide bond Asp-Lys - parameters?
(Wed Jun 04 2014 - 05:08:17 PDT)
Arunima Shilpi
[AMBER] Hbond analysi
(Sun Jun 08 2014 - 16:41:45 PDT)
[AMBER] hbond analysis
(Sun Jun 08 2014 - 06:05:47 PDT)
[AMBER] error in hydrogen bond
(Fri Jun 06 2014 - 21:48:04 PDT)
[AMBER] error in hbond analysis
(Thu Jun 05 2014 - 23:51:22 PDT)
[AMBER] donor and acceptor group in hbond
(Tue Jun 03 2014 - 21:59:17 PDT)
[AMBER] plot in xmgrace (interaction energy per residues)
(Sun Jun 01 2014 - 23:45:18 PDT)
[AMBER] error in plot of interaction energy in xmgrace
(Sun Jun 01 2014 - 09:05:15 PDT)
Asaminew Haile
Re: [AMBER] error in plot of interaction energy in xmgrace
(Sun Jun 01 2014 - 09:30:24 PDT)
Asmita Gupta
Re: [AMBER] fitting of atomic structures to cryo-em maps
(Mon Jun 16 2014 - 06:36:41 PDT)
[AMBER] fitting of atomic structures to cryo-em maps
(Mon Jun 16 2014 - 06:12:02 PDT)
[AMBER] principal axes error using cpptraj
(Wed Jun 04 2014 - 03:16:43 PDT)
Ben Roberts
Re: [AMBER] metal ion parameterisation problem
(Sun Jun 22 2014 - 14:57:11 PDT)
Benjamin D Madej
Re: [AMBER] Falling apart of membrane
(Mon Jun 30 2014 - 13:58:14 PDT)
Re: [AMBER] Setting up z-constraint
(Thu Jun 19 2014 - 19:40:27 PDT)
Re: [AMBER] charmmlipid2amber.py
(Thu Jun 12 2014 - 11:27:54 PDT)
Re: [AMBER] charmmlipid2amber.py
(Wed Jun 11 2014 - 13:47:58 PDT)
Re: [AMBER] charmmlipid2amber.py
(Tue Jun 10 2014 - 13:38:54 PDT)
Re: [AMBER] charmmlipid2amber.py
(Tue Jun 10 2014 - 12:16:41 PDT)
Re: [AMBER] Equilibration of membrane protein
(Tue Jun 10 2014 - 12:04:41 PDT)
Re: [AMBER] charmmlipid2amber.py
(Tue Jun 10 2014 - 11:51:40 PDT)
Re: [AMBER] Problem using charmmlipid2amber.py with VMD
(Mon Jun 09 2014 - 17:10:36 PDT)
Re: [AMBER] Constant surface tension on the membrane
(Mon Jun 09 2014 - 16:19:53 PDT)
Re: [AMBER] charmmlipid2amber.py
(Mon Jun 09 2014 - 15:48:20 PDT)
Re: [AMBER] Problem using charmmlipid2amber.py with VMD
(Mon Jun 09 2014 - 12:18:57 PDT)
Re: [AMBER] Problem using charmmlipid2amber.py with VMD
(Mon Jun 09 2014 - 12:03:13 PDT)
Re: [AMBER] charmmlipid2amber.py
(Mon Jun 09 2014 - 12:02:09 PDT)
Re: [AMBER] Constant surface tension on the membrane
(Mon Jun 09 2014 - 11:53:29 PDT)
Re: [AMBER] GAFFlipid parameters
(Wed Jun 04 2014 - 14:13:51 PDT)
Re: [AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10
(Wed Jun 04 2014 - 13:43:33 PDT)
Bill Miller III
Re: [AMBER] MMPBSA - calculating energy decomposition by residue in a trajectory without a ligand
(Wed Jun 18 2014 - 15:40:42 PDT)
Bill Ross
Re: [AMBER] Problem in creating prmtop inpcrd file in leap
(Tue Jun 24 2014 - 18:06:02 PDT)
Re: [AMBER] On the usage of the position restrains during equilibration
(Fri Jun 20 2014 - 18:57:36 PDT)
Re: [AMBER] On the usage of the position restrains during equilibration
(Fri Jun 20 2014 - 18:48:33 PDT)
Re: [AMBER] On the usage of the position restrains during equilibration
(Fri Jun 20 2014 - 08:36:06 PDT)
Re: [AMBER] "Invalid start to time: 28..." error
(Fri Jun 13 2014 - 18:21:38 PDT)
Re: [AMBER] "Invalid start to time: 28..." error
(Thu Jun 12 2014 - 17:20:10 PDT)
Re: [AMBER] charmmlipid2amber.py
(Tue Jun 10 2014 - 13:43:35 PDT)
Re: [AMBER] Simulation of the protein with internal water
(Thu Jun 05 2014 - 19:04:21 PDT)
Re: [AMBER] SolvateBox command
(Mon Jun 02 2014 - 17:18:41 PDT)
Brian Radak
[AMBER] cpptraj: arithmetic on data sets?
(Mon Jun 30 2014 - 07:24:47 PDT)
Re: [AMBER] Analyze properties of in parallel MD
(Fri Jun 27 2014 - 08:09:00 PDT)
[AMBER] 3D-RISM: charge density, charge distribution, and electrostatic potential
(Thu Jun 26 2014 - 14:06:16 PDT)
Re: [AMBER] Setting up z-constraint
(Wed Jun 18 2014 - 09:11:22 PDT)
Re: [AMBER] different number of waters
(Wed Jun 18 2014 - 08:01:27 PDT)
Re: [AMBER] different number of waters
(Wed Jun 18 2014 - 07:09:48 PDT)
Re: [AMBER] Queries about QM/MM
(Wed Jun 18 2014 - 07:03:36 PDT)
Re: [AMBER] QM/MMPBSA
(Wed Jun 11 2014 - 09:24:26 PDT)
Re: [AMBER] Membrane protein tutorial
(Tue Jun 10 2014 - 10:03:45 PDT)
Re: [AMBER] Membrane protein tutorial
(Tue Jun 10 2014 - 09:19:08 PDT)
Re: [AMBER] On the choosing of coordinate for the umbrella sampling
(Thu Jun 05 2014 - 06:37:29 PDT)
[AMBER] (probably) benign error when writing iapbs-pot.dx files with sander.APBS
(Tue Jun 03 2014 - 10:03:21 PDT)
Re: [AMBER] QM/MM and spin parameter
(Tue Jun 03 2014 - 08:16:36 PDT)
Carlos Simmerling
Re: [AMBER] On the choosing of coordinate for the umbrella sampling
(Thu Jun 05 2014 - 12:28:32 PDT)
Re: [AMBER] FF12SB (and FF14?) - any benchmarks/evidence of its quality?
(Sun Jun 01 2014 - 12:59:19 PDT)
Chinthaka Ratnaweera
Re: [AMBER] Per residue rmsd
(Fri Jun 27 2014 - 14:46:58 PDT)
[AMBER] Per residue rmsd
(Fri Jun 27 2014 - 13:59:49 PDT)
[AMBER] GLYCAM_06 reference
(Tue Jun 17 2014 - 00:18:35 PDT)
Daniel Roe
Re: [AMBER] Printing out matrix labels
(Mon Jun 30 2014 - 06:41:12 PDT)
Re: [AMBER] Printing out matrix labels
(Fri Jun 27 2014 - 21:13:10 PDT)
Re: [AMBER] Per residue rmsd
(Fri Jun 27 2014 - 16:07:53 PDT)
Re: [AMBER] filter trajectory with modes same number of frames
(Tue Jun 24 2014 - 08:42:55 PDT)
Re: [AMBER] about setting iwrap
(Tue Jun 24 2014 - 08:27:59 PDT)
Re: [AMBER] Clustering using CPPTRAJ
(Mon Jun 23 2014 - 06:58:50 PDT)
Re: [AMBER] Low performance in multi-pmemd.mpi
(Mon Jun 23 2014 - 06:52:58 PDT)
Re: [AMBER] filter trajectory with modes same number of frames
(Sat Jun 21 2014 - 13:48:33 PDT)
Re: [AMBER] Derive charge of multiple molecules
(Sat Jun 21 2014 - 08:45:29 PDT)
Re: [AMBER] bash scripting for MD tasks
(Fri Jun 20 2014 - 07:47:22 PDT)
Re: [AMBER] Topology issue with MMPBSA.py
(Thu Jun 19 2014 - 14:24:40 PDT)
Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems
(Thu Jun 19 2014 - 14:17:33 PDT)
Re: [AMBER] Hi
(Thu Jun 19 2014 - 13:58:44 PDT)
Re: [AMBER] remd
(Thu Jun 19 2014 - 13:57:09 PDT)
Re: [AMBER] bash scripting for MD tasks
(Mon Jun 16 2014 - 14:11:03 PDT)
Re: [AMBER] Deleting Box info from trajectory
(Sat Jun 14 2014 - 14:27:11 PDT)
Re: [AMBER] "Invalid start to time: 28..." error
(Sat Jun 14 2014 - 11:41:58 PDT)
Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems
(Sat Jun 14 2014 - 10:49:48 PDT)
Re: [AMBER] "Invalid start to time: 28..." error
(Thu Jun 12 2014 - 13:09:06 PDT)
Re: [AMBER] NVT equilibration crash using CUDA
(Tue Jun 10 2014 - 07:39:26 PDT)
Re: [AMBER] zlib issues during compilation.
(Mon Jun 09 2014 - 20:17:41 PDT)
Re: [AMBER] zlib issues during compilation.
(Mon Jun 09 2014 - 14:44:56 PDT)
Re: [AMBER] Hbond analysi
(Sun Jun 08 2014 - 19:23:24 PDT)
Re: [AMBER] 【amber】center of mass&umbrella sampling
(Fri Jun 06 2014 - 06:57:16 PDT)
Re: [AMBER] cpptraj error : not parsing mdvel file
(Fri Jun 06 2014 - 06:53:53 PDT)
Re: [AMBER] Analysis of CHARMM DNA trajectory using nastruct
(Wed Jun 04 2014 - 12:06:06 PDT)
Re: [AMBER] image distances
(Wed Jun 04 2014 - 11:06:55 PDT)
Re: [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1.
(Wed Jun 04 2014 - 10:54:02 PDT)
Re: [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1.
(Wed Jun 04 2014 - 10:15:58 PDT)
Re: [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1.
(Wed Jun 04 2014 - 08:26:12 PDT)
Re: [AMBER] donor and acceptor group in hbond
(Wed Jun 04 2014 - 06:47:16 PDT)
Re: [AMBER] principal axes error using cpptraj
(Wed Jun 04 2014 - 06:05:24 PDT)
Re: [AMBER] Error in cpptraj remlog command
(Tue Jun 03 2014 - 12:20:05 PDT)
Re: [AMBER] Distance matrix time series
(Tue Jun 03 2014 - 07:22:47 PDT)
Re: [AMBER] sudden and rapid configuration change in NVT simulation
(Tue Jun 03 2014 - 07:12:07 PDT)
Re: [AMBER] Error in cpptraj remlog command
(Mon Jun 02 2014 - 19:54:21 PDT)
Re: [AMBER] image distances
(Mon Jun 02 2014 - 07:50:22 PDT)
Re: [AMBER] request for help in plotting distance matrix plot
(Sun Jun 01 2014 - 09:35:30 PDT)
David A Case
Re: [AMBER] periodic box drifted during NVE run
(Sat Jun 28 2014 - 08:45:39 PDT)
Re: [AMBER] Sirius executable not available anymore?
(Thu Jun 26 2014 - 04:30:55 PDT)
Re: [AMBER] Issues in .out trying to simulat a polymer in AMBER
(Wed Jun 25 2014 - 04:42:05 PDT)
Re: [AMBER] Problem in creating prmtop inpcrd file in leap
(Tue Jun 24 2014 - 18:20:52 PDT)
Re: [AMBER] Sirius executable not available anymore?
(Tue Jun 24 2014 - 04:53:18 PDT)
Re: [AMBER] Se atom type
(Mon Jun 23 2014 - 05:04:42 PDT)
Re: [AMBER] EAMBER (non-restraint) in sander output
(Wed Jun 18 2014 - 20:25:07 PDT)
Re: [AMBER] Leapfrog algorithm
(Wed Jun 18 2014 - 13:34:09 PDT)
Re: [AMBER] different number of waters
(Wed Jun 18 2014 - 07:49:05 PDT)
Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14
(Wed Jun 18 2014 - 06:02:45 PDT)
Re: [AMBER] Queries about QM/MM
(Wed Jun 18 2014 - 05:54:51 PDT)
Re: [AMBER] different number of waters
(Sun Jun 15 2014 - 08:52:48 PDT)
Re: [AMBER] Deleting Box info from trajectory
(Sat Jun 14 2014 - 20:32:31 PDT)
Re: [AMBER] Deleting Box info from trajectory
(Sat Jun 14 2014 - 13:51:36 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 12:08:35 PDT)
Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems
(Thu Jun 12 2014 - 13:39:40 PDT)
Re: [AMBER] "Invalid start to time: 28..." error
(Thu Jun 12 2014 - 13:37:13 PDT)
Re: [AMBER] Magnesium FATAL error
(Thu Jun 12 2014 - 04:10:36 PDT)
Re: [AMBER] restarting MDs generated in Amber10 with Amber12
(Wed Jun 11 2014 - 04:29:24 PDT)
Re: [AMBER] problem during add ions
(Mon Jun 09 2014 - 05:02:49 PDT)
Re: [AMBER] calculating absolute binding free energy using MMPBSA
(Wed Jun 04 2014 - 12:24:46 PDT)
Re: [AMBER] sander14 MPI produces different results depending on number of used cores
(Tue Jun 03 2014 - 06:10:59 PDT)
Re: [AMBER] Mistake in water density
(Tue Jun 03 2014 - 05:14:20 PDT)
Re: [AMBER] WaterBox Dimensions
(Tue Jun 03 2014 - 05:10:35 PDT)
Re: [AMBER] plot in xmgrace (interaction energy per residues)
(Mon Jun 02 2014 - 04:07:10 PDT)
Re: [AMBER] calculation diffusion coefficient
(Sun Jun 01 2014 - 04:37:50 PDT)
David Abia
[AMBER] sander14 MPI produces different results depending on number of used cores
(Tue Jun 03 2014 - 05:00:53 PDT)
Dickson, Callum J
Re: [AMBER] GAFFlipid parameters
(Wed Jun 11 2014 - 04:25:31 PDT)
Re: [AMBER] GAFFlipid parameters
(Wed Jun 04 2014 - 05:52:44 PDT)
Re: [AMBER] GAFFlipid parameters
(Wed Jun 04 2014 - 04:37:42 PDT)
Dr. Vitaly Chaban
Re: [AMBER] Question about how a charged system can be simulated using PBC?
(Sun Jun 08 2014 - 03:27:05 PDT)
Duggan, Brendan
Re: [AMBER] EAMBER (non-restraint) in sander output
(Thu Jun 19 2014 - 14:55:12 PDT)
[AMBER] torsion restraint violation reporting
(Wed Jun 18 2014 - 11:36:08 PDT)
[AMBER] EAMBER (non-restraint) in sander output
(Wed Jun 18 2014 - 11:26:37 PDT)
Eugene Yedvabny
Re: [AMBER] Printing out matrix labels
(Sun Jun 29 2014 - 21:51:09 PDT)
Re: [AMBER] Printing out matrix labels
(Sun Jun 29 2014 - 21:44:08 PDT)
[AMBER] Printing out matrix labels
(Fri Jun 27 2014 - 18:09:12 PDT)
[AMBER] Error in cpptraj remlog command
(Mon Jun 02 2014 - 17:25:04 PDT)
[AMBER] Distance matrix time series
(Mon Jun 02 2014 - 15:19:35 PDT)
Felix Terwesten
Re: [AMBER] Sirius executable not available anymore?
(Thu Jun 26 2014 - 04:05:23 PDT)
[AMBER] Sirius executable not available anymore?
(Tue Jun 24 2014 - 04:19:57 PDT)
FyD
Re: [AMBER] Torsional profile of butane
(Thu Jun 26 2014 - 22:55:02 PDT)
Re: [AMBER] Force field for carbohydrates-Reg.
(Tue Jun 24 2014 - 23:14:23 PDT)
Re: [AMBER] Glycophosphate parametrization using GLYCAM
(Fri Jun 20 2014 - 01:46:35 PDT)
Re: [AMBER] Glycophosphate parametrization using GLYCAM
(Thu Jun 19 2014 - 01:53:30 PDT)
Re: [AMBER] Glycophosphate parametrization using GLYCAM
(Tue Jun 17 2014 - 23:34:08 PDT)
Re: [AMBER] Adding residue in two end of DNA
(Sat Jun 14 2014 - 10:08:01 PDT)
Re: [AMBER] Isopeptide bond Asp-Lys - parameters?
(Wed Jun 04 2014 - 22:56:03 PDT)
Geoffrey Gray
Re: [AMBER] Analysis of CHARMM DNA trajectory using nastruct
(Wed Jun 04 2014 - 12:11:48 PDT)
[AMBER] Analysis of CHARMM DNA trajectory using nastruct
(Wed Jun 04 2014 - 08:38:07 PDT)
George Tzotzos
Re: [AMBER] Amber scaling on culster
(Wed Jun 25 2014 - 06:29:56 PDT)
[AMBER] Amber scaling on culster
(Tue Jun 24 2014 - 13:19:24 PDT)
Gerald Monard
Re: [AMBER] AmberTools14 installation
(Fri Jun 20 2014 - 02:12:56 PDT)
Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14
(Thu Jun 19 2014 - 03:09:55 PDT)
Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14
(Wed Jun 18 2014 - 12:44:13 PDT)
Re: [AMBER] MPI and parallel installation
(Wed Jun 18 2014 - 12:06:49 PDT)
Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14
(Mon Jun 16 2014 - 06:04:37 PDT)
Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14
(Sun Jun 15 2014 - 00:27:25 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 12:39:14 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 06:48:11 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 02:31:17 PDT)
Guo, Zhuyan
[AMBER] Efficient, accurate estimation of relative binding free energies
(Mon Jun 30 2014 - 05:13:50 PDT)
Guqin Shi
Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems
(Tue Jun 17 2014 - 14:15:49 PDT)
Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems
(Tue Jun 17 2014 - 14:11:23 PDT)
Gözde YALÇIN
Re: [AMBER] Falling apart of membrane
(Mon Jun 30 2014 - 07:07:26 PDT)
Hai Nguyen
Re: [AMBER] FF12SB (and FF14?) - any benchmarks/evidence of its quality?
(Sun Jun 01 2014 - 12:09:44 PDT)
Hannes Loeffler
Re: [AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10
(Wed Jun 04 2014 - 03:07:33 PDT)
Harris, Danni
Re: [AMBER] zlib issues during compilation.
(Tue Jun 10 2014 - 04:56:02 PDT)
Re: [AMBER] zlib issues during compilation.
(Mon Jun 09 2014 - 16:29:24 PDT)
[AMBER] zlib issues during compilation.
(Mon Jun 09 2014 - 12:46:51 PDT)
Hector A. Baldoni
Re: [AMBER] Could not find angle parameter: S - S - S
(Tue Jun 03 2014 - 03:47:48 PDT)
Him Shweta
Re: [AMBER] MM/PBSA calculation.
(Mon Jun 23 2014 - 23:02:51 PDT)
Re: [AMBER] MM/PBSA calculation.
(Mon Jun 23 2014 - 10:21:17 PDT)
[AMBER] MM/PBSA calculation.
(Mon Jun 23 2014 - 03:09:47 PDT)
[AMBER] Hi
(Thu Jun 19 2014 - 12:30:32 PDT)
Himanshu Joshi
Re: [AMBER] cpptraj error : not parsing mdvel file
(Sat Jun 07 2014 - 05:17:41 PDT)
[AMBER] cpptraj error : not parsing mdvel file
(Fri Jun 06 2014 - 04:00:17 PDT)
Indrajit Deb
Re: [AMBER] Query about GPU model
(Tue Jun 10 2014 - 12:25:16 PDT)
[AMBER] Query about GPU model
(Tue Jun 10 2014 - 01:19:19 PDT)
James Starlight
Re: [AMBER] bash scripting for MD tasks
(Mon Jun 23 2014 - 04:48:29 PDT)
[AMBER] Low performance in multi-pmemd.mpi
(Mon Jun 23 2014 - 04:38:32 PDT)
Re: [AMBER] bash scripting for MD tasks
(Sun Jun 22 2014 - 06:24:34 PDT)
Re: [AMBER] On the usage of the position restrains during equilibration
(Fri Jun 20 2014 - 22:23:38 PDT)
Re: [AMBER] On the usage of the position restrains during equilibration
(Fri Jun 20 2014 - 11:31:33 PDT)
[AMBER] On the usage of the position restrains during equilibration
(Fri Jun 20 2014 - 07:30:50 PDT)
Re: [AMBER] bash scripting for MD tasks
(Fri Jun 20 2014 - 07:25:06 PDT)
Re: [AMBER] bash scripting for MD tasks
(Thu Jun 19 2014 - 06:52:51 PDT)
Re: [AMBER] bash scripting for MD tasks
(Tue Jun 17 2014 - 11:16:31 PDT)
[AMBER] bash scripting for MD tasks
(Mon Jun 16 2014 - 12:59:08 PDT)
Re: [AMBER] Loop refirement
(Sat Jun 14 2014 - 13:21:02 PDT)
Re: [AMBER] Loop refirement
(Fri Jun 13 2014 - 12:50:36 PDT)
Re: [AMBER] charmmlipid2amber.py
(Thu Jun 12 2014 - 12:49:23 PDT)
Re: [AMBER] charmmlipid2amber.py
(Wed Jun 11 2014 - 22:45:00 PDT)
Re: [AMBER] charmmlipid2amber.py
(Wed Jun 11 2014 - 00:16:33 PDT)
Re: [AMBER] charmmlipid2amber.py
(Tue Jun 10 2014 - 23:54:48 PDT)
Re: [AMBER] charmmlipid2amber.py
(Tue Jun 10 2014 - 22:15:49 PDT)
Re: [AMBER] Equilibration of membrane protein
(Tue Jun 10 2014 - 22:13:36 PDT)
Re: [AMBER] charmmlipid2amber.py
(Tue Jun 10 2014 - 12:39:24 PDT)
Re: [AMBER] charmmlipid2amber.py
(Tue Jun 10 2014 - 12:04:30 PDT)
Re: [AMBER] Membrane protein tutorial
(Tue Jun 10 2014 - 11:36:59 PDT)
Re: [AMBER] charmmlipid2amber.py
(Tue Jun 10 2014 - 09:06:49 PDT)
[AMBER] Membrane protein tutorial
(Tue Jun 10 2014 - 08:58:13 PDT)
Re: [AMBER] NVT equilibration crash using CUDA
(Tue Jun 10 2014 - 02:36:04 PDT)
[AMBER] Equilibration of membrane protein
(Tue Jun 10 2014 - 00:05:13 PDT)
Re: [AMBER] charmmlipid2amber.py
(Mon Jun 09 2014 - 22:47:52 PDT)
Re: [AMBER] charmmlipid2amber.py
(Mon Jun 09 2014 - 22:36:06 PDT)
Re: [AMBER] Constant surface tension on the membrane
(Mon Jun 09 2014 - 12:24:08 PDT)
Re: [AMBER] charmmlipid2amber.py
(Mon Jun 09 2014 - 12:18:47 PDT)
Re: [AMBER] NVT equilibration crash using CUDA
(Mon Jun 09 2014 - 11:13:26 PDT)
Re: [AMBER] NVT equilibration crash using CUDA
(Mon Jun 09 2014 - 07:59:44 PDT)
Re: [AMBER] NVT equilibration crash using CUDA
(Mon Jun 09 2014 - 03:26:08 PDT)
Re: [AMBER] NVT equilibration crash using CUDA
(Mon Jun 09 2014 - 01:34:29 PDT)
[AMBER] NVT equilibration crash using CUDA
(Mon Jun 09 2014 - 01:17:04 PDT)
Re: [AMBER] Problem using charmmlipid2amber.py with VMD
(Sun Jun 08 2014 - 00:52:22 PDT)
Re: [AMBER] charmmlipid2amber.py
(Fri Jun 06 2014 - 09:26:53 PDT)
[AMBER] charmmlipid2amber.py
(Fri Jun 06 2014 - 07:40:45 PDT)
[AMBER] Constant surface tension on the membrane
(Fri Jun 06 2014 - 01:28:27 PDT)
Re: [AMBER] VMD and binary trajectories
(Thu Jun 05 2014 - 07:19:08 PDT)
[AMBER] On the choosing of coordinate for the umbrella sampling
(Thu Jun 05 2014 - 04:03:46 PDT)
[AMBER] VMD and binary trajectories
(Thu Jun 05 2014 - 01:00:45 PDT)
Re: [AMBER] Parametrization of the protein with the assigned protonation states
(Wed Jun 04 2014 - 06:43:53 PDT)
[AMBER] Parametrization of the protein with the assigned protonation states
(Tue Jun 03 2014 - 10:44:07 PDT)
Re: [AMBER] Parametrization of non-standart residues
(Tue Jun 03 2014 - 08:15:55 PDT)
Re: [AMBER] Parametrization of non-standart residues
(Tue Jun 03 2014 - 05:57:57 PDT)
Jason Swails
Re: [AMBER] Printing out matrix labels
(Mon Jun 30 2014 - 06:37:50 PDT)
Re: [AMBER] Early termination of parallel MD
(Mon Jun 30 2014 - 06:30:44 PDT)
Re: [AMBER] Efficient, accurate estimation of relative binding free energies
(Mon Jun 30 2014 - 06:17:01 PDT)
Re: [AMBER] QMMM NEB reaction pathway calculation with AMBER
(Sun Jun 29 2014 - 17:52:49 PDT)
Re: [AMBER] Per residue rmsd
(Fri Jun 27 2014 - 15:50:54 PDT)
Re: [AMBER] Analyze properties of in parallel MD
(Fri Jun 27 2014 - 08:41:38 PDT)
Re: [AMBER] formal charge of the ligand
(Fri Jun 27 2014 - 06:52:36 PDT)
Re: [AMBER] formal charge of the ligand
(Fri Jun 27 2014 - 05:05:29 PDT)
Re: [AMBER] Torsional profile of butane
(Thu Jun 26 2014 - 15:14:00 PDT)
Re: [AMBER] Torsional profile of butane
(Thu Jun 26 2014 - 11:54:25 PDT)
Re: [AMBER] Clustering using CPPTRAJ
(Mon Jun 23 2014 - 12:35:25 PDT)
Re: [AMBER] MM/PBSA calculation.
(Mon Jun 23 2014 - 12:01:27 PDT)
Re: [AMBER] Some error in output file and restart
(Mon Jun 23 2014 - 09:54:08 PDT)
Re: [AMBER] Clustering using CPPTRAJ
(Mon Jun 23 2014 - 08:19:04 PDT)
Re: [AMBER] MM/PBSA calculation.
(Mon Jun 23 2014 - 05:51:47 PDT)
Re: [AMBER] On the usage of the position restrains during equilibration
(Sun Jun 22 2014 - 12:34:06 PDT)
Re: [AMBER] Se atom type
(Sat Jun 21 2014 - 20:16:18 PDT)
Re: [AMBER] Derive charge of multiple molecules
(Thu Jun 19 2014 - 12:02:16 PDT)
Re: [AMBER] MPI and parallel installation
(Wed Jun 18 2014 - 12:09:36 PDT)
Re: [AMBER] Leapfrog algorithm
(Wed Jun 18 2014 - 11:12:35 PDT)
Re: [AMBER] cpptraj hbond - warning message
(Wed Jun 18 2014 - 08:13:00 PDT)
Re: [AMBER] Queries about QM/MM
(Wed Jun 18 2014 - 05:41:31 PDT)
Re: [AMBER] bash scripting for MD tasks
(Tue Jun 17 2014 - 12:25:49 PDT)
Re: [AMBER] fitting of atomic structures to cryo-em maps
(Mon Jun 16 2014 - 07:07:03 PDT)
Re: [AMBER] Topology issue with MMPBSA.py
(Mon Jun 16 2014 - 07:03:43 PDT)
Re: [AMBER] fitting of atomic structures to cryo-em maps
(Mon Jun 16 2014 - 06:17:41 PDT)
Re: [AMBER] Topology issue with MMPBSA.py
(Mon Jun 16 2014 - 05:27:52 PDT)
Re: [AMBER] different number of waters
(Sat Jun 14 2014 - 22:07:41 PDT)
Re: [AMBER] Deleting Box info from trajectory
(Sat Jun 14 2014 - 22:03:19 PDT)
Re: [AMBER] Integration scheme used in Amber 9 and 11 ?
(Sat Jun 14 2014 - 06:07:45 PDT)
Re: [AMBER] The linkage of Amber and Gaussian in Amber 14.
(Sat Jun 14 2014 - 06:05:39 PDT)
Re: [AMBER] "Invalid start to time: 28..." error
(Fri Jun 13 2014 - 16:05:22 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 03:54:41 PDT)
Re: [AMBER] Metal Center Parameter Builder (MCPB) manual
(Thu Jun 12 2014 - 10:32:53 PDT)
Re: [AMBER] MMPBSA huge VDW values
(Thu Jun 12 2014 - 04:11:39 PDT)
Re: [AMBER] QM/MMPBSA
(Wed Jun 11 2014 - 10:14:06 PDT)
Re: [AMBER] QM/MMPBSA
(Wed Jun 11 2014 - 09:32:02 PDT)
Re: [AMBER] QM/MMPBSA
(Wed Jun 11 2014 - 05:35:07 PDT)
Re: [AMBER] Side chain and backbone-specific parameters.
(Tue Jun 10 2014 - 12:07:35 PDT)
Re: [AMBER] Side chain and backbone-specific parameters.
(Tue Jun 10 2014 - 11:30:03 PDT)
Re: [AMBER] Membrane protein tutorial
(Tue Jun 10 2014 - 10:48:31 PDT)
Re: [AMBER] Side chain and backbone-specific parameters.
(Tue Jun 10 2014 - 10:46:32 PDT)
Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py
(Tue Jun 10 2014 - 10:06:17 PDT)
Re: [AMBER] Membrane protein tutorial
(Tue Jun 10 2014 - 09:35:56 PDT)
Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py
(Tue Jun 10 2014 - 09:26:48 PDT)
Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py
(Tue Jun 10 2014 - 08:39:03 PDT)
Re: [AMBER] error in using pmemd
(Tue Jun 10 2014 - 08:22:20 PDT)
Re: [AMBER] NVT equilibration crash using CUDA
(Tue Jun 10 2014 - 05:10:03 PDT)
Re: [AMBER] NVT equilibration crash using CUDA
(Mon Jun 09 2014 - 08:39:34 PDT)
Re: [AMBER] Is it possible to tleap a protein molecule without adding terminal atoms?
(Mon Jun 09 2014 - 05:33:49 PDT)
Re: [AMBER] Fwd: Substrate moving out of the box during MD simulation-- reg
(Mon Jun 09 2014 - 05:24:05 PDT)
Re: [AMBER] NVT equilibration crash using CUDA
(Mon Jun 09 2014 - 05:21:06 PDT)
Re: [AMBER] Question about how a charged system can be simulated using PBC?
(Sun Jun 08 2014 - 18:26:37 PDT)
Re: [AMBER] error in hydrogen bond
(Sat Jun 07 2014 - 04:24:26 PDT)
Re: [AMBER] Constant surface tension on the membrane
(Fri Jun 06 2014 - 05:27:01 PDT)
Re: [AMBER] Density Plot
(Fri Jun 06 2014 - 05:21:43 PDT)
Re: [AMBER] 【amber】center of mass&umbrella sampling
(Fri Jun 06 2014 - 05:20:20 PDT)
Re: [AMBER] error in hbond analysis
(Fri Jun 06 2014 - 05:15:25 PDT)
Re: [AMBER] sudden and rapid configuration change in NVT simulation
(Thu Jun 05 2014 - 05:40:17 PDT)
Re: [AMBER] On the choosing of coordinate for the umbrella sampling
(Thu Jun 05 2014 - 04:45:56 PDT)
Re: [AMBER] VMD and binary trajectories
(Thu Jun 05 2014 - 04:39:54 PDT)
Re: [AMBER] Analysis of CHARMM DNA trajectory using nastruct
(Wed Jun 04 2014 - 12:40:11 PDT)
Re: [AMBER] RDF Plot
(Wed Jun 04 2014 - 09:08:42 PDT)
Re: [AMBER] Parametrization of the protein with the assigned protonation states
(Wed Jun 04 2014 - 07:35:02 PDT)
Re: [AMBER] MMPBSA error
(Wed Jun 04 2014 - 06:02:14 PDT)
Re: [AMBER] Ligand movement in protein cavatiy
(Wed Jun 04 2014 - 05:55:59 PDT)
Re: [AMBER] calculating absolute binding free energy using MMPBSA
(Wed Jun 04 2014 - 04:55:57 PDT)
Re: [AMBER] MTKPP installation error
(Wed Jun 04 2014 - 04:39:45 PDT)
Re: [AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10
(Tue Jun 03 2014 - 14:58:11 PDT)
Re: [AMBER] MTKPP installation error
(Tue Jun 03 2014 - 12:52:03 PDT)
Re: [AMBER] Parametrization of the protein with the assigned protonation states
(Tue Jun 03 2014 - 10:59:34 PDT)
Re: [AMBER] QM/MM and spin parameter
(Tue Jun 03 2014 - 08:18:47 PDT)
Re: [AMBER] MMPBSA error
(Tue Jun 03 2014 - 08:11:32 PDT)
Re: [AMBER] sudden and rapid configuration change in NVT simulation
(Tue Jun 03 2014 - 06:23:09 PDT)
Re: [AMBER] help in grid command
(Tue Jun 03 2014 - 05:52:56 PDT)
Re: [AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex
(Mon Jun 02 2014 - 05:15:48 PDT)
Re: [AMBER] Regarding molecule's breaking during simulation.
(Mon Jun 02 2014 - 05:12:38 PDT)
Re: [AMBER] Ligand movement in protein cavatiy
(Mon Jun 02 2014 - 04:47:37 PDT)
Re: [AMBER] Pressure fluctuation problem during NPT simulation
(Mon Jun 02 2014 - 04:35:00 PDT)
Re: [AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex
(Mon Jun 02 2014 - 04:27:13 PDT)
Re: [AMBER] Ligand movement in protein cavatiy
(Mon Jun 02 2014 - 04:25:24 PDT)
Re: [AMBER] sudden and rapid configuration change in NVT simulation
(Mon Jun 02 2014 - 04:20:43 PDT)
Re: [AMBER] Contributing new water models
(Mon Jun 02 2014 - 04:18:52 PDT)
Re: [AMBER] defining reaction coordinate for umbrella sampling
(Sun Jun 01 2014 - 19:09:50 PDT)
Jinfeng Huang
[AMBER] The linkage of Amber and Gaussian in Amber 14.
(Sat Jun 14 2014 - 01:41:41 PDT)
[AMBER] QM/MM and spin parameter
(Tue Jun 03 2014 - 07:39:10 PDT)
Jochen Heil
Re: [AMBER] Glycophosphate parametrization using GLYCAM
(Thu Jun 19 2014 - 04:57:00 PDT)
Re: [AMBER] Glycophosphate parametrization using GLYCAM
(Wed Jun 18 2014 - 02:23:33 PDT)
John Smith
Re: [AMBER] QM/MMPBSA
(Wed Jun 11 2014 - 09:53:15 PDT)
Re: [AMBER] QM/MMPBSA
(Wed Jun 11 2014 - 09:01:42 PDT)
[AMBER] QM/MMPBSA
(Wed Jun 11 2014 - 04:31:29 PDT)
Jorgen Simonsen
[AMBER] defining reaction coordinate for umbrella sampling
(Sun Jun 01 2014 - 18:12:32 PDT)
JPB
[AMBER] No VDWAALS EEL in PB MMPBSA.py job
(Fri Jun 27 2014 - 08:27:25 PDT)
Re: [AMBER] Topology issue with MMPBSA.py
(Mon Jun 16 2014 - 06:37:06 PDT)
[AMBER] Topology issue with MMPBSA.py
(Mon Jun 16 2014 - 03:29:39 PDT)
Jurgens de Bruin
[AMBER] Density Plot
(Fri Jun 06 2014 - 00:58:32 PDT)
Re: [AMBER] Ligand movement in protein cavatiy
(Wed Jun 04 2014 - 05:56:18 PDT)
Re: [AMBER] Ligand movement in protein cavatiy
(Wed Jun 04 2014 - 05:14:19 PDT)
Re: [AMBER] Ligand movement in protein cavatiy
(Mon Jun 02 2014 - 23:09:41 PDT)
Re: [AMBER] Ligand movement in protein cavatiy
(Mon Jun 02 2014 - 05:22:59 PDT)
Re: [AMBER] Ligand movement in protein cavatiy
(Mon Jun 02 2014 - 04:31:09 PDT)
Re: [AMBER] Ligand movement in protein cavatiy
(Sun Jun 01 2014 - 22:22:41 PDT)
[AMBER] Ligand movement in protein cavatiy
(Sun Jun 01 2014 - 19:20:10 PDT)
Keiran Rowell
Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure."
(Thu Jun 12 2014 - 18:40:14 PDT)
Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure."
(Mon Jun 02 2014 - 18:34:17 PDT)
Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure."
(Mon Jun 02 2014 - 16:54:55 PDT)
Keisuke Aono
[AMBER] [Amber 14] multi-GPU calculation error occers when specify eight GPUs with Tesla K20Xm
(Mon Jun 09 2014 - 04:17:52 PDT)
Ken Merz
Re: [AMBER] metal ion parameterisation problem
(Mon Jun 23 2014 - 07:10:40 PDT)
kirtana S
[AMBER] about setting iwrap
(Tue Jun 24 2014 - 08:04:15 PDT)
Re: [AMBER] Some error in output file and restart
(Mon Jun 23 2014 - 21:42:24 PDT)
[AMBER] Some error in output file and restart
(Mon Jun 23 2014 - 08:40:35 PDT)
Krisztina Feher
Re: [AMBER] Se atom type
(Mon Jun 23 2014 - 04:43:35 PDT)
[AMBER] Se atom type
(Sat Jun 21 2014 - 05:37:34 PDT)
[AMBER] Se atom type
(Thu Jun 19 2014 - 11:29:18 PDT)
[AMBER] Se atom type
(Thu Jun 19 2014 - 08:32:24 PDT)
Kshatresh Dutta Dubey
Re: [AMBER] Query about parallel GPU multijob
(Mon Jun 23 2014 - 14:27:35 PDT)
Re: [AMBER] Query about parallel GPU multijob
(Mon Jun 23 2014 - 13:54:22 PDT)
Re: [AMBER] Query about parallel GPU multijob
(Mon Jun 23 2014 - 13:44:14 PDT)
Re: [AMBER] Query about parallel GPU multijob
(Mon Jun 23 2014 - 13:36:45 PDT)
Re: [AMBER] Query about parallel GPU multijob
(Mon Jun 23 2014 - 13:25:18 PDT)
Re: [AMBER] metal ion parameterisation problem
(Mon Jun 23 2014 - 12:52:07 PDT)
[AMBER] Query about parallel GPU multijob
(Mon Jun 23 2014 - 12:43:59 PDT)
Re: [AMBER] metal ion parameterisation problem
(Mon Jun 23 2014 - 08:02:06 PDT)
Re: [AMBER] MTK++ Error
(Sat Jun 21 2014 - 16:00:46 PDT)
[AMBER] MTK++ Error
(Sat Jun 21 2014 - 13:43:44 PDT)
[AMBER] metal ion parameterisation problem
(Fri Jun 20 2014 - 14:29:30 PDT)
Re: [AMBER] Deleting Box info from trajectory
(Sun Jun 15 2014 - 00:47:00 PDT)
Re: [AMBER] Deleting Box info from trajectory
(Sat Jun 14 2014 - 20:53:05 PDT)
Re: [AMBER] Deleting Box info from trajectory
(Sat Jun 14 2014 - 14:40:35 PDT)
[AMBER] Deleting Box info from trajectory
(Sat Jun 14 2014 - 13:09:26 PDT)
Re: [AMBER] Integration scheme used in Amber 9 and 11 ?
(Sat Jun 14 2014 - 06:28:40 PDT)
Re: [AMBER] Integration scheme used in Amber 9 and 11 ?
(Sat Jun 14 2014 - 02:03:56 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 14:24:54 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 07:58:59 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 06:01:00 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 04:44:39 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 04:31:51 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 04:26:48 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 02:50:31 PDT)
[AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 02:16:03 PDT)
Re: [AMBER] MTKPP installation error
(Wed Jun 04 2014 - 04:46:23 PDT)
Re: [AMBER] MTKPP installation error
(Tue Jun 03 2014 - 22:07:44 PDT)
Re: [AMBER] MTKPP installation error
(Tue Jun 03 2014 - 13:04:09 PDT)
[AMBER] MTKPP installation error
(Tue Jun 03 2014 - 12:47:12 PDT)
Lachele Foley
Re: [AMBER] Fwd: problem while USING GLYCAM for Gammacyclodextrin-Reg.
(Thu Jun 26 2014 - 11:13:14 PDT)
Re: [AMBER] Force field for carbohydrates-Reg.
(Wed Jun 25 2014 - 07:46:57 PDT)
Re: [AMBER] Force field for carbohydrates-Reg.
(Wed Jun 25 2014 - 07:46:20 PDT)
Re: [AMBER] tleap for gammacyclodextrin-Reg.
(Tue Jun 24 2014 - 10:54:54 PDT)
Re: [AMBER] tleap for gammacyclodextrin-Reg.
(Tue Jun 24 2014 - 10:32:00 PDT)
Re: [AMBER] Condensed Glycam notation for gammacyclodextrin
(Mon Jun 23 2014 - 10:49:16 PDT)
Re: [AMBER] tleap using GLYCAM force field
(Mon Jun 23 2014 - 08:32:51 PDT)
Re: [AMBER] Glycophosphate parametrization using GLYCAM
(Thu Jun 19 2014 - 08:46:31 PDT)
Re: [AMBER] Glycophosphate parametrization using GLYCAM
(Wed Jun 18 2014 - 10:48:44 PDT)
Re: [AMBER] bash scripting for MD tasks
(Tue Jun 17 2014 - 11:38:30 PDT)
Re: [AMBER] Glycophosphate parametrization using GLYCAM
(Tue Jun 17 2014 - 09:57:47 PDT)
Re: [AMBER] GLYCAM_06 reference
(Tue Jun 17 2014 - 07:55:59 PDT)
Re: [AMBER] GLYCAM parameter ATOM TYPE
(Wed Jun 11 2014 - 12:34:17 PDT)
Lara rajam
[AMBER] error in MMPBSA
(Mon Jun 02 2014 - 13:48:47 PDT)
Lee-Ping Wang
Re: [AMBER] Side chain and backbone-specific parameters.
(Tue Jun 10 2014 - 11:50:40 PDT)
Re: [AMBER] Side chain and backbone-specific parameters.
(Tue Jun 10 2014 - 10:50:35 PDT)
[AMBER] Side chain and backbone-specific parameters.
(Tue Jun 10 2014 - 10:25:24 PDT)
loue chen
[AMBER] AMBER 12 Nucleic Acid Builder (NAB) language
(Sun Jun 22 2014 - 08:50:09 PDT)
Mahendra B Thapa
[AMBER] cpptraj hbond - warning message
(Tue Jun 17 2014 - 16:16:16 PDT)
Manikanthan Bhavaraju
Re: [AMBER] simulation differences in pmemd.MPI and pmemd.cuda
(Wed Jun 25 2014 - 18:33:00 PDT)
[AMBER] simulation differences in pmemd.MPI and pmemd.cuda
(Wed Jun 25 2014 - 14:56:45 PDT)
Marc van der Kamp
[AMBER] FF12SB (and FF14?) - any benchmarks/evidence of its quality?
(Sun Jun 01 2014 - 07:39:27 PDT)
Mary Varughese
Re: [AMBER] formal charge of the ligand
(Fri Jun 27 2014 - 23:13:21 PDT)
[AMBER] formal charge of the ligand
(Fri Jun 27 2014 - 02:35:55 PDT)
maryam azimzadehirani
Re: [AMBER] MMPBSA huge VDW values
(Thu Jun 12 2014 - 04:44:16 PDT)
[AMBER] MMPBSA huge VDW values
(Thu Jun 12 2014 - 00:28:36 PDT)
mehdi bagherpoor
[AMBER] Adding residue in two end of DNA
(Thu Jun 12 2014 - 09:59:50 PDT)
menwer momo
[AMBER] calculating absolute binding free energy using MMPBSA
(Wed Jun 04 2014 - 02:17:49 PDT)
[AMBER] Calculating absolute binding free energy
(Wed Jun 04 2014 - 00:04:41 PDT)
mish
Re: [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1.
(Thu Jun 05 2014 - 07:49:33 PDT)
Re: [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1.
(Wed Jun 04 2014 - 08:43:48 PDT)
[AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1.
(Wed Jun 04 2014 - 08:11:47 PDT)
MURAT OZTURK
Re: [AMBER] different number of waters
(Sat Jun 14 2014 - 16:07:34 PDT)
Neha Gandhi
Re: [AMBER] set up for the ScaledMD
(Wed Jun 04 2014 - 00:10:49 PDT)
newamber list
Re: [AMBER] filter trajectory with modes same number of frames
(Tue Jun 24 2014 - 17:28:08 PDT)
Re: [AMBER] filter trajectory with modes same number of frames
(Sat Jun 21 2014 - 18:34:01 PDT)
[AMBER] filter trajectory with modes same number of frames
(Sat Jun 21 2014 - 10:07:53 PDT)
Re: [AMBER] different number of waters
(Wed Jun 18 2014 - 07:30:05 PDT)
Re: [AMBER] different number of waters
(Wed Jun 18 2014 - 06:43:34 PDT)
Re: [AMBER] different number of waters
(Sun Jun 15 2014 - 08:06:10 PDT)
Re: [AMBER] different number of waters
(Sun Jun 15 2014 - 07:18:48 PDT)
[AMBER] different number of waters
(Fri Jun 13 2014 - 06:04:22 PDT)
Re: [AMBER] image distances
(Wed Jun 04 2014 - 07:06:05 PDT)
Re: [AMBER] image distances
(Mon Jun 02 2014 - 08:36:34 PDT)
[AMBER] image distances
(Mon Jun 02 2014 - 07:46:38 PDT)
Parker de Waal
Re: [AMBER] bash scripting for MD tasks
(Mon Jun 23 2014 - 07:30:54 PDT)
Re: [AMBER] bash scripting for MD tasks
(Sun Jun 22 2014 - 07:07:17 PDT)
Re: [AMBER] bash scripting for MD tasks
(Sun Jun 22 2014 - 07:04:13 PDT)
Re: [AMBER] Parametrization of non-standart residues
(Tue Jun 03 2014 - 06:15:30 PDT)
Parvesh Singh
Re: [AMBER] problem during add ions
(Mon Jun 09 2014 - 07:08:50 PDT)
Pengfei Li
Re: [AMBER] metal ion parameterisation problem
(Wed Jun 25 2014 - 13:25:54 PDT)
Re: [AMBER] metal ion parameterisation problem
(Mon Jun 23 2014 - 11:53:46 PDT)
Pierpaolo Cacciotto
Re: [AMBER] Setting up z-constraint
(Mon Jun 23 2014 - 03:20:29 PDT)
Re: [AMBER] Setting up z-constraint
(Fri Jun 20 2014 - 03:26:48 PDT)
Re: [AMBER] Setting up z-constraint
(Wed Jun 18 2014 - 10:03:31 PDT)
Quynh Vo
[AMBER] periodic box drifted during NVE run
(Thu Jun 26 2014 - 15:56:25 PDT)
Raj Schneider
[AMBER] Glycophosphate parametrization using GLYCAM
(Tue Jun 17 2014 - 09:26:51 PDT)
Rajeswari A.
Re: [AMBER] Rmsd with reference structure having different number of total atoms
(Fri Jun 13 2014 - 07:26:25 PDT)
[AMBER] Rmsd with reference structure having different number of total atoms
(Fri Jun 13 2014 - 07:13:05 PDT)
[AMBER] Fwd: Substrate moving out of the box during MD simulation-- reg
(Mon Jun 09 2014 - 04:10:35 PDT)
Ravi Tripathi
Re: [AMBER] Integration scheme used in Amber 9 and 11 ?
(Sun Jun 15 2014 - 21:14:00 PDT)
[AMBER] Integration scheme used in Amber 9 and 11 ?
(Fri Jun 13 2014 - 23:30:57 PDT)
Ray Luo, Ph.D.
Re: [AMBER] No VDWAALS EEL in PB MMPBSA.py job
(Fri Jun 27 2014 - 09:57:28 PDT)
Re: [AMBER] MMPBSA error
(Tue Jun 10 2014 - 12:58:53 PDT)
Re: [AMBER] Is it possible to tleap a protein molecule without adding terminal atoms?
(Mon Jun 09 2014 - 10:13:40 PDT)
Re: [AMBER] MMPBSA error
(Thu Jun 05 2014 - 16:25:43 PDT)
Re: [AMBER] MMPBSA error
(Wed Jun 04 2014 - 10:52:40 PDT)
Re: [AMBER] error in MMPBSA
(Mon Jun 02 2014 - 15:39:54 PDT)
richa anand
[AMBER] Regarding molecule's breaking during simulation.
(Mon Jun 02 2014 - 04:52:09 PDT)
Robin Jain
[AMBER] help in calculating Angular distribution function
(Tue Jun 03 2014 - 00:12:16 PDT)
[AMBER] help in grid command
(Mon Jun 02 2014 - 23:17:08 PDT)
Roitberg,Adrian E
Re: [AMBER] Amber scaling on culster
(Tue Jun 24 2014 - 13:39:18 PDT)
Ross Walker
Re: [AMBER] simulation differences in pmemd.MPI and pmemd.cuda
(Wed Jun 25 2014 - 17:57:26 PDT)
Re: [AMBER] Amber scaling on culster
(Tue Jun 24 2014 - 14:11:49 PDT)
Re: [AMBER] Amber scaling on culster
(Tue Jun 24 2014 - 13:48:46 PDT)
Re: [AMBER] Sirius executable not available anymore?
(Tue Jun 24 2014 - 11:09:49 PDT)
Re: [AMBER] Some error in output file and restart
(Tue Jun 24 2014 - 09:59:27 PDT)
Re: [AMBER] Query about parallel GPU multijob
(Mon Jun 23 2014 - 14:15:11 PDT)
Re: [AMBER] Query about parallel GPU multijob
(Mon Jun 23 2014 - 13:45:57 PDT)
Re: [AMBER] Query about parallel GPU multijob
(Mon Jun 23 2014 - 13:37:43 PDT)
Re: [AMBER] Some error in output file and restart
(Mon Jun 23 2014 - 13:11:59 PDT)
Re: [AMBER] Query about parallel GPU multijob
(Mon Jun 23 2014 - 13:04:44 PDT)
Re: [AMBER] Setting up z-constraint
(Mon Jun 23 2014 - 08:04:56 PDT)
Re: [AMBER] Setting up z-constraint
(Fri Jun 20 2014 - 08:57:56 PDT)
Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure."
(Thu Jun 12 2014 - 19:10:20 PDT)
Re: [AMBER] Query about GPU model
(Tue Jun 10 2014 - 09:27:10 PDT)
Re: [AMBER] [Amber 14] multi-GPU calculation error occers when specify eight GPUs with Tesla K20Xm
(Mon Jun 09 2014 - 05:42:42 PDT)
Roza M
[AMBER] Using MM-PBSA to find binding free energy for Zif268-DNA complex
(Mon Jun 02 2014 - 06:20:04 PDT)
Re: [AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex
(Mon Jun 02 2014 - 05:02:15 PDT)
[AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex
(Mon Jun 02 2014 - 04:04:28 PDT)
Saikat Dutta chowdhury
Re: [AMBER] Pressure fluctuation problem during NPT simulation
(Mon Jun 02 2014 - 04:41:19 PDT)
[AMBER] Pressure fluctuation problem during NPT simulation
(Mon Jun 02 2014 - 03:53:30 PDT)
Sangita Kachhap
Re: [AMBER] Could not find angle parameter: S - S - S
(Tue Jun 03 2014 - 03:55:30 PDT)
[AMBER] Could not find angle parameter: S - S - S
(Tue Jun 03 2014 - 02:49:52 PDT)
Scott Le Grand
Re: [AMBER] Setting up z-constraint
(Fri Jun 20 2014 - 09:16:37 PDT)
Re: [AMBER] Setting up z-constraint
(Fri Jun 20 2014 - 09:13:01 PDT)
Re: [AMBER] Query about GPU model
(Tue Jun 10 2014 - 10:28:21 PDT)
Re: [AMBER] [Amber 14] multi-GPU calculation error occers when specify eight GPUs with Tesla K20Xm
(Mon Jun 09 2014 - 09:50:56 PDT)
Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure."
(Mon Jun 02 2014 - 22:45:38 PDT)
Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure."
(Mon Jun 02 2014 - 17:05:22 PDT)
Senthil Natesan
Re: [AMBER] Metal Center Parameter Builder (MCPB) manual
(Thu Jun 12 2014 - 11:24:00 PDT)
Re: [AMBER] Metal Center Parameter Builder (MCPB) manual
(Thu Jun 12 2014 - 10:47:07 PDT)
[AMBER] Metal Center Parameter Builder (MCPB) manual
(Wed Jun 11 2014 - 14:49:41 PDT)
[AMBER] Metal Center Parameter Builder (MCPB) manual
(Wed Jun 11 2014 - 10:19:27 PDT)
Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py
(Tue Jun 10 2014 - 11:08:01 PDT)
Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py
(Tue Jun 10 2014 - 08:57:51 PDT)
[AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py
(Tue Jun 10 2014 - 08:22:38 PDT)
Shomesankar Bhunia
Re: [AMBER] segmentation_fault_loading_pdb in tleap
(Sat Jun 21 2014 - 06:45:30 PDT)
[AMBER] segmentation_fault_loading_pdb in tleap
(Sat Jun 21 2014 - 05:56:11 PDT)
Shreeramesh
[AMBER] Fwd: problem while USING GLYCAM for Gammacyclodextrin-Reg.
(Thu Jun 26 2014 - 05:46:31 PDT)
[AMBER] tleap for gammacyclodextrin-Reg.
(Tue Jun 24 2014 - 08:18:25 PDT)
[AMBER] Force field for carbohydrates-Reg.
(Tue Jun 24 2014 - 01:56:11 PDT)
[AMBER] Condensed Glycam notation for gammacyclodextrin
(Mon Jun 23 2014 - 05:08:09 PDT)
[AMBER] tleap using GLYCAM force field
(Mon Jun 23 2014 - 05:00:49 PDT)
Silvia Bonomo
[AMBER] restarting MDs generated in Amber10 with Amber12
(Wed Jun 11 2014 - 01:52:29 PDT)
Simone Fulle
[AMBER] MPI and parallel installation
(Wed Jun 18 2014 - 10:44:26 PDT)
Sohag Biswas
[AMBER] problem during add ions
(Mon Jun 09 2014 - 03:21:02 PDT)
[AMBER] calculation diffusion coefficient
(Sun Jun 01 2014 - 02:28:21 PDT)
Soumendranath Bhakat
Re: [AMBER] Per residue rmsd
(Fri Jun 27 2014 - 15:56:31 PDT)
Re: [AMBER] Per residue rmsd
(Fri Jun 27 2014 - 14:19:40 PDT)
Re: [AMBER] formal charge of the ligand
(Fri Jun 27 2014 - 09:40:19 PDT)
Re: [AMBER] formal charge of the ligand
(Fri Jun 27 2014 - 05:33:59 PDT)
Re: [AMBER] simulation differences in pmemd.MPI and pmemd.cuda
(Wed Jun 25 2014 - 15:13:53 PDT)
Re: [AMBER] Clustering using CPPTRAJ
(Mon Jun 23 2014 - 12:08:50 PDT)
Re: [AMBER] Clustering using CPPTRAJ
(Mon Jun 23 2014 - 07:45:54 PDT)
Re: [AMBER] Clustering using CPPTRAJ
(Mon Jun 23 2014 - 07:07:47 PDT)
[AMBER] Clustering using CPPTRAJ
(Mon Jun 23 2014 - 06:51:15 PDT)
Re: [AMBER] Derive charge of multiple molecules
(Sun Jun 22 2014 - 06:44:31 PDT)
Re: [AMBER] Derive charge of multiple molecules
(Sun Jun 22 2014 - 06:34:13 PDT)
Re: [AMBER] segmentation_fault_loading_pdb in tleap
(Sat Jun 21 2014 - 06:34:50 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 04:42:31 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 04:34:47 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 04:36:26 PDT)
Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface
(Fri Jun 13 2014 - 04:01:44 PDT)
[AMBER] Magnesium FATAL error
(Thu Jun 12 2014 - 01:46:00 PDT)
Re: [AMBER] GLYCAM parameter ATOM TYPE
(Thu Jun 12 2014 - 01:42:07 PDT)
[AMBER] GLYCAM parameter ATOM TYPE
(Wed Jun 11 2014 - 11:54:15 PDT)
Re: [AMBER] NVT equilibration crash using CUDA
(Mon Jun 09 2014 - 02:15:27 PDT)
Re: [AMBER] error in hydrogen bond
(Sat Jun 07 2014 - 06:43:18 PDT)
Re: [AMBER] sudden and rapid configuration change in NVT simulation
(Tue Jun 03 2014 - 06:46:30 PDT)
Re: [AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex
(Mon Jun 02 2014 - 05:10:57 PDT)
Re: [AMBER] Ligand movement in protein cavatiy
(Mon Jun 02 2014 - 04:59:04 PDT)
Re: [AMBER] error in plot of interaction energy in xmgrace
(Sun Jun 01 2014 - 13:24:11 PDT)
Re: [AMBER] request for help in plotting distance matrix plot
(Sun Jun 01 2014 - 09:53:55 PDT)
sunita gupta
Re: [AMBER] Derive charge of multiple molecules
(Fri Jun 20 2014 - 22:29:14 PDT)
[AMBER] Derive charge of multiple molecules
(Thu Jun 19 2014 - 11:38:45 PDT)
T Luchko (Lists)
Re: [AMBER] 3D-RISM: charge density, charge distribution, and electrostatic potential
(Fri Jun 27 2014 - 11:53:33 PDT)
Tanmoy Paul
[AMBER] Queries about QM/MM
(Tue Jun 17 2014 - 23:36:51 PDT)
Teerapong Pirojsirikul
Re: [AMBER] QMMM NEB reaction pathway calculation with AMBER
(Mon Jun 30 2014 - 11:17:51 PDT)
[AMBER] QMMM NEB reaction pathway calculation with AMBER
(Sat Jun 28 2014 - 17:50:17 PDT)
Thomas Evangelidis
Re: [AMBER] Problem using charmmlipid2amber.py with VMD
(Mon Jun 09 2014 - 12:48:40 PDT)
Re: [AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10
(Wed Jun 04 2014 - 04:03:04 PDT)
[AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10
(Tue Jun 03 2014 - 14:30:21 PDT)
Thomas Pochapsky
Re: [AMBER] Glycophosphate parametrization using GLYCAM
(Wed Jun 18 2014 - 11:15:10 PDT)
Re: [AMBER] Glycophosphate parametrization using GLYCAM
(Wed Jun 18 2014 - 11:13:31 PDT)
Valentina Romano
Re: [AMBER] Early termination of parallel MD
(Mon Jun 30 2014 - 01:49:07 PDT)
[AMBER] Early termination of parallel MD
(Mon Jun 30 2014 - 00:52:24 PDT)
[AMBER] Analyze properties of in parallel MD
(Fri Jun 27 2014 - 07:37:34 PDT)
[AMBER] error in using pmemd
(Tue Jun 10 2014 - 08:13:26 PDT)
Vu Truong
Re: [AMBER] "Invalid start to time: 28..." error
(Fri Jun 13 2014 - 14:35:42 PDT)
[AMBER] "Invalid start to time: 28..." error
(Thu Jun 12 2014 - 11:43:21 PDT)
[AMBER] Mistake in water density
(Mon Jun 02 2014 - 15:50:08 PDT)
whb
[AMBER] remd
(Wed Jun 18 2014 - 17:35:19 PDT)
[AMBER] 【amber】center of mass&umbrella sampling
(Fri Jun 06 2014 - 00:11:40 PDT)
wmsmith.uci.edu
[AMBER] Problem using charmmlipid2amber.py with VMD
(Fri Jun 06 2014 - 09:27:59 PDT)
Yingjie Wang
Re: [AMBER] Torsional profile of butane
(Fri Jun 27 2014 - 07:38:41 PDT)
Re: [AMBER] Torsional profile of butane
(Thu Jun 26 2014 - 13:08:32 PDT)
[AMBER] Torsional profile of butane
(Thu Jun 26 2014 - 10:57:32 PDT)
yjlee
Re: [AMBER] sudden and rapid configuration change in NVT simulation
(Fri Jun 06 2014 - 05:46:03 PDT)
Re: [AMBER] sudden and rapid configuration change in NVT simulation
(Thu Jun 05 2014 - 04:47:02 PDT)
Re: [AMBER] sudden and rapid configuration change in NVT simulation
(Mon Jun 02 2014 - 23:43:02 PDT)
Re: [AMBER] sudden and rapid configuration change in NVT simulation
(Sun Jun 01 2014 - 23:47:17 PDT)
Ylenia Cau
[AMBER] Setting up z-constraint
(Wed Jun 18 2014 - 08:47:03 PDT)
yuandandan05.gmail.com
Re: [AMBER] Question about how a charged system can be simulated using PBC?
(Sun Jun 08 2014 - 18:13:31 PDT)
[AMBER] Question about how a charged system can be simulated using PBC?
(Sat Jun 07 2014 - 21:12:27 PDT)
zahra khatti
Re: [AMBER] MMPBSA error
(Fri Jun 20 2014 - 08:03:32 PDT)
[AMBER] AmberTools14 installation
(Fri Jun 20 2014 - 01:30:18 PDT)
[AMBER] Leapfrog algorithm
(Wed Jun 18 2014 - 10:20:48 PDT)
Re: [AMBER] MMPBSA error
(Fri Jun 06 2014 - 05:57:41 PDT)
Re: [AMBER] MMPBSA error
(Thu Jun 05 2014 - 00:28:06 PDT)
Re: [AMBER] MMPBSA error
(Wed Jun 04 2014 - 11:43:38 PDT)
[AMBER] Fw: RDF Plot
(Wed Jun 04 2014 - 08:13:45 PDT)
[AMBER] RDF Plot
(Wed Jun 04 2014 - 08:04:57 PDT)
Re: [AMBER] MMPBSA error
(Wed Jun 04 2014 - 05:46:48 PDT)
Re: [AMBER] MMPBSA error
(Tue Jun 03 2014 - 13:17:48 PDT)
[AMBER] MMPBSA error
(Tue Jun 03 2014 - 07:15:45 PDT)
[AMBER] mmpbsa.py
(Mon Jun 02 2014 - 07:54:40 PDT)
zhou gong
[AMBER] set up for the ScaledMD
(Tue Jun 03 2014 - 23:55:06 PDT)
Антипина Александра
Re: [AMBER] GAFFlipid parameters
(Wed Jun 04 2014 - 05:24:17 PDT)
[AMBER] GAFFlipid parameters
(Wed Jun 04 2014 - 02:01:16 PDT)
余青芬
Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14
(Thu Jun 19 2014 - 02:27:21 PDT)
Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14
(Wed Jun 18 2014 - 03:03:55 PDT)
Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14
(Mon Jun 16 2014 - 02:26:38 PDT)
[AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14
(Sat Jun 14 2014 - 23:26:54 PDT)
肖立
Re: [AMBER] Problem in creating prmtop inpcrd file in leap
(Wed Jun 25 2014 - 10:25:42 PDT)
[AMBER] Problem in creating prmtop inpcrd file in leap
(Tue Jun 24 2014 - 17:31:37 PDT)
Last message date
:
Mon Jun 30 2014 - 14:30:02 PDT
Archived on
: Fri Nov 15 2024 - 05:55:02 PST
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