Amber Archive Nov 2013 by thread
414 messages
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Starting
Thu Oct 31 2013 - 21:00:02 PDT,
Ending
Sat Nov 30 2013 - 09:00:03 PST
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Re: [AMBER] Installation error
Dhananjay
(Thu Oct 31 2013 - 20:54:38 PDT)
Re: [AMBER] Installation error
David A Case
(Fri Nov 01 2013 - 05:11:43 PDT)
Re: [AMBER] Installation error
Dhananjay
(Mon Nov 04 2013 - 05:24:46 PST)
Re: [AMBER] Installation error
Jason Swails
(Mon Nov 04 2013 - 06:14:06 PST)
Re: [AMBER] Installation error
Dhananjay
(Tue Nov 05 2013 - 20:57:11 PST)
Re: [AMBER] mdcrd to dcd
石坪江梨花
(Thu Oct 31 2013 - 22:54:14 PDT)
Re: [AMBER] Sander error (AmberTools 13 & Amber10)
David A Case
(Fri Nov 01 2013 - 05:06:17 PDT)
Re: [AMBER] TI soft-core parameters
David A Case
(Fri Nov 01 2013 - 05:12:15 PDT)
[AMBER] Multidihedral and histogram analysis
Fabrício Bracht
(Fri Nov 01 2013 - 08:48:14 PDT)
Re: [AMBER] Multidihedral and histogram analysis
Daniel Roe
(Fri Nov 01 2013 - 09:20:37 PDT)
Re: [AMBER] Multidihedral and histogram analysis
Fabrício Bracht
(Fri Nov 01 2013 - 12:21:21 PDT)
Re: [AMBER] Amber 12 Updater error on Arch linux
M. Reza Ganjalikhany
(Sat Nov 02 2013 - 05:52:23 PDT)
[AMBER] Hybrid QM/MM Convergence
Ahmed Ayoub
(Sat Nov 02 2013 - 21:25:51 PDT)
Re: [AMBER] Hybrid QM/MM Convergence
Brian Radak
(Sun Nov 03 2013 - 10:53:38 PST)
Re: [AMBER] Hybrid QM/MM Convergence
Tanmoy Paul
(Fri Nov 08 2013 - 05:28:17 PST)
[AMBER] Sulfonamide parameters,
loue chen
(Sat Nov 02 2013 - 23:16:55 PDT)
Re: [AMBER] Sulfonamide parameters,
Karl N. Kirschner
(Mon Nov 04 2013 - 06:12:06 PST)
Re: [AMBER] Sulfonamide parameters,
Hector A. Baldoni
(Mon Nov 04 2013 - 14:00:49 PST)
Re: [AMBER] Sulfonamide parameters,
Karl N. Kirschner
(Tue Nov 05 2013 - 02:31:54 PST)
[AMBER] Temperature raises abnormally during accelerated MD
O Z
(Sun Nov 03 2013 - 23:41:07 PST)
Re: [AMBER] Temperature raises abnormally during accelerated MD
Daniel Roe
(Mon Nov 04 2013 - 10:22:57 PST)
Re: [AMBER] Temperature raises abnormally during accelerated MD
Daniel Roe
(Tue Nov 05 2013 - 07:19:26 PST)
Re: [AMBER] Temperature raises abnormally during accelerated MD
O Z
(Wed Nov 13 2013 - 22:24:25 PST)
Re: [AMBER] Temperature raises abnormally during accelerated MD
O Z
(Thu Nov 21 2013 - 17:29:42 PST)
Re: [AMBER] Temperature raises abnormally during accelerated MD
Ross Walker
(Thu Nov 21 2013 - 18:05:08 PST)
[AMBER] PBC-connectivity
Rasha Alqus
(Mon Nov 04 2013 - 09:16:49 PST)
Re: [AMBER] PBC-connectivity
Jason Swails
(Mon Nov 04 2013 - 09:28:28 PST)
[AMBER] Running Amber in GPU cluster
Soumendranath Bhakat
(Tue Nov 05 2013 - 00:25:46 PST)
Re: [AMBER] Running Amber in GPU cluster
Jason Swails
(Tue Nov 05 2013 - 04:24:58 PST)
Re: [AMBER] Running Amber in GPU cluster
David A Case
(Tue Nov 05 2013 - 04:26:37 PST)
Re: [AMBER] Running Amber in GPU cluster
Ross Walker
(Tue Nov 05 2013 - 10:36:54 PST)
[AMBER] nmode and newton optimization divergence
maghtar
(Tue Nov 05 2013 - 00:35:09 PST)
Re: [AMBER] nmode and newton optimization divergence
David A Case
(Tue Nov 05 2013 - 04:34:56 PST)
Re: [AMBER] nmode and newton optimization divergence
maghtar
(Tue Nov 05 2013 - 06:16:12 PST)
[AMBER] nmode and newton optimization divergence
maghtar
(Tue Nov 05 2013 - 02:05:24 PST)
Re: [AMBER] MMPBSA.py MPI problem on TACC Stampede
Sorensen, Jesper
(Tue Nov 05 2013 - 05:04:52 PST)
Re: [AMBER] MMPBSA.py MPI problem on TACC Stampede
Jason Swails
(Tue Nov 05 2013 - 05:14:13 PST)
[AMBER] Location of MMPBSA temporary files
rohitarora10.gmail.com
(Tue Nov 05 2013 - 05:18:42 PST)
Re: [AMBER] Location of MMPBSA temporary files
Jason Swails
(Tue Nov 05 2013 - 05:49:50 PST)
Re: [AMBER] Location of MMPBSA temporary files
rohitarora10.gmail.com
(Tue Nov 05 2013 - 06:47:01 PST)
[AMBER] Ligand has no type
kanika sharma
(Tue Nov 05 2013 - 09:57:00 PST)
Re: [AMBER] Ligand has no type
David A Case
(Tue Nov 05 2013 - 12:15:13 PST)
Re: [AMBER] Ligand has no type
Jason Swails
(Tue Nov 05 2013 - 12:22:41 PST)
[AMBER] Fwd: Ligand has no type
kanika sharma
(Wed Nov 06 2013 - 05:19:36 PST)
Re: [AMBER] Fwd: Ligand has no type
Karl N. Kirschner
(Wed Nov 06 2013 - 05:25:31 PST)
Re: [AMBER] Fwd: Ligand has no type
kanika sharma
(Wed Nov 06 2013 - 06:13:05 PST)
Re: [AMBER] Fwd: Ligand has no type
Karl N. Kirschner
(Wed Nov 06 2013 - 06:34:20 PST)
[AMBER] Parmed.py script generates additional dihedral terms
Meekyum Olivia Kim
(Tue Nov 05 2013 - 10:10:53 PST)
Re: [AMBER] Parmed.py script generates additional dihedral terms
Jason Swails
(Tue Nov 05 2013 - 12:21:00 PST)
[AMBER] normal mode analysis, AmberTools13, vecs
maghtar
(Wed Nov 06 2013 - 03:20:38 PST)
Re: [AMBER] normal mode analysis, AmberTools13, vecs
David A Case
(Wed Nov 06 2013 - 04:35:50 PST)
Re: [AMBER] normal mode analysis, AmberTools13, vecs
maghtar
(Thu Nov 07 2013 - 02:17:13 PST)
Re: [AMBER] normal mode analysis, AmberTools13, vecs
case
(Thu Nov 07 2013 - 04:54:20 PST)
[AMBER] help!!! I got a error when I used mmpbsa calculate the binding freeenergy
David Chen
(Wed Nov 06 2013 - 05:18:27 PST)
Re: [AMBER] help!!! I got a error when I used mmpbsa calculate the binding freeenergy
Jason Swails
(Wed Nov 06 2013 - 05:41:31 PST)
Re: [AMBER] help!!! I got a error when I used mmpbsa calculate the binding freeenergy
Hannes Loeffler
(Wed Nov 06 2013 - 05:51:00 PST)
Re: [AMBER] help!!! I got a error when I used mmpbsa calculate the binding freeenergy
Jason Swails
(Wed Nov 06 2013 - 06:17:52 PST)
Re: [AMBER] help!!! I got a error when I used mmpbsa calculate the binding freeenergy
David Chen
(Fri Nov 08 2013 - 23:11:58 PST)
Re: [AMBER] help!!! I got a error when I used mmpbsa calculate the binding freeenergy
hannes.loeffler.stfc.ac.uk
(Sat Nov 09 2013 - 02:33:05 PST)
Re: [AMBER] help!!! I got a error when I used mmpbsa calculate the binding freeenergy
David Chen
(Sat Nov 09 2013 - 03:32:24 PST)
[AMBER] Building AMBER/MMPBSA.py.MPI with intel MPI
Vlad Cojocaru
(Thu Nov 07 2013 - 02:45:39 PST)
Re: [AMBER] Building AMBER/MMPBSA.py.MPI with intel MPI
Jason Swails
(Thu Nov 07 2013 - 04:34:08 PST)
Re: [AMBER] Building AMBER/MMPBSA.py.MPI with intel MPI
Vlad Cojocaru
(Thu Nov 07 2013 - 04:42:41 PST)
[AMBER] error while executing sander.MPI
sunita.tifrh.res.in
(Thu Nov 07 2013 - 04:52:36 PST)
Re: [AMBER] error while executing sander.MPI
Daniel Roe
(Thu Nov 07 2013 - 07:30:55 PST)
Re: [AMBER] error while executing sander.MPI
sunita.tifrh.res.in
(Fri Nov 08 2013 - 22:10:55 PST)
[AMBER] MMPBSA.py.MPI: mpi4py not imported via LSF
Vlad Cojocaru
(Thu Nov 07 2013 - 10:34:44 PST)
Re: [AMBER] MMPBSA.py.MPI: mpi4py not imported via LSF
Vlad Cojocaru
(Fri Nov 08 2013 - 01:28:53 PST)
[AMBER] hexagonal unit cell for membrane simulation with NAMD
Thomas Evangelidis
(Thu Nov 07 2013 - 16:37:19 PST)
Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD
Brian Radak
(Fri Nov 08 2013 - 06:32:14 PST)
Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD
Pawel
(Fri Nov 08 2013 - 14:03:40 PST)
Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD
Thomas Evangelidis
(Tue Nov 12 2013 - 04:11:47 PST)
Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD
Thomas Evangelidis
(Tue Nov 12 2013 - 04:28:57 PST)
Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD
Pawel
(Tue Nov 12 2013 - 07:41:59 PST)
Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD
Thomas Evangelidis
(Tue Nov 12 2013 - 09:31:20 PST)
Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD
Thomas Evangelidis
(Tue Nov 12 2013 - 13:11:22 PST)
Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD
Jason Swails
(Tue Nov 12 2013 - 14:06:30 PST)
Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD
Daniel Roe
(Tue Nov 12 2013 - 14:27:32 PST)
Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD
Thomas Evangelidis
(Tue Nov 12 2013 - 15:02:04 PST)
Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD
Jason Swails
(Tue Nov 12 2013 - 16:51:16 PST)
Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD
Pawel
(Wed Nov 13 2013 - 05:07:43 PST)
Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD
Thomas Evangelidis
(Wed Nov 13 2013 - 07:27:15 PST)
Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD
Pawel Janowski
(Wed Nov 13 2013 - 07:34:57 PST)
[AMBER] TI tutorial
Terry M. Gray
(Thu Nov 07 2013 - 20:53:15 PST)
Re: [AMBER] TI tutorial
David A Case
(Fri Nov 08 2013 - 04:09:10 PST)
Re: [AMBER] TI tutorial
Terry M. Gray
(Fri Nov 08 2013 - 15:16:31 PST)
[AMBER] Nonbond cells Problem How to restart?
Soumendranath Bhakat
(Thu Nov 07 2013 - 23:27:23 PST)
Re: [AMBER] Nonbond cells Problem How to restart?
Daniel Roe
(Fri Nov 08 2013 - 06:54:22 PST)
[AMBER] parameters for F-
Mannan
(Thu Nov 07 2013 - 23:46:59 PST)
Re: [AMBER] parameters for F-
David A Case
(Fri Nov 08 2013 - 04:13:03 PST)
[AMBER] writing out atom radii optimized for PBSA (radiopt=1)
Vlad Cojocaru
(Fri Nov 08 2013 - 00:50:19 PST)
Re: [AMBER] writing out atom radii optimized for PBSA (radiopt=1)
Jason Swails
(Fri Nov 08 2013 - 04:11:53 PST)
Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much!
Yongxiu Li
(Fri Nov 08 2013 - 01:19:40 PST)
Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much!
Pawel
(Fri Nov 08 2013 - 06:11:27 PST)
[AMBER] QMMM with Gaussian 09 not writing structures in mdcrd
Claire Coderch Boué
(Fri Nov 08 2013 - 01:55:03 PST)
Re: [AMBER] QMMM with Gaussian 09 not writing structures in mdcrd
David A Case
(Fri Nov 08 2013 - 04:16:58 PST)
[AMBER] ph md simulation
Necmettin Pirinccioglu
(Fri Nov 08 2013 - 02:00:27 PST)
Re: [AMBER] ph md simulation
Jason Swails
(Fri Nov 08 2013 - 04:22:17 PST)
[AMBER] creation of disulfide bonds
Beale, John
(Fri Nov 08 2013 - 02:18:57 PST)
Re: [AMBER] creation of disulfide bonds
Hannes Loeffler
(Fri Nov 08 2013 - 02:46:51 PST)
[AMBER] MMPBSA.py.MPI
Anthony Cruz Balberdi
(Fri Nov 08 2013 - 08:01:37 PST)
Re: [AMBER] MMPBSA.py.MPI
David A Case
(Fri Nov 08 2013 - 09:16:53 PST)
Re: [AMBER] MMPBSA.py.MPI
Anthony Cruz-Balberdy
(Sat Nov 09 2013 - 15:57:25 PST)
Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"
冉挺
(Fri Nov 08 2013 - 09:10:10 PST)
Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"
case
(Sat Nov 09 2013 - 07:30:32 PST)
Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"
冉挺
(Sun Nov 10 2013 - 20:20:16 PST)
Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"
David A Case
(Mon Nov 11 2013 - 06:18:23 PST)
Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"
Ying-Chieh Sun
(Sat Nov 09 2013 - 23:50:07 PST)
[AMBER] Input file (_MMPBSA_gb.mdin) doesn't exist
Mu Xia
(Fri Nov 08 2013 - 18:19:35 PST)
Re: [AMBER] Input file (_MMPBSA_gb.mdin) doesn't exist
Jason Swails
(Sat Nov 09 2013 - 06:45:27 PST)
[AMBER] Problem of calculating the Van der Waals energy between two proteins
Tan-MIng Chi
(Fri Nov 08 2013 - 19:33:14 PST)
[AMBER] Temperature and TI with qm/mm
Fabrício Bracht
(Fri Nov 08 2013 - 23:33:09 PST)
Re: [AMBER] Temperature and TI with qm/mm
case
(Sat Nov 09 2013 - 07:25:45 PST)
Re: [AMBER] Temperature and TI with qm/mm
Fabrício Bracht
(Sat Nov 09 2013 - 10:01:18 PST)
Re: [AMBER] Temperature and TI with qm/mm
case
(Sun Nov 10 2013 - 13:20:39 PST)
[AMBER] dna with different base pairs/turn
Jio M
(Sun Nov 10 2013 - 09:09:40 PST)
Re: [AMBER] dna with different base pairs/turn
ros
(Sun Nov 10 2013 - 10:01:50 PST)
Re: [AMBER] dna with different base pairs/turn
David A Case
(Mon Nov 11 2013 - 06:23:36 PST)
Re: [AMBER] dna with different base pairs/turn
Jio M
(Mon Nov 11 2013 - 10:01:33 PST)
Re: [AMBER] dna with different base pairs/turn
David A Case
(Mon Nov 11 2013 - 12:22:55 PST)
Re: [AMBER] update error
Raman Parkesh
(Sun Nov 10 2013 - 22:25:42 PST)
Re: [AMBER] update error
Raman Parkesh
(Mon Nov 11 2013 - 01:44:58 PST)
Re: [AMBER] update error
Jason Swails
(Mon Nov 11 2013 - 04:12:10 PST)
Re: [AMBER] update error
Raman Parkesh
(Mon Nov 11 2013 - 05:12:52 PST)
Re: [AMBER] update error
Raman Parkesh
(Mon Nov 11 2013 - 06:24:12 PST)
Re: [AMBER] update error
Jason Swails
(Mon Nov 11 2013 - 06:37:26 PST)
Re: [AMBER] update error
Jason Swails
(Mon Nov 11 2013 - 04:16:38 PST)
[AMBER] estimate memory requirements for MMPBSA.py.MPI
Vlad Cojocaru
(Mon Nov 11 2013 - 06:52:24 PST)
Re: [AMBER] estimate memory requirements for MMPBSA.py.MPI
Jason Swails
(Mon Nov 11 2013 - 08:50:10 PST)
Re: [AMBER] estimate memory requirements for MMPBSA.py.MPI
Vlad Cojocaru
(Tue Nov 12 2013 - 00:17:44 PST)
[AMBER] R.E.D. server updating
psu4.uic.edu
(Mon Nov 11 2013 - 13:24:33 PST)
Re: [AMBER] R.E.D. server updating
FyD
(Mon Nov 11 2013 - 14:51:47 PST)
Re: [AMBER] R.E.D. server updating
psu4.uic.edu
(Tue Nov 12 2013 - 12:20:39 PST)
[AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory"
Vlad Cojocaru
(Tue Nov 12 2013 - 02:53:24 PST)
Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory"
Jason Swails
(Tue Nov 12 2013 - 05:17:09 PST)
Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory"
Vlad Cojocaru
(Tue Nov 12 2013 - 05:36:23 PST)
Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory"
Vlad Cojocaru
(Tue Nov 12 2013 - 06:22:50 PST)
Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory"
Jason Swails
(Tue Nov 12 2013 - 07:22:40 PST)
Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory"
Vlad Cojocaru
(Tue Nov 12 2013 - 07:41:41 PST)
Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory"
Jason Swails
(Tue Nov 12 2013 - 08:17:54 PST)
Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory"
Vlad Cojocaru
(Thu Nov 14 2013 - 06:35:48 PST)
Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory"
Jason Swails
(Thu Nov 14 2013 - 07:53:26 PST)
Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory"
Vlad Cojocaru
(Thu Nov 14 2013 - 08:49:48 PST)
[AMBER] Questions about pmemd.cuda and prmtop file with modified A COEF.
X Sun
(Tue Nov 12 2013 - 00:13:01 PST)
Re: [AMBER] Questions about pmemd.cuda and prmtop file with modified A COEF.
Jason Swails
(Tue Nov 12 2013 - 17:04:13 PST)
Re: [AMBER] Questions about pmemd.cuda and prmtop file with modified A COEF.
X Sun
(Tue Nov 12 2013 - 05:03:15 PST)
Re: [AMBER] Questions about pmemd.cuda and prmtop file with modified A COEF.
case
(Wed Nov 13 2013 - 00:40:45 PST)
Re: [AMBER] Questions about pmemd.cuda and prmtop file with modified A COEF.
Scott Le Grand
(Wed Nov 13 2013 - 13:14:38 PST)
Re: [AMBER] Questions about pmemd.cuda and prmtop file with modified A COEF.
Ross Walker
(Wed Nov 13 2013 - 13:53:13 PST)
[AMBER] Currently only GPU version 1.3 and 2.x are supported
Ashutosh Shandilya
(Tue Nov 12 2013 - 23:02:42 PST)
Re: [AMBER] Currently only GPU version 1.3 and 2.x are supported
Ashutosh Shandilya
(Wed Nov 13 2013 - 02:35:02 PST)
Re: [AMBER] Currently only GPU version 1.3 and 2.x are supported
Jason Swails
(Wed Nov 13 2013 - 02:41:15 PST)
Re: [AMBER] Currently only GPU version 1.3 and 2.x are supported
Ashutosh Shandilya
(Wed Nov 13 2013 - 02:49:57 PST)
Re: [AMBER] Currently only GPU version 1.3 and 2.x are supported
Jason Swails
(Wed Nov 13 2013 - 03:17:16 PST)
Re: [AMBER] Currently only GPU version 1.3 and 2.x are supported
Ashutosh Shandilya
(Wed Nov 13 2013 - 05:01:53 PST)
Re: [AMBER] Currently only GPU version 1.3 and 2.x are supported
Jason Swails
(Wed Nov 13 2013 - 07:18:00 PST)
Re: [AMBER] Currently only GPU version 1.3 and 2.x are supported
Ashutosh Shandilya
(Thu Nov 14 2013 - 23:33:20 PST)
[AMBER] How to calculate charges for a beta peptide
Lalita Shaki
(Wed Nov 13 2013 - 05:05:58 PST)
[AMBER] ambpdb problem with binary restart file
Date, Mihir
(Wed Nov 13 2013 - 10:43:02 PST)
Re: [AMBER] ambpdb problem with binary restart file
Daniel Roe
(Wed Nov 13 2013 - 11:14:55 PST)
Re: [AMBER] ambpdb problem with binary restart file. .
Date, Mihir
(Wed Nov 13 2013 - 11:38:39 PST)
Re: [AMBER] ambpdb problem with binary restart file. .
Daniel Roe
(Wed Nov 13 2013 - 11:45:46 PST)
Re: [AMBER] ambpdb problem with binary restart file. .
Jason Swails
(Wed Nov 13 2013 - 11:57:47 PST)
Re: [AMBER] ambpdb problem with binary restart file
Jason Swails
(Wed Nov 13 2013 - 11:16:45 PST)
[AMBER] Positional restraints
George Tzotzos
(Wed Nov 13 2013 - 12:41:50 PST)
Re: [AMBER] Positional restraints
Jason Swails
(Wed Nov 13 2013 - 13:18:59 PST)
Re: [AMBER] Positional restraints
George Tzotzos
(Wed Nov 13 2013 - 16:10:22 PST)
Re: [AMBER] Positional restraints
Jason Swails
(Thu Nov 14 2013 - 04:26:02 PST)
[AMBER] saquinavir.prep
andrea
(Thu Nov 14 2013 - 03:26:01 PST)
[AMBER] minimization/equilibration amber 12 - wont generate .mdcrd and .ene files
Amparo Garcia Lopez
(Thu Nov 14 2013 - 04:16:19 PST)
Re: [AMBER] minimization/equilibration amber 12 - wont generate .mdcrd and .ene files
Jason Swails
(Thu Nov 14 2013 - 04:38:35 PST)
Re: [AMBER] minimization/equilibration amber 12 - wont generate .mdcrd and .ene files
Amparo Garcia Lopez
(Thu Nov 14 2013 - 04:54:20 PST)
[AMBER] MMPBSA.py calculation
Fernando Martín García
(Thu Nov 14 2013 - 05:32:32 PST)
[AMBER] protonation of protein-ligand complex
Thomas Evangelidis
(Thu Nov 14 2013 - 11:30:45 PST)
Re: [AMBER] protonation of protein-ligand complex
Dwight McGee
(Thu Nov 14 2013 - 11:50:42 PST)
Re: [AMBER] protonation of protein-ligand complex
Thomas Evangelidis
(Thu Nov 14 2013 - 12:14:24 PST)
Re: [AMBER] protonation of protein-ligand complex
Brian Radak
(Thu Nov 14 2013 - 12:21:59 PST)
Re: [AMBER] protonation of protein-ligand complex
Thomas Evangelidis
(Thu Nov 14 2013 - 12:52:41 PST)
Re: [AMBER] protonation of protein-ligand complex
Jason Swails
(Thu Nov 14 2013 - 13:33:58 PST)
Re: [AMBER] protonation of protein-ligand complex
Adrian Roitberg
(Thu Nov 14 2013 - 13:22:51 PST)
Re: [AMBER] protonation of protein-ligand complex
Jason Swails
(Thu Nov 14 2013 - 13:29:27 PST)
[AMBER] Mac OS X Mavericks
Julio Dominguez
(Thu Nov 14 2013 - 20:29:18 PST)
[AMBER] Inquiring abt the use of NOE pairs in analysis of MD simulations
Yew Mun Yip
(Fri Nov 15 2013 - 00:32:07 PST)
Re: [AMBER] Inquiring abt the use of NOE pairs in analysis of MD simulations
case
(Fri Nov 15 2013 - 02:05:12 PST)
[AMBER] Qns abt REMD simulations
Yew Mun Yip
(Fri Nov 15 2013 - 02:51:49 PST)
[AMBER] ff12 references
Jacopo Sgrignani
(Fri Nov 15 2013 - 04:47:30 PST)
[AMBER] QMMM of Ca containing protein
Thomas Exner
(Fri Nov 15 2013 - 08:10:23 PST)
Re: [AMBER] QMMM of Ca containing protein
Thomas Exner
(Fri Nov 15 2013 - 08:30:49 PST)
Re: [AMBER] QMMM of Ca containing protein
Brian Radak
(Fri Nov 15 2013 - 09:12:59 PST)
[AMBER] charmmlipid2amber.x: Permission denied
Yuan Lyu
(Fri Nov 15 2013 - 13:41:46 PST)
Re: [AMBER] charmmlipid2amber.x: Permission denied
Ross Walker
(Fri Nov 15 2013 - 13:48:42 PST)
Re: [AMBER] charmmlipid2amber.x: Permission denied
Yuan Lyu
(Fri Nov 15 2013 - 14:08:50 PST)
Re: [AMBER] charmmlipid2amber.x: Permission denied
Ross Walker
(Fri Nov 15 2013 - 14:27:35 PST)
Re: [AMBER] charmmlipid2amber.x: Permission denied
Yuan Lyu
(Fri Nov 15 2013 - 14:45:31 PST)
[AMBER] Does anyone know how to use nab to generate a single RNA chain
肖立
(Fri Nov 15 2013 - 14:00:32 PST)
Re: [AMBER] Does anyone know how to use nab to generate a single RNA chain
Brian Radak
(Fri Nov 15 2013 - 14:09:52 PST)
Re: [AMBER] Does anyone know how to use nab to generate a single RNA chain
肖立
(Fri Nov 15 2013 - 14:13:45 PST)
Re: [AMBER] Does anyone know how to use nab to generate a single RNA chain
Brian Radak
(Fri Nov 15 2013 - 14:25:30 PST)
[AMBER] Problem with penta coordinated HEME-HIS
moitrayee.mbu.iisc.ernet.in
(Fri Nov 15 2013 - 15:59:56 PST)
Re: [AMBER] Problem with penta coordinated HEME-HIS
case
(Sat Nov 16 2013 - 01:13:06 PST)
Re: [AMBER] Problem with penta coordinated HEME-HIS
moitrayee.mbu.iisc.ernet.in
(Sat Nov 16 2013 - 13:06:14 PST)
Re: [AMBER] Problem with penta coordinated HEME-HIS
Jason Swails
(Sun Nov 17 2013 - 08:38:44 PST)
Re: [AMBER] Problem with penta coordinated HEME-HIS
moitrayee.mbu.iisc.ernet.in
(Wed Nov 20 2013 - 18:48:37 PST)
Re: [AMBER] Problem with penta coordinated HEME-HIS
Jason Swails
(Thu Nov 21 2013 - 04:52:03 PST)
[AMBER] Dump vector problem
Indrajit Deb
(Fri Nov 15 2013 - 20:50:20 PST)
Re: [AMBER] Dump vector problem
Daniel Roe
(Sun Nov 17 2013 - 09:26:27 PST)
[AMBER] Enquiries about running a simulation in vacuum
Yip Yew Mun
(Sat Nov 16 2013 - 06:57:49 PST)
Re: [AMBER] Enquiries about running a simulation in vacuum
Jason Swails
(Sat Nov 16 2013 - 09:25:53 PST)
[AMBER] Amber 12 pmemd.MPI doesn't produce distance output
Sajeewa Pemasinghe
(Sat Nov 16 2013 - 08:26:07 PST)
Re: [AMBER] Amber 12 pmemd.MPI doesn't produce distance output
Jason Swails
(Sat Nov 16 2013 - 09:19:52 PST)
Re: [AMBER] Amber 12 pmemd.MPI doesn't produce distance output
Sajeewa Pemasinghe
(Sat Nov 16 2013 - 10:01:37 PST)
[AMBER] atom does not have a type
Helen Lvy
(Sat Nov 16 2013 - 13:17:45 PST)
Re: [AMBER] atom does not have a type
Daniel Roe
(Mon Nov 18 2013 - 09:18:53 PST)
[AMBER] Query about MM-PBSA free energy calculation for multiple ligand binding
Vaibhav Jain
(Sat Nov 16 2013 - 21:03:27 PST)
Re: [AMBER] Query about MM-PBSA free energy calculation for multiple ligand binding
Jason Swails
(Sun Nov 17 2013 - 08:33:43 PST)
Re: [AMBER] Query about MM-PBSA free energy calculation for multiple ligand binding
Vaibhav Jain
(Mon Nov 18 2013 - 03:04:38 PST)
Re: [AMBER] Query about MM-PBSA free energy calculation for multiple ligand binding
Jason Swails
(Mon Nov 18 2013 - 04:49:08 PST)
Re: [AMBER] Query about MM-PBSA free energy calculation for multiple ligand binding
Vaibhav Dixit
(Tue Nov 19 2013 - 13:50:05 PST)
[AMBER] RMS2D maybe?
Fabrício Bracht
(Sun Nov 17 2013 - 11:06:33 PST)
Re: [AMBER] RMS2D maybe?
Daniel Roe
(Mon Nov 18 2013 - 07:33:58 PST)
[AMBER] making a box with restraints so ligand does not float away
ranjit pillai
(Sun Nov 17 2013 - 11:55:08 PST)
Re: [AMBER] making a box with restraints so ligand does not float away
case
(Sun Nov 17 2013 - 14:35:14 PST)
Re: [AMBER] making a box with restraints so ligand does not float away
ranjit pillai
(Mon Nov 18 2013 - 09:30:59 PST)
[AMBER] Cannot turn on column_fft?
yunshi11 .
(Sun Nov 17 2013 - 15:17:40 PST)
Re: [AMBER] Cannot turn on column_fft?
Adrian Roitberg
(Sun Nov 17 2013 - 15:23:51 PST)
[AMBER] gpu_download_partial_forces: download failed unspecified launch failure
Ashutosh Shandilya
(Sun Nov 17 2013 - 21:41:19 PST)
Re: [AMBER] gpu_download_partial_forces: download failed unspecified launch failure
Daniel Roe
(Mon Nov 18 2013 - 09:32:26 PST)
Re: [AMBER] gpu_download_partial_forces: download failed unspecified launch failure
Ashutosh Shandilya
(Tue Nov 19 2013 - 07:47:48 PST)
Re: [AMBER] gpu_download_partial_forces: download failed unspecified launch failure
Niel Henriksen
(Tue Nov 19 2013 - 08:17:59 PST)
Re: [AMBER] gpu_download_partial_forces: download failed unspecified launch failure
Jason Swails
(Tue Nov 19 2013 - 08:18:46 PST)
Re: [AMBER] gpu_download_partial_forces: download failed unspecified launch failure
Ross Walker
(Tue Nov 19 2013 - 08:14:33 PST)
[AMBER] which PBRadii is best when we use PBSA method to calculate the bonding affinity
fjliu
(Sun Nov 17 2013 - 23:32:41 PST)
[AMBER] CL vs Cl & more...
FyD
(Mon Nov 18 2013 - 02:45:34 PST)
Re: [AMBER] CL vs Cl & more...
case
(Mon Nov 18 2013 - 04:10:05 PST)
Re: [AMBER] CL vs Cl & more...
FyD
(Mon Nov 18 2013 - 04:37:47 PST)
Re: [AMBER] which PBRadii is best when we use PBSA method to calculate the bonding affinity
Jason Swails
(Mon Nov 18 2013 - 04:47:39 PST)
[AMBER] Freezing the angle during the simulation
anu chandra
(Mon Nov 18 2013 - 04:57:54 PST)
Re: [AMBER] Freezing the angle during the simulation
Jason Swails
(Mon Nov 18 2013 - 05:19:36 PST)
[AMBER] Substructure potential energy
Toomas Kaevand
(Mon Nov 18 2013 - 08:32:47 PST)
Re: [AMBER] Substructure potential energy
Carlos Simmerling
(Mon Nov 18 2013 - 08:38:54 PST)
Re: [AMBER] Substructure potential energy
Toomas Kaevand
(Mon Nov 18 2013 - 08:44:27 PST)
[AMBER] Bug in ptraj (Ambertools 13 patch 20)
Åke Sandgren
(Mon Nov 18 2013 - 09:08:23 PST)
[AMBER] PME Direct Force takes up 40% CPU time?
yunshi11 .
(Mon Nov 18 2013 - 09:46:35 PST)
Re: [AMBER] PME Direct Force takes up 40% CPU time?
Jason Swails
(Mon Nov 18 2013 - 10:10:56 PST)
Re: [AMBER] PME Direct Force takes up 40% CPU time?
yunshi11 .
(Tue Nov 19 2013 - 08:35:51 PST)
Re: [AMBER] PME Direct Force takes up 40% CPU time?
Jason Swails
(Tue Nov 19 2013 - 09:17:51 PST)
[AMBER] Wham tolerance
Fabrício Bracht
(Mon Nov 18 2013 - 13:38:53 PST)
Re: [AMBER] Wham tolerance
Adrian Roitberg
(Mon Nov 18 2013 - 13:41:16 PST)
Re: [AMBER] Wham tolerance
Fabrício Bracht
(Mon Nov 18 2013 - 14:17:34 PST)
Re: [AMBER] Wham tolerance
Jason Swails
(Mon Nov 18 2013 - 14:41:21 PST)
Re: [AMBER] Wham tolerance
Brian Radak
(Tue Nov 19 2013 - 07:21:05 PST)
[AMBER] CUDA driver insufficient
wei zhang
(Mon Nov 18 2013 - 14:08:30 PST)
Re: [AMBER] CUDA driver insufficient
Jason Swails
(Mon Nov 18 2013 - 14:32:59 PST)
Re: [AMBER] CUDA driver insufficient
wei zhang
(Mon Nov 18 2013 - 15:35:30 PST)
Re: [AMBER] CUDA driver insufficient
Ross Walker
(Mon Nov 18 2013 - 20:26:17 PST)
Re: [AMBER] CUDA driver insufficient
Scott Le Grand
(Mon Nov 18 2013 - 21:13:54 PST)
Re: [AMBER] CUDA driver insufficient
wei zhang
(Tue Nov 19 2013 - 07:19:16 PST)
Re: [AMBER] CUDA driver insufficient
wei zhang
(Wed Nov 20 2013 - 07:09:27 PST)
Re: [AMBER] CUDA driver insufficient
wei zhang
(Tue Nov 26 2013 - 15:35:55 PST)
Re: [AMBER] CUDA driver insufficient
Ross Walker
(Tue Nov 26 2013 - 16:31:22 PST)
Re: [AMBER] CUDA driver insufficient
wei zhang
(Wed Nov 27 2013 - 11:45:24 PST)
[AMBER] PARSE radii and effective radii IN MM/PBSA & MM/GBSA
psu4.uic.edu
(Mon Nov 18 2013 - 15:50:56 PST)
Re: [AMBER] PARSE radii and effective radii IN MM/PBSA & MM/GBSA
Ray Luo, Ph.D.
(Mon Nov 18 2013 - 16:09:12 PST)
[AMBER] Res-Res energy shows different value with or without explicit solvent
kurisaki
(Tue Nov 19 2013 - 04:06:05 PST)
Re: [AMBER] Res-Res energy shows different value with or without explicit solvent
Jason Swails
(Tue Nov 19 2013 - 04:53:48 PST)
Re: [AMBER] Res-Res energy shows different value with or without explicit solvent
kurisaki
(Tue Nov 19 2013 - 05:06:22 PST)
Re: [AMBER] Res-Res energy shows different value with or without explicit solvent
Carlos Simmerling
(Tue Nov 19 2013 - 05:13:58 PST)
Re: [AMBER] Res-Res energy shows different value with or without explicit solvent
kurisaki
(Tue Nov 19 2013 - 16:45:24 PST)
Re: [AMBER] Res-Res energy shows different value with or without explicit solvent
Carlos Simmerling
(Tue Nov 19 2013 - 17:00:17 PST)
Re: [AMBER] Res-Res energy shows different value with or without explicit solvent
kurisaki
(Tue Nov 19 2013 - 18:12:09 PST)
Re: [AMBER] Res-Res energy shows different value with or without explicit solvent
Jason Swails
(Tue Nov 19 2013 - 18:43:20 PST)
Re: [AMBER] Res-Res energy shows different value with or without explicit solvent
Jason Swails
(Tue Nov 19 2013 - 17:10:18 PST)
Re: [AMBER] Fwd: which PBRadii is best when we use PBSA method to calculate the bonding affinity
Jason Swails
(Tue Nov 19 2013 - 05:15:01 PST)
[AMBER] how to calculate electron density and order parameters of lipid11 membrane
Thomas Evangelidis
(Tue Nov 19 2013 - 05:33:01 PST)
Re: [AMBER] how to calculate electron density and order parameters of lipid11 membrane
Thomas Evangelidis
(Tue Nov 19 2013 - 13:43:22 PST)
Re: [AMBER] how to calculate electron density and order parameters of lipid11 membrane
Jason Swails
(Tue Nov 19 2013 - 17:16:01 PST)
[AMBER] README under pmemd/src?
yunshi11 .
(Tue Nov 19 2013 - 08:45:45 PST)
Re: [AMBER] README under pmemd/src?
Ross Walker
(Tue Nov 19 2013 - 10:35:28 PST)
Re: [AMBER] README under pmemd/src?
yunshi11 .
(Wed Nov 20 2013 - 09:21:41 PST)
Re: [AMBER] README under pmemd/src?
Jason Swails
(Wed Nov 20 2013 - 10:14:21 PST)
[AMBER] Hill coef in constant ph calculation fit
Fabrício Bracht
(Tue Nov 19 2013 - 09:23:15 PST)
Re: [AMBER] Hill coef in constant ph calculation fit
Jason Swails
(Tue Nov 19 2013 - 10:16:52 PST)
[AMBER] van der Waals energy component calculation
Dennis Stauffer
(Tue Nov 19 2013 - 14:36:52 PST)
Re: [AMBER] van der Waals energy component calculation
David A Case
(Wed Nov 20 2013 - 05:16:02 PST)
[AMBER] About turning off energy terms between selected atoms
Mo Chen
(Tue Nov 19 2013 - 15:27:26 PST)
Re: [AMBER] About turning off energy terms between selected atoms
David A Case
(Thu Nov 21 2013 - 04:33:49 PST)
Re: [AMBER] About turning off energy terms between selected atoms
Jason Swails
(Thu Nov 21 2013 - 04:44:31 PST)
[AMBER] the dielectric constant for mixed solvent in mmpbsa
Fengxue Li
(Tue Nov 19 2013 - 16:39:48 PST)
Re: [AMBER] the dielectric constant for mixed solvent in mmpbsa
Jason Swails
(Tue Nov 19 2013 - 17:02:32 PST)
[AMBER] Analysis of REMD trajectories (YM)
Yip Yew Mun
(Tue Nov 19 2013 - 23:45:34 PST)
Re: [AMBER] Analysis of REMD trajectories (YM)
Jason Swails
(Wed Nov 20 2013 - 14:28:57 PST)
[AMBER] Error with angle restrain in CUDA PMEMD
anu chandra
(Wed Nov 20 2013 - 03:26:46 PST)
Re: [AMBER] Error with angle restrain in CUDA PMEMD
Jason Swails
(Wed Nov 20 2013 - 04:35:13 PST)
Re: [AMBER] Error with angle restrain in CUDA PMEMD
anu chandra
(Thu Nov 21 2013 - 23:06:32 PST)
Re: [AMBER] Error with angle restrain in CUDA PMEMD
Jason Swails
(Fri Nov 22 2013 - 06:27:11 PST)
Re: [AMBER] Error with angle restrain in CUDA PMEMD
David A Case
(Wed Nov 20 2013 - 05:26:36 PST)
Re: [AMBER] Error with angle restrain in CUDA PMEMD
anu chandra
(Thu Nov 21 2013 - 23:18:38 PST)
[AMBER] RTIL simulation
Saeed Nasiri
(Wed Nov 20 2013 - 05:09:35 PST)
Re: [AMBER] RTIL simulation
David A Case
(Thu Nov 21 2013 - 04:52:47 PST)
[AMBER] ante-MMPBSA
Milo Westler
(Wed Nov 20 2013 - 08:34:23 PST)
Re: [AMBER] ante-MMPBSA
Milo Westler
(Wed Nov 20 2013 - 08:38:12 PST)
Re: [AMBER] ante-MMPBSA
Milo Westler
(Wed Nov 20 2013 - 08:43:33 PST)
Re: [AMBER] ante-MMPBSA
Jason Swails
(Wed Nov 20 2013 - 08:54:03 PST)
Re: [AMBER] ante-MMPBSA
Milo Westler
(Wed Nov 20 2013 - 09:10:55 PST)
[AMBER] Fwd: gpu_download_partial_forces: download failed unspecified launch failure
Ashutosh Shandilya
(Wed Nov 20 2013 - 09:19:10 PST)
Re: [AMBER] Fwd: gpu_download_partial_forces: download failed unspecified launch failure
Jason Swails
(Wed Nov 20 2013 - 10:17:01 PST)
Re: [AMBER] Fwd: gpu_download_partial_forces: download failed unspecified launch failure
Niel Henriksen
(Wed Nov 20 2013 - 10:17:53 PST)
[AMBER] C2H2 zinc finger stability
Michael Garton
(Wed Nov 20 2013 - 10:42:12 PST)
[AMBER] Nudged Elastic Band with Explicit Solvent for a Larger Protein
James W. Snyder, Jr.
(Wed Nov 20 2013 - 12:40:11 PST)
Re: [AMBER] Nudged Elastic Band with Explicit Solvent for a Larger Protein
Daniel Roe
(Wed Nov 20 2013 - 12:57:44 PST)
Re: [AMBER] Nudged Elastic Band with Explicit Solvent for a Larger Protein
James W. Snyder, Jr.
(Wed Nov 20 2013 - 13:34:32 PST)
Re: [AMBER] Nudged Elastic Band with Explicit Solvent for a Larger Protein
Daniel Roe
(Wed Nov 20 2013 - 14:35:27 PST)
Re: [AMBER] Nudged Elastic Band with Explicit Solvent for a Larger Protein
James W. Snyder, Jr.
(Wed Nov 20 2013 - 16:33:46 PST)
[AMBER] How do I know if QM is working in sander.MPI?
yunshi11 .
(Wed Nov 20 2013 - 19:23:11 PST)
Re: [AMBER] How do I know if QM is working in sander.MPI?
Ross Walker
(Wed Nov 20 2013 - 19:33:14 PST)
Re: [AMBER] How do I know if QM is working in sander.MPI?
Brian Radak
(Thu Nov 21 2013 - 06:00:32 PST)
Re: [AMBER] How do I know if QM is working in sander.MPI?
Jason Swails
(Thu Nov 21 2013 - 06:53:05 PST)
Re: [AMBER] How do I know if QM is working in sander.MPI?
Brian Radak
(Thu Nov 21 2013 - 07:07:23 PST)
Re: [AMBER] How do I know if QM is working in sander.MPI?
Gustavo Seabra
(Thu Nov 21 2013 - 07:24:33 PST)
Re: [AMBER] How do I know if QM is working in sander.MPI?
Jason Swails
(Thu Nov 21 2013 - 07:46:09 PST)
Re: [AMBER] How do I know if QM is working in sander.MPI?
Jan-Philip Gehrcke
(Fri Nov 22 2013 - 04:02:13 PST)
Re: [AMBER] How do I know if QM is working in sander.MPI?
yunshi11 .
(Fri Nov 22 2013 - 10:04:34 PST)
[AMBER] maximum simulated annealing temperature in explicit solvent
Thomas Evangelidis
(Thu Nov 21 2013 - 02:23:25 PST)
Re: [AMBER] maximum simulated annealing temperature in explicit solvent
Carlos Simmerling
(Thu Nov 21 2013 - 03:33:50 PST)
[AMBER] GTX 780 Ti
filip fratev
(Fri Nov 22 2013 - 00:03:44 PST)
Re: [AMBER] GTX 780 Ti
Scott Le Grand
(Fri Nov 22 2013 - 09:46:23 PST)
Re: [AMBER] GTX 780 Ti
Ross Walker
(Fri Nov 22 2013 - 09:54:37 PST)
Re: [AMBER] GTX 780 Ti
filip fratev
(Fri Nov 22 2013 - 20:50:44 PST)
Re: [AMBER] GTX 780 Ti
Ross Walker
(Sat Nov 23 2013 - 14:14:54 PST)
Re: [AMBER] GTX 780 Ti
filip fratev
(Sun Nov 24 2013 - 00:15:40 PST)
Re: [AMBER] GTX 780 Ti
Bill Ross
(Mon Nov 25 2013 - 20:39:20 PST)
[AMBER] New empirical force field tools: Release of R.E.D. Server Dev./R.E.D. Python
FyD
(Fri Nov 22 2013 - 02:22:40 PST)
[AMBER] Query about residue decomposition energy
Kshatresh Dutta Dubey
(Fri Nov 22 2013 - 02:58:41 PST)
Re: [AMBER] Query about residue decomposition energy
Jason Swails
(Fri Nov 22 2013 - 04:51:30 PST)
Re: [AMBER] Query about residue decomposition energy
Kshatresh Dutta Dubey
(Fri Nov 22 2013 - 06:41:13 PST)
Re: [AMBER] Query about residue decomposition energy
Jason Swails
(Fri Nov 22 2013 - 07:17:32 PST)
Re: [AMBER] AMBER CUDA Installation
Massimiliano Porrini
(Fri Nov 22 2013 - 03:38:44 PST)
Re: [AMBER] AMBER CUDA Installation
Jason Swails
(Fri Nov 22 2013 - 04:32:18 PST)
[AMBER] REMD mdout file in AMBER12 do not show REMD EXCHANGE CALCULATION section
sunita.tifrh.res.in
(Fri Nov 22 2013 - 06:07:01 PST)
Re: [AMBER] REMD mdout file in AMBER12 do not show REMD EXCHANGE CALCULATION section
Jason Swails
(Fri Nov 22 2013 - 06:40:43 PST)
Re: [AMBER] REMD mdout file in AMBER12 do not show REMD EXCHANGE CALCULATION section
sunita.tifrh.res.in
(Fri Nov 22 2013 - 08:36:12 PST)
Re: [AMBER] REMD mdout file in AMBER12 do not show REMD EXCHANGE CALCULATION section
Jason Swails
(Fri Nov 22 2013 - 06:42:15 PST)
[AMBER] Fwd: Amber 11 with AM1/d and PM6
Jianzhuang Yao
(Fri Nov 22 2013 - 09:33:27 PST)
Re: [AMBER] Fwd: Amber 11 with AM1/d and PM6
Jason Swails
(Fri Nov 22 2013 - 09:40:35 PST)
Re: [AMBER] Fwd: Amber 11 with AM1/d and PM6
Jianzhuang Yao
(Fri Nov 22 2013 - 09:46:52 PST)
[AMBER] Wanna run nanoseconds of QM/MM MD?
yunshi11 .
(Fri Nov 22 2013 - 10:19:34 PST)
Re: [AMBER] Wanna run nanoseconds of QM/MM MD?
Jason Swails
(Fri Nov 22 2013 - 10:32:54 PST)
Re: [AMBER] Wanna run nanoseconds of QM/MM MD?
Ross Walker
(Fri Nov 22 2013 - 10:59:30 PST)
Re: [AMBER] Wanna run nanoseconds of QM/MM MD?
yunshi11 .
(Fri Nov 22 2013 - 11:47:04 PST)
Re: [AMBER] Wanna run nanoseconds of QM/MM MD?
Jason Swails
(Fri Nov 22 2013 - 12:04:43 PST)
Re: [AMBER] Wanna run nanoseconds of QM/MM MD?
Brian Radak
(Fri Nov 22 2013 - 11:48:46 PST)
[AMBER] SQM file format
Geoffrey Gray
(Fri Nov 22 2013 - 10:48:38 PST)
Re: [AMBER] SQM file format
Brian Radak
(Fri Nov 22 2013 - 11:41:48 PST)
Re: [AMBER] SQM file format
Brian Radak
(Fri Nov 22 2013 - 11:54:23 PST)
Re: [AMBER] SQM file format
Geoffrey Gray
(Sat Nov 23 2013 - 07:10:10 PST)
[AMBER] tleap command
Saeed Nasiri
(Sat Nov 23 2013 - 02:46:34 PST)
Re: [AMBER] tleap command
case
(Sat Nov 23 2013 - 13:32:32 PST)
[AMBER] query about atom nomenclature in NOE restraints
Thomas Evangelidis
(Sat Nov 23 2013 - 04:26:28 PST)
Re: [AMBER] query about atom nomenclature in NOE restraints
Thomas Evangelidis
(Sat Nov 23 2013 - 08:12:31 PST)
Re: [AMBER] query about atom nomenclature in NOE restraints
case
(Sat Nov 23 2013 - 13:35:40 PST)
[AMBER] Fix a atom??
X Sun
(Fri Nov 22 2013 - 18:11:16 PST)
Re: [AMBER] Fix a atom??
case
(Sat Nov 23 2013 - 13:28:43 PST)
[AMBER] Detailed. Fix a atom??
X Sun
(Fri Nov 22 2013 - 23:50:00 PST)
Re: [AMBER] Detailed. Fix a atom??
case
(Sat Nov 23 2013 - 17:08:42 PST)
[AMBER] About Cv in _MMPBSA_complex_nm.out.0
赵媛
(Mon Nov 25 2013 - 08:52:23 PST)
Re: [AMBER] About Cv in _MMPBSA_complex_nm.out.0
Ray Luo, Ph.D.
(Mon Nov 25 2013 - 09:03:25 PST)
Re: [AMBER] About Cv in _MMPBSA_complex_nm.out.0
赵媛
(Mon Nov 25 2013 - 18:57:38 PST)
[AMBER] pbsa: solvation radius from topology file not used when radiopt=0
Jan-Philip Gehrcke
(Mon Nov 25 2013 - 09:38:43 PST)
Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0
Jan-Philip Gehrcke
(Mon Nov 25 2013 - 10:04:08 PST)
Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0
Ray Luo, Ph.D.
(Mon Nov 25 2013 - 10:13:18 PST)
Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0
Jan-Philip Gehrcke
(Mon Nov 25 2013 - 10:52:26 PST)
Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0
Ray Luo, Ph.D.
(Mon Nov 25 2013 - 11:16:11 PST)
Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0
wmsmith.uci.edu
(Mon Nov 25 2013 - 12:00:00 PST)
Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0
Ray Luo, Ph.D.
(Tue Nov 26 2013 - 10:49:17 PST)
Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0
Jason Swails
(Mon Nov 25 2013 - 10:38:05 PST)
[AMBER] error while loading shared libraries: libgfortran.so.3
Jio M
(Mon Nov 25 2013 - 11:43:19 PST)
Re: [AMBER] error while loading shared libraries: libgfortran.so.3
Jason Swails
(Mon Nov 25 2013 - 12:10:38 PST)
Re: [AMBER] error while loading shared libraries: libgfortran.so.3
Jio M
(Mon Nov 25 2013 - 13:21:51 PST)
[AMBER] MMPBSA.py strip_mask issue
psu4.uic.edu
(Mon Nov 25 2013 - 12:24:22 PST)
Re: [AMBER] MMPBSA.py strip_mask issue
Jason Swails
(Mon Nov 25 2013 - 15:08:35 PST)
[AMBER] Multiple restraint masks
Michael Garton
(Tue Nov 26 2013 - 07:34:47 PST)
Re: [AMBER] Multiple restraint masks
Jason Swails
(Tue Nov 26 2013 - 08:29:42 PST)
Re: [AMBER] Multiple restraint masks
case
(Tue Nov 26 2013 - 14:52:54 PST)
Re: [AMBER] Multiple restraint masks
Jio M
(Tue Nov 26 2013 - 20:19:00 PST)
Re: [AMBER] Multiple restraint masks
case
(Wed Nov 27 2013 - 18:23:44 PST)
[AMBER] internal geometry restraint
Jio M
(Tue Nov 26 2013 - 08:06:20 PST)
Re: [AMBER] internal geometry restraint
Jason Swails
(Tue Nov 26 2013 - 08:31:35 PST)
Re: [AMBER] internal geometry restraint
case
(Tue Nov 26 2013 - 14:56:11 PST)
Re: [AMBER] internal geometry restraint
Jio M
(Tue Nov 26 2013 - 19:09:18 PST)
Re: [AMBER] internal geometry restraint
Jio M
(Thu Nov 28 2013 - 07:40:28 PST)
Re: [AMBER] About the Mg charge in AMBER FF
George Patargias
(Wed Nov 27 2013 - 03:07:33 PST)
[AMBER] AMBER 2 LAMMPS
Arjun Sharma
(Wed Nov 27 2013 - 08:40:48 PST)
Re: [AMBER] AMBER 2 LAMMPS
Brian Radak
(Wed Nov 27 2013 - 12:20:18 PST)
[AMBER] ff99SB with nmr and ildn corrections
Norah Schlacter
(Wed Nov 27 2013 - 13:10:33 PST)
Re: [AMBER] ff99SB with nmr and ildn corrections
case
(Wed Nov 27 2013 - 18:31:07 PST)
[AMBER] Atom types for "alkene carbons", R.E.D.
Cecilia Lindgren
(Thu Nov 28 2013 - 06:40:34 PST)
Re: [AMBER] Atom types for "alkene carbons", R.E.D.
FyD
(Thu Nov 28 2013 - 08:06:34 PST)
Re: [AMBER] Atom types for "alkene carbons", R.E.D.
case
(Fri Nov 29 2013 - 06:30:34 PST)
Re: [AMBER] Atom types for "alkene carbons", R.E.D.
FyD
(Fri Nov 29 2013 - 08:50:54 PST)
Re: [AMBER] Atom types for "alkene carbons", R.E.D.
FyD
(Sat Nov 30 2013 - 01:04:49 PST)
[AMBER] Trying to relax selected residues in tleap gives a null list error
Sajeewa Pemasinghe
(Thu Nov 28 2013 - 20:50:05 PST)
Re: [AMBER] Trying to relax selected residues in tleap gives a null list error
FyD
(Thu Nov 28 2013 - 21:41:59 PST)
Re: [AMBER] Trying to relax selected residues in tleap gives a null list error
Sajeewa Pemasinghe
(Fri Nov 29 2013 - 12:35:58 PST)
[AMBER] Error "glibc detected" sander
Souvik Sur
(Fri Nov 29 2013 - 01:18:11 PST)
Re: [AMBER] Error "glibc detected" sander
Jan-Philip Gehrcke
(Fri Nov 29 2013 - 02:09:22 PST)
[AMBER] Volume calculation
Sanjib Paul
(Fri Nov 29 2013 - 04:47:05 PST)
[AMBER] RE : Volume calculation
ABEL Stephane 175950
(Fri Nov 29 2013 - 05:05:08 PST)
[AMBER] TR : [PROVENANCE INTERNET] RE : Volume calculation
ABEL Stephane 175950
(Fri Nov 29 2013 - 05:09:36 PST)
Re: [AMBER] TR : [PROVENANCE INTERNET] RE : Volume calculation
Sanjib Paul
(Fri Nov 29 2013 - 06:35:53 PST)
[AMBER] Topology files of homodimer-ligand complex
George Tzotzos
(Fri Nov 29 2013 - 11:02:18 PST)
[AMBER] planarity of Trp side chain and improper torsion term
Jorge Iulek
(Fri Nov 29 2013 - 14:15:31 PST)
Re: [AMBER] planarity of Trp side chain and improper torsion term
case
(Sat Nov 30 2013 - 06:13:41 PST)
Re: [AMBER] Does pmemd or pmemd.mpi support center of mass restraint?
case
(Sat Nov 30 2013 - 08:39:44 PST)
Re: [AMBER] Does pmemd or pmemd.mpi support center of mass restraint?
Jason Swails
(Sat Nov 30 2013 - 08:42:56 PST)
Last message date
:
Sat Nov 30 2013 - 09:00:03 PST
Archived on
: Fri Apr 19 2024 - 05:54:38 PDT
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