Amber Archive Jun 2012 by author
767 messages
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Starting
Thu May 31 2012 - 10:30:03 PDT,
Ending
Sat Jun 30 2012 - 15:30:03 PDT
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Acoot Brett
[AMBER] Which server can give the series of PDB files for the energy equivalent conformations
(Wed Jun 27 2012 - 17:30:16 PDT)
[AMBER] a question on molecular dynamics simulation of key residue mutated protein
(Wed Jun 27 2012 - 16:42:22 PDT)
Re: [AMBER] How to explain this phenomenon is production MD
(Sat Jun 23 2012 - 18:12:33 PDT)
Re: [AMBER] How to explain this phenomenon is production MD
(Sat Jun 23 2012 - 01:51:01 PDT)
[AMBER] How to explain this phenomenon is production MD
(Thu Jun 21 2012 - 23:31:17 PDT)
[AMBER] partial charge, charge radius and epsilon
(Fri Jun 08 2012 - 04:45:24 PDT)
[AMBER] how to change the namme of the terminal OXT so that it can be recoginized by MOLMOL
(Sun Jun 03 2012 - 23:57:53 PDT)
Adam Jion
[AMBER] Pressure Regulaton Under Position Restraint
(Sun Jun 24 2012 - 10:06:45 PDT)
[AMBER] How does 'restraint' work in Amber?
(Sat Jun 23 2012 - 02:04:29 PDT)
[AMBER] Switching-off the partial charges
(Tue Jun 19 2012 - 22:56:08 PDT)
Re: [AMBER] GPU kernel error
(Tue Jun 19 2012 - 22:51:36 PDT)
Re: [AMBER] Problems installing AmberTools12 on Ubuntu
(Thu Jun 07 2012 - 19:32:29 PDT)
Re: [AMBER] Problems installing AmberTools12 on Ubuntu
(Thu Jun 07 2012 - 18:41:55 PDT)
Re: [AMBER] Problems installing AmberTools12 on Ubuntu
(Thu Jun 07 2012 - 18:22:42 PDT)
[AMBER] Problems installing AmberTools12 on Ubuntu
(Thu Jun 07 2012 - 01:47:19 PDT)
Re: [AMBER] Removing finite number of solvent particles from simulation box
(Wed Jun 06 2012 - 21:49:22 PDT)
[AMBER] Removing finite number of solvent particles from simulation box
(Wed Jun 06 2012 - 18:12:44 PDT)
Adrian Roitberg
Re: [AMBER] Script error to restart MD automatically
(Tue Jun 19 2012 - 06:03:49 PDT)
Re: [AMBER] Problem of Force filed (Calculate the dihedral parameter)
(Sat Jun 16 2012 - 22:31:16 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 15 2012 - 06:46:23 PDT)
Re: [AMBER] QM/MM minimization
(Mon Jun 11 2012 - 08:38:14 PDT)
Re: [AMBER] Distance constraints not working..
(Mon Jun 04 2012 - 09:58:49 PDT)
Alan
Re: [AMBER] acpye for CHARMM?
(Fri Jun 15 2012 - 04:11:17 PDT)
Albert
Re: [AMBER] update for POPE test
(Fri Jun 29 2012 - 07:16:46 PDT)
[AMBER] update for POPE test
(Fri Jun 29 2012 - 05:32:16 PDT)
[AMBER] update for POPE test
(Fri Jun 29 2012 - 05:28:44 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Mon Jun 25 2012 - 10:52:42 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 22 2012 - 01:50:32 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Thu Jun 21 2012 - 22:51:50 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Thu Jun 21 2012 - 22:41:02 PDT)
[AMBER] strange ion location
(Thu Jun 21 2012 - 06:22:07 PDT)
[AMBER] strange ion location
(Wed Jun 20 2012 - 23:56:01 PDT)
Re: [AMBER] POPE lipids is too 'ordered'
(Tue Jun 19 2012 - 05:42:18 PDT)
Re: [AMBER] POPE lipids is too 'ordered'
(Tue Jun 19 2012 - 05:14:38 PDT)
Re: [AMBER] ptraj vector error
(Tue Jun 19 2012 - 04:42:03 PDT)
Re: [AMBER] ptraj vector error
(Tue Jun 19 2012 - 02:13:09 PDT)
[AMBER] ptraj vector error
(Tue Jun 19 2012 - 01:04:40 PDT)
Re: [AMBER] POPE lipids is too 'ordered'
(Mon Jun 18 2012 - 11:27:12 PDT)
Re: [AMBER] POPE lipids is too 'ordered'
(Mon Jun 18 2012 - 11:16:09 PDT)
[AMBER] POPE lipids is too 'ordered'
(Mon Jun 18 2012 - 07:02:29 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Sat Jun 16 2012 - 12:15:53 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Sat Jun 16 2012 - 10:01:33 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 15 2012 - 11:07:08 PDT)
[AMBER] why cut off is so small for CUDA running?
(Fri Jun 15 2012 - 05:18:00 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 15 2012 - 03:35:38 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 15 2012 - 03:28:45 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 15 2012 - 02:48:54 PDT)
[AMBER] acpye for CHARMM?
(Thu Jun 14 2012 - 08:18:54 PDT)
[AMBER] strange POPC under lipids 11 FF
(Thu Jun 14 2012 - 06:17:20 PDT)
[AMBER] how to assign bond order for the output of RED .mol2?
(Tue Jun 12 2012 - 23:35:43 PDT)
[AMBER] where is velocity information?
(Tue Jun 12 2012 - 23:31:40 PDT)
Re: [AMBER] up coming workshop?
(Fri Jun 08 2012 - 02:51:44 PDT)
Re: [AMBER] up coming workshop?
(Fri Jun 08 2012 - 00:17:11 PDT)
[AMBER] up coming workshop?
(Thu Jun 07 2012 - 10:06:55 PDT)
Aldo Segura
Re: [AMBER] Trouble calculating free energy
(Fri Jun 01 2012 - 22:48:34 PDT)
Alex Rodriguez
Re: [AMBER] Problem in parameter file generation
(Mon Jun 04 2012 - 03:30:17 PDT)
Re: [AMBER] Problem in parameter file generation
(Mon Jun 04 2012 - 03:09:36 PDT)
Re: [AMBER] Problem in parameter file generation
(Mon Jun 04 2012 - 02:54:25 PDT)
Andre Serobian
[AMBER] Monitoring formation of Water bridges in ptraj
(Wed Jun 27 2012 - 23:46:45 PDT)
Anna Bauß
Re: [AMBER] TI calculation Amber 12
(Thu Jun 21 2012 - 05:53:54 PDT)
Re: [AMBER] TI calculation Amber 12
(Thu Jun 21 2012 - 04:31:35 PDT)
[AMBER] TI calculation Amber 12
(Thu Jun 21 2012 - 02:42:53 PDT)
Anselm Horn
[AMBER] Salt concentration: general question
(Sat Jun 30 2012 - 07:20:06 PDT)
Re: [AMBER] Specifying disulfide bonds in a protein model
(Thu Jun 21 2012 - 03:45:22 PDT)
Re: [AMBER] Script error to restart MD automatically
(Tue Jun 19 2012 - 00:05:01 PDT)
Re: [AMBER] is there a batch queue app?
(Fri Jun 01 2012 - 13:02:17 PDT)
arun kumar
Re: [AMBER] Amber11 Installation Problem
(Wed Jun 06 2012 - 05:51:10 PDT)
[AMBER] Amber11 Installation Problem
(Tue Jun 05 2012 - 23:35:20 PDT)
[AMBER] Amber11 Installation Problem
(Tue Jun 05 2012 - 00:46:47 PDT)
Ashutosh Shandilya
[AMBER] Error in writing of coordinate file after simulation
(Wed Jun 20 2012 - 12:34:12 PDT)
Asma Abro 28-FBAS/MSBI/F09
Re: [AMBER] AMBER Error: unable to achieve consistency
(Thu Jun 28 2012 - 20:51:15 PDT)
Re: [AMBER] AMBER Error: unable to achieve consistency
(Wed Jun 27 2012 - 21:57:27 PDT)
Re: [AMBER] AMBER Error: unable to achieve consistency
(Tue Jun 26 2012 - 23:45:40 PDT)
Re: [AMBER] AMBER Error: unable to achieve consistency
(Tue Jun 26 2012 - 22:20:21 PDT)
Re: [AMBER] AMBER Error: unable to achieve consistency
(Tue Jun 26 2012 - 22:19:27 PDT)
[AMBER] AMBER Error: unable to achieve consistency
(Tue Jun 26 2012 - 20:40:12 PDT)
Re: [AMBER] Error in minimization
(Tue Jun 12 2012 - 04:00:29 PDT)
Re: [AMBER] Error in minimization
(Sun Jun 10 2012 - 22:24:54 PDT)
Re: [AMBER] Error in minimization
(Sun Jun 10 2012 - 22:10:27 PDT)
Re: [AMBER] Error in minimization
(Fri Jun 08 2012 - 10:25:16 PDT)
Re: [AMBER] Error in minimization
(Thu Jun 07 2012 - 22:49:36 PDT)
Re: [AMBER] Error in minimization
(Thu Jun 07 2012 - 22:20:17 PDT)
Re: [AMBER] Error in minimization
(Wed Jun 06 2012 - 21:18:58 PDT)
Re: [AMBER] Error in minimization
(Wed Jun 06 2012 - 00:32:41 PDT)
Re: [AMBER] Error in minimization
(Tue Jun 05 2012 - 21:28:18 PDT)
Re: [AMBER] Error in minimization
(Tue Jun 05 2012 - 00:37:00 PDT)
[AMBER] Error in minimization
(Mon Jun 04 2012 - 23:24:49 PDT)
Re: [AMBER] Problem in parameter file generation
(Mon Jun 04 2012 - 03:33:19 PDT)
Re: [AMBER] Problem in parameter file generation
(Mon Jun 04 2012 - 03:22:32 PDT)
Re: [AMBER] Problem in parameter file generation
(Mon Jun 04 2012 - 03:02:35 PDT)
[AMBER] Problem in parameter file generation
(Mon Jun 04 2012 - 02:47:19 PDT)
Asmita Gupta
[AMBER] all_prot_nucleic10.lib file in amber12
(Wed Jun 27 2012 - 23:44:29 PDT)
Re: [AMBER] force field library for protonated cytosine
(Mon Jun 25 2012 - 11:42:22 PDT)
Re: [AMBER] force field library for protonated cytosine
(Mon Jun 25 2012 - 10:28:18 PDT)
[AMBER] force field library for protonated cytosine
(Thu Jun 14 2012 - 11:24:32 PDT)
barb fr
[AMBER] binding energy of duplex DNA by mm-pbsa
(Mon Jun 25 2012 - 07:28:04 PDT)
Bashford, Donald
[AMBER] GBSA for simulation of disordered proteins
(Thu Jun 07 2012 - 19:07:20 PDT)
Beale, John
[AMBER] Specifying disulfide bonds in a protein model
(Thu Jun 21 2012 - 02:18:09 PDT)
Ben Roberts
Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
(Sat Jun 23 2012 - 21:17:24 PDT)
Re: [AMBER] undefined reference error in compiling
(Thu Jun 14 2012 - 18:12:45 PDT)
Re: [AMBER] Help with Zn parameters after MCPB parameterization
(Thu Jun 14 2012 - 13:37:00 PDT)
Re: [AMBER] Error in minimization
(Mon Jun 11 2012 - 16:56:42 PDT)
Re: [AMBER] Error in minimization
(Tue Jun 05 2012 - 00:26:05 PDT)
Benjamin D Madej
Re: [AMBER] POPE lipids is too 'ordered'
(Mon Jun 18 2012 - 11:25:02 PDT)
Re: [AMBER] POPE lipids is too 'ordered'
(Mon Jun 18 2012 - 09:28:46 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Sat Jun 16 2012 - 11:17:28 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Sat Jun 16 2012 - 10:37:09 PDT)
Re: [AMBER] R: R: strange POPC under lipids 11 FF
(Sat Jun 16 2012 - 09:59:45 PDT)
Benjamin Haley
[AMBER] Configurational bias Monte Carlo
(Fri Jun 01 2012 - 09:19:01 PDT)
Benjamin Madej
Re: [AMBER] R: strange POPC under lipids 11 FF
(Mon Jun 25 2012 - 11:33:08 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Mon Jun 25 2012 - 10:14:56 PDT)
Benjamin Stauch
[AMBER] ptraj behaves differently on Mac and Linux
(Thu Jun 07 2012 - 02:23:33 PDT)
BERGY
Re: [AMBER] CHAMBER with RNA
(Fri Jun 29 2012 - 00:28:15 PDT)
[AMBER] Amber12 Compilation Error in CENTOS 4.5
(Mon Jun 11 2012 - 02:41:15 PDT)
Bill Miller III
Re: [AMBER] warning during nmode calulation - Not all of your snapshots minimized within tolerable limits for nmode
(Fri Jun 22 2012 - 11:11:53 PDT)
Re: [AMBER] MMPBSA problem
(Tue Jun 19 2012 - 18:59:39 PDT)
Re: [AMBER] MMPBSA.py.MPI
(Sat Jun 16 2012 - 20:38:19 PDT)
Re: [AMBER] The VDWAALS is huge in MMPBSA calculation.
(Fri Jun 15 2012 - 05:08:20 PDT)
Re: [AMBER] The VDWAALS is huge in MMPBSA calculation.
(Wed Jun 13 2012 - 04:53:23 PDT)
Re: [AMBER] The VDWAALS is huge in MMPBSA calculation.
(Tue Jun 12 2012 - 23:07:19 PDT)
Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11
(Wed Jun 06 2012 - 08:32:09 PDT)
Re: [AMBER] MMPBSA.py - problem with complex.prmtop
(Wed Jun 06 2012 - 04:53:13 PDT)
Re: [AMBER] MMPBSA_Error: Could not find necessary program [sander]
(Fri Jun 01 2012 - 07:46:28 PDT)
Bill Ross
Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
(Wed Jun 27 2012 - 14:34:04 PDT)
Re: [AMBER] problem with solvateShell command
(Tue Jun 19 2012 - 16:31:31 PDT)
Re: [AMBER] protein misplaced into the water box
(Tue Jun 12 2012 - 15:52:44 PDT)
Re: [AMBER] protein misplaced into the water box
(Mon Jun 11 2012 - 14:08:44 PDT)
Re: [AMBER] LEaP misplaces ions
(Sat Jun 09 2012 - 10:45:05 PDT)
Re: [AMBER] LEaP misplaces ions
(Sat Jun 09 2012 - 09:51:30 PDT)
Re: [AMBER] Problems matching atom names to PREP files
(Fri Jun 08 2012 - 14:16:19 PDT)
bmartini
Re: [AMBER] Small molecule simulations
(Mon Jun 04 2012 - 22:11:36 PDT)
[AMBER] Trouble calculating free energy
(Sat Jun 02 2012 - 06:43:14 PDT)
Brandon Sim
Re: [AMBER] sander termination upon reaching end temperature
(Sat Jun 30 2012 - 15:06:49 PDT)
Re: [AMBER] sander termination upon reaching end temperature
(Fri Jun 29 2012 - 15:05:59 PDT)
Re: [AMBER] sander termination upon reaching end temperature
(Fri Jun 29 2012 - 03:39:01 PDT)
Re: [AMBER] sander termination upon reaching end temperature
(Fri Jun 29 2012 - 03:14:59 PDT)
[AMBER] sander termination upon reaching end temperature
(Fri Jun 29 2012 - 02:17:05 PDT)
Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop?
(Wed Jun 27 2012 - 23:51:42 PDT)
Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop?
(Wed Jun 27 2012 - 20:19:08 PDT)
Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop?
(Wed Jun 27 2012 - 13:12:50 PDT)
Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop?
(Wed Jun 27 2012 - 12:11:53 PDT)
Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop?
(Wed Jun 27 2012 - 12:10:20 PDT)
[AMBER] tleap adds in "missing" terminal hydrogens - how to stop?
(Wed Jun 27 2012 - 12:09:48 PDT)
Re: [AMBER] Solvent box specification for sander
(Thu Jun 21 2012 - 10:33:47 PDT)
Re: [AMBER] Solvent box specification for sander
(Thu Jun 21 2012 - 08:37:17 PDT)
[AMBER] Solvent box specification for sander
(Thu Jun 21 2012 - 05:31:01 PDT)
Re: [AMBER] modeling GDP
(Tue Jun 19 2012 - 22:23:09 PDT)
Re: [AMBER] modeling GDP
(Mon Jun 18 2012 - 15:38:47 PDT)
[AMBER] modeling GDP
(Mon Jun 18 2012 - 11:43:52 PDT)
Brian Radak
Re: [AMBER] Solvent box specification for sander
(Thu Jun 21 2012 - 06:17:30 PDT)
Re: [AMBER] where is velocity information?
(Wed Jun 13 2012 - 06:26:39 PDT)
Re: [AMBER] Fwd: problem with running equilibration MD in an LES system
(Fri Jun 01 2012 - 15:51:40 PDT)
Cao Yang
[AMBER] Bad atom MN in free energy decomposition with MMPBSA.py
(Tue Jun 19 2012 - 07:26:08 PDT)
[AMBER] Slow jobs
(Tue Jun 19 2012 - 03:52:20 PDT)
Re: [AMBER] The VDWAALS is huge in MMPBSA calculation.
(Wed Jun 13 2012 - 20:11:42 PDT)
[AMBER] Abnormally Slow NMode entropy calculation
(Mon Jun 11 2012 - 21:02:40 PDT)
Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0
(Fri Jun 01 2012 - 06:42:30 PDT)
Re: [AMBER] MMPBSA_Error: Could not find necessary program [sander]
(Fri Jun 01 2012 - 06:29:34 PDT)
Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0
(Fri Jun 01 2012 - 06:03:50 PDT)
[AMBER] MMPBSA_Error: Could not find necessary program [sander]
(Fri Jun 01 2012 - 00:58:05 PDT)
Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0
(Thu May 31 2012 - 20:50:54 PDT)
Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0
(Thu May 31 2012 - 19:13:06 PDT)
Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0
(Thu May 31 2012 - 18:05:31 PDT)
[AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0
(Thu May 31 2012 - 10:02:48 PDT)
caobb0214
[AMBER] decomposition of potential of mean force into free energy contribution
(Fri Jun 01 2012 - 21:50:22 PDT)
Carlos Simmerling
Re: [AMBER] Salt concentration: general question
(Sat Jun 30 2012 - 07:52:19 PDT)
Re: [AMBER] trajectory imaging results in structural clashes in protein-ligand complexes
(Fri Jun 29 2012 - 07:43:37 PDT)
Re: [AMBER] sander termination upon reaching end temperature
(Fri Jun 29 2012 - 04:48:57 PDT)
Re: [AMBER] sander termination upon reaching end temperature
(Fri Jun 29 2012 - 03:42:40 PDT)
Re: [AMBER] sander termination upon reaching end temperature
(Fri Jun 29 2012 - 03:24:38 PDT)
Re: [AMBER] sander termination upon reaching end temperature
(Fri Jun 29 2012 - 02:59:27 PDT)
Re: [AMBER] rmsd
(Thu Jun 28 2012 - 12:53:32 PDT)
Re: [AMBER] rmsd
(Thu Jun 28 2012 - 12:45:10 PDT)
Re: [AMBER] rmsd
(Thu Jun 28 2012 - 12:25:10 PDT)
Re: [AMBER] a question on molecular dynamics simulation of key residue mutated protein
(Wed Jun 27 2012 - 16:51:21 PDT)
Re: [AMBER] problem in running LES calculation with a solvated shell system
(Tue Jun 26 2012 - 06:13:21 PDT)
Re: [AMBER] problem in running LES calculation with a solvated shell system
(Tue Jun 26 2012 - 02:49:13 PDT)
Re: [AMBER] REMD structure failure
(Mon Jun 25 2012 - 09:50:59 PDT)
Re: [AMBER] idea of RMSD calculation in AMBER
(Thu Jun 21 2012 - 15:52:18 PDT)
Re: [AMBER] REMD equilibration
(Sat Jun 16 2012 - 04:03:10 PDT)
Re: [AMBER] REMD equilibration
(Fri Jun 15 2012 - 08:09:05 PDT)
Re: [AMBER] long range LJ correction; surface tension; trajectory
(Fri Jun 15 2012 - 03:41:09 PDT)
Re: [AMBER] REMD equilibration
(Fri Jun 15 2012 - 03:38:11 PDT)
Re: [AMBER] REMD equilibration
(Thu Jun 14 2012 - 11:11:34 PDT)
Re: [AMBER] unfolding with iwrap=1, 500K heating is enough?
(Thu Jun 14 2012 - 08:58:18 PDT)
Re: [AMBER] REMD equilibration
(Fri Jun 08 2012 - 02:59:51 PDT)
Re: [AMBER] unfolding with iwrap=1, 500K heating is enough?
(Fri Jun 08 2012 - 02:57:06 PDT)
Re: [AMBER] Fwd: Fwd: problem with running equilibration MD in an LES system
(Mon Jun 04 2012 - 09:44:10 PDT)
case
Re: [AMBER] atom type specification for chlorine
(Sat Jun 30 2012 - 05:27:35 PDT)
Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop?
(Wed Jun 27 2012 - 17:44:21 PDT)
Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
(Tue Jun 26 2012 - 18:21:44 PDT)
Re: [AMBER] using bellymask and group specification together
(Mon Jun 25 2012 - 18:03:22 PDT)
Re: [AMBER] force field library for protonated cytosine
(Mon Jun 25 2012 - 15:12:37 PDT)
Re: [AMBER] undefined reference error in compiling
(Thu Jun 14 2012 - 18:35:33 PDT)
Re: [AMBER] mmpbsa
(Mon Jun 11 2012 - 18:48:04 PDT)
Re: [AMBER] QM/MM periodic boundary conditions in Amber
(Mon Jun 11 2012 - 18:37:16 PDT)
Re: [AMBER] restraining residues with a gpu cluster
(Wed Jun 06 2012 - 19:10:24 PDT)
Re: [AMBER] rocks cluster: MD is much slower when using more than one node
(Sat Jun 02 2012 - 06:06:10 PDT)
Catein Catherine
[AMBER] How to call up ptraj in supercomputer facilities? should I use mpi?
(Sat Jun 30 2012 - 03:28:30 PDT)
[AMBER] How to get starting geometry for <10 AA peptides?
(Mon Jun 11 2012 - 03:09:06 PDT)
[AMBER] Error in new installation.
(Wed Jun 06 2012 - 02:09:08 PDT)
Chinh Su Tran To
Re: [AMBER] unfolding with iwrap=1, 500K heating is enough?
(Sun Jun 17 2012 - 20:05:40 PDT)
Re: [AMBER] unfolding with iwrap=1, 500K heating is enough?
(Sun Jun 10 2012 - 23:52:01 PDT)
[AMBER] unfolding with iwrap=1, 500K heating is enough?
(Thu Jun 07 2012 - 20:17:15 PDT)
chirag740.gmail.com
Re: [AMBER] problem during heating up the system
(Wed Jun 20 2012 - 04:50:40 PDT)
Chris Chris
[AMBER] Small molecule simulations
(Mon Jun 04 2012 - 21:37:51 PDT)
Chris Whittleston
[AMBER] Problems matching atom names to PREP files
(Fri Jun 08 2012 - 05:35:34 PDT)
cieplak.cgl.ucsf.edu
Re: [AMBER] binding energy of duplex DNA by mm-pbsa
(Tue Jun 26 2012 - 14:24:45 PDT)
Re: [AMBER] Problem with NAB: "Residue g not in library rna.amber94.rlb."
(Tue Jun 05 2012 - 13:07:06 PDT)
colvin
Re: [AMBER] MMPBSA.py - problem with complex.prmtop
(Wed Jun 06 2012 - 20:01:32 PDT)
[AMBER] MMPBSA.py - problem with complex.prmtop
(Wed Jun 06 2012 - 01:49:25 PDT)
Damodaran, Komath
Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11
(Thu Jun 07 2012 - 09:09:16 PDT)
[AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11
(Wed Jun 06 2012 - 08:18:00 PDT)
Daniel Roe
Re: [AMBER] using "append" in trajout
(Wed Jun 27 2012 - 05:51:56 PDT)
Re: [AMBER] valence not found for for [Na+ ]
(Mon Jun 25 2012 - 19:35:20 PDT)
Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
(Fri Jun 22 2012 - 08:38:31 PDT)
Re: [AMBER] is the 'image' behavior of cpptraj's 'distance' command correct?
(Fri Jun 22 2012 - 08:19:11 PDT)
Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
(Fri Jun 22 2012 - 06:17:53 PDT)
Re: [AMBER] hydrogen bond analysis
(Fri Jun 22 2012 - 06:15:58 PDT)
Re: [AMBER] C-H...O hydrogen bonds?
(Fri Jun 22 2012 - 06:10:00 PDT)
Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
(Fri Jun 22 2012 - 06:06:57 PDT)
Re: [AMBER] Error in writing of coordinate file after simulation
(Thu Jun 21 2012 - 04:39:49 PDT)
Re: [AMBER] Job running problem in sander
(Sat Jun 16 2012 - 04:52:56 PDT)
Re: [AMBER] REMD equilibration
(Fri Jun 15 2012 - 06:29:03 PDT)
Re: [AMBER] why cut off is so small for CUDA running?
(Fri Jun 15 2012 - 06:07:48 PDT)
Re: [AMBER] ptraj cannot handle large crd file
(Wed Jun 13 2012 - 11:58:47 PDT)
Re: [AMBER] Problems matching atom names to PREP files
(Fri Jun 08 2012 - 06:23:01 PDT)
Re: [AMBER] ptraj behaves differently on Mac and Linux
(Thu Jun 07 2012 - 06:24:29 PDT)
Re: [AMBER] Error in minimization
(Tue Jun 05 2012 - 04:18:32 PDT)
Re: [AMBER] Amber11 Installation Problem
(Tue Jun 05 2012 - 04:16:57 PDT)
Re: [AMBER] inpcrd
(Sun Jun 03 2012 - 13:04:23 PDT)
Daniel Sindhikara
Re: [AMBER] Switching-off the partial charges
(Tue Jun 19 2012 - 23:17:30 PDT)
Re: [AMBER] Ion clumping in large protein-RNA systems
(Sun Jun 17 2012 - 18:32:23 PDT)
Re: [AMBER] REMD equilibration
(Fri Jun 15 2012 - 02:25:51 PDT)
Re: [AMBER] REMD equilibration
(Thu Jun 14 2012 - 18:36:05 PDT)
[AMBER] A small point of confusion in 3DRISM outfiles
(Wed Jun 13 2012 - 02:54:31 PDT)
Re: [AMBER] Error in minimization
(Sun Jun 10 2012 - 23:29:21 PDT)
Re: [AMBER] Error in minimization
(Sun Jun 10 2012 - 22:20:39 PDT)
Re: [AMBER] REMD equilibration
(Sat Jun 09 2012 - 02:56:03 PDT)
David A Case
Re: [AMBER] Fw: set box problem
(Fri Jun 29 2012 - 09:02:01 PDT)
Re: [AMBER] Fw: set box problem
(Fri Jun 29 2012 - 06:46:55 PDT)
Re: [AMBER] no hydrogen added with xleap
(Fri Jun 29 2012 - 05:24:45 PDT)
Re: [AMBER] force field library for protonated cytosine
(Thu Jun 28 2012 - 10:50:04 PDT)
Re: [AMBER] AMBER Error: unable to achieve consistency
(Thu Jun 28 2012 - 07:42:50 PDT)
Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
(Thu Jun 28 2012 - 07:39:14 PDT)
Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop?
(Wed Jun 27 2012 - 12:51:22 PDT)
Re: [AMBER] gaff.dat column and preference to frcmod file params
(Wed Jun 27 2012 - 05:05:38 PDT)
Re: [AMBER] MMPBSA calculation of DNA solvation
(Wed Jun 27 2012 - 04:58:36 PDT)
Re: [AMBER] force field library for protonated cytosine
(Mon Jun 25 2012 - 11:16:01 PDT)
Re: [AMBER] binding energy of duplex DNA by mm-pbsa
(Mon Jun 25 2012 - 08:38:16 PDT)
Re: [AMBER] Doubt about ligand preparation in Gaussian and tleap
(Mon Jun 25 2012 - 08:30:12 PDT)
Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
(Mon Jun 25 2012 - 04:58:56 PDT)
Re: [AMBER] Fwd: Mn2+ parameter and crystal water
(Mon Jun 25 2012 - 04:42:31 PDT)
Re: [AMBER] Pressure Regulaton Under Position Restraint
(Mon Jun 25 2012 - 04:40:54 PDT)
Re: [AMBER] problem in antechamber
(Mon Jun 25 2012 - 04:35:21 PDT)
Re: [AMBER] Error with box parameters
(Fri Jun 15 2012 - 05:21:03 PDT)
Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc.
(Thu Jun 14 2012 - 13:23:11 PDT)
Re: [AMBER] force field library for protonated cytosine
(Thu Jun 14 2012 - 13:09:57 PDT)
Re: [AMBER] mmpbsa
(Thu Jun 14 2012 - 05:11:55 PDT)
Re: [AMBER] what is vlimit error?
(Wed Jun 13 2012 - 04:59:09 PDT)
Re: [AMBER] mmpbsa
(Tue Jun 12 2012 - 10:50:36 PDT)
Re: [AMBER] FF12SB + GLYCAM_06h + Fluorine
(Tue Jun 12 2012 - 07:51:25 PDT)
Re: [AMBER] FIX for Mac OS X Lion with Xcode 4.3.2
(Fri Jun 08 2012 - 13:18:26 PDT)
Re: [AMBER] FIX for Mac OS X Lion with Xcode 4.3.2
(Fri Jun 08 2012 - 07:11:47 PDT)
Re: [AMBER] Error in minimization
(Fri Jun 08 2012 - 05:20:22 PDT)
Re: [AMBER] Error in minimization
(Thu Jun 07 2012 - 04:49:58 PDT)
Re: [AMBER] compiling parallel on centOS5 - rocks with intel
(Mon Jun 04 2012 - 11:54:32 PDT)
Re: [AMBER] Antechamber problem
(Mon Jun 04 2012 - 09:49:32 PDT)
Re: [AMBER] Distance constraints not working..
(Mon Jun 04 2012 - 04:57:17 PDT)
Re: [AMBER] how to change the namme of the terminal OXT so that it can be recoginized by MOLMOL
(Mon Jun 04 2012 - 04:55:03 PDT)
Re: [AMBER] Configurational bias Monte Carlo
(Fri Jun 01 2012 - 09:50:29 PDT)
Re: [AMBER] cuda parallel - can't find mpi.h
(Fri Jun 01 2012 - 09:49:34 PDT)
Re: [AMBER] Fwd: problem with running equilibration MD in an LES system
(Fri Jun 01 2012 - 08:42:19 PDT)
Re: [AMBER] Fwd: problem with running equilibration MD in an LES system
(Fri Jun 01 2012 - 06:47:18 PDT)
David A. Case
Re: [AMBER] Making a complex
(Sat Jun 23 2012 - 06:37:29 PDT)
Re: [AMBER] Question on Ig=-1 usage
(Sat Jun 23 2012 - 06:33:28 PDT)
Re: [AMBER] (no subject)
(Fri Jun 22 2012 - 15:41:21 PDT)
Re: [AMBER] Issues with library location on compiling AmberTools12
(Fri Jun 22 2012 - 15:41:14 PDT)
Re: [AMBER] Specifying disulfide bonds in a protein model
(Thu Jun 21 2012 - 04:36:30 PDT)
Re: [AMBER] problem during heating up the system
(Wed Jun 20 2012 - 05:13:03 PDT)
Re: [AMBER] Switching-off the partial charges
(Tue Jun 19 2012 - 23:43:39 PDT)
Re: [AMBER] modeling GDP
(Tue Jun 19 2012 - 01:24:13 PDT)
Re: [AMBER] modeling GDP
(Mon Jun 18 2012 - 14:27:37 PDT)
Re: [AMBER] (no subject)
(Mon Jun 18 2012 - 10:42:18 PDT)
Re: [AMBER] Atom type for oxygen bound to Phosphate
(Mon Jun 18 2012 - 05:02:47 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Sat Jun 16 2012 - 09:20:17 PDT)
Re: [AMBER] undefined reference error in compiling
(Fri Jun 15 2012 - 18:24:38 PDT)
Re: [AMBER] umbrella sampling -- centroid or center of mass
(Fri Jun 15 2012 - 18:21:13 PDT)
Re: [AMBER] Problem with NAB: "Residue g not in library rna.amber94.rlb."
(Tue Jun 05 2012 - 10:50:47 PDT)
Debolina Mitra
[AMBER] Generation of ESP files
(Thu Jun 07 2012 - 23:26:14 PDT)
[AMBER] Reallocation of memory space
(Mon Jun 04 2012 - 05:38:32 PDT)
DEBOSTUTI GHOSHDASTIDAR
Re: [AMBER] (no subject)
(Mon Jun 25 2012 - 23:09:17 PDT)
Re: [AMBER] (no subject)
(Mon Jun 25 2012 - 11:00:31 PDT)
Re: [AMBER] (no subject)
(Wed Jun 20 2012 - 09:56:38 PDT)
Re: [AMBER] (no subject)
(Mon Jun 18 2012 - 06:51:01 PDT)
Delwar Hossain
[AMBER] MMPBSA.py.MPI and MMPBSA.py
(Wed Jun 20 2012 - 12:24:51 PDT)
[AMBER] MMPBSA.py.MPI
(Sat Jun 16 2012 - 20:30:01 PDT)
[AMBER] MMPBSA.py
(Fri Jun 15 2012 - 16:05:07 PDT)
[AMBER] Why calcualted energy difference betwwen MM-PBSA and MM-GBSA is so large
(Wed Jun 06 2012 - 13:01:20 PDT)
Dilraj LAMA
[AMBER] Question on Ig=-1 usage
(Sat Jun 23 2012 - 01:05:55 PDT)
[AMBER] Atom type for oxygen bound to Phosphate
(Tue Jun 19 2012 - 06:03:03 PDT)
[AMBER] Atom type for oxygen bound to Phosphate
(Mon Jun 18 2012 - 04:25:12 PDT)
Dmitry Mukha
Re: [AMBER] GPU kernel error
(Mon Jun 18 2012 - 23:27:19 PDT)
Re: [AMBER] GPU kernel error
(Sun Jun 17 2012 - 08:56:11 PDT)
Re: [AMBER] GPU kernel error
(Sun Jun 17 2012 - 05:53:56 PDT)
Re: [AMBER] rocks cluster: MD is much slower when using more than one node
(Sat Jun 02 2012 - 02:35:38 PDT)
Do Yong Kim
[AMBER] REMD structure failure
(Mon Jun 25 2012 - 09:48:02 PDT)
Do-Yong Kim
[AMBER] ptraj: combine pdb's to mdcrd
(Mon Jun 11 2012 - 15:45:45 PDT)
Dr. Vitaly V. Chaban
Re: [AMBER] DMSO parameters
(Tue Jun 05 2012 - 17:05:32 PDT)
Re: [AMBER] Small molecule simulations
(Mon Jun 04 2012 - 22:17:48 PDT)
Re: [AMBER] inpcrd
(Sun Jun 03 2012 - 14:24:51 PDT)
[AMBER] inpcrd
(Sun Jun 03 2012 - 12:08:29 PDT)
Dwight McGee
Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc.
(Thu Jun 14 2012 - 09:43:05 PDT)
E. Nihal Korkmaz
[AMBER] MMPBSA.py gbsa unrecognized
(Wed Jun 27 2012 - 13:39:09 PDT)
[AMBER] rdf/count of ions around a protein
(Wed Jun 20 2012 - 13:40:42 PDT)
Elisa Frezza
Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
(Fri Jun 22 2012 - 06:38:18 PDT)
Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
(Fri Jun 22 2012 - 06:11:03 PDT)
[AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
(Fri Jun 22 2012 - 03:36:04 PDT)
Ewa Chudyk
[AMBER] QM/MM minimization
(Mon Jun 11 2012 - 08:17:43 PDT)
Fabrício Bracht
Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
(Thu Jun 28 2012 - 14:43:24 PDT)
Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
(Thu Jun 28 2012 - 13:29:04 PDT)
Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
(Thu Jun 28 2012 - 12:09:21 PDT)
Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
(Thu Jun 28 2012 - 05:01:13 PDT)
Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
(Tue Jun 26 2012 - 16:57:51 PDT)
Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
(Sun Jun 24 2012 - 08:23:45 PDT)
[AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
(Sat Jun 23 2012 - 06:43:48 PDT)
[AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
(Mon Jun 18 2012 - 12:10:37 PDT)
[AMBER] Help with Zn parameters after MCPB parameterization
(Thu Jun 14 2012 - 09:44:04 PDT)
[AMBER] Convergence problems with rism1d and water model other than SPC
(Wed Jun 06 2012 - 10:33:57 PDT)
[AMBER] Convergence problems with rism1d and water model other than SPC
(Wed Jun 06 2012 - 10:26:23 PDT)
Fernando Martín García
Re: [AMBER] GPU kernel error
(Fri Jun 15 2012 - 05:39:18 PDT)
[AMBER] GPU kernel error
(Fri Jun 15 2012 - 03:01:19 PDT)
Francesco Pietra
Re: [AMBER] Issues with library location on compiling AmberTools12
(Fri Jun 22 2012 - 22:21:37 PDT)
[AMBER] SOLVED Fwd: Issues with library location on compiling AmberTools12
(Thu Jun 21 2012 - 22:48:30 PDT)
[AMBER] Issues with library location on compiling AmberTools12
(Thu Jun 21 2012 - 11:57:59 PDT)
Re: [AMBER] protein misplaced into the water box
(Tue Jun 12 2012 - 02:25:12 PDT)
[AMBER] protein misplaced into the water box
(Mon Jun 11 2012 - 00:17:48 PDT)
Re: [AMBER] LEaP misplaces ions
(Sun Jun 10 2012 - 03:37:23 PDT)
Re: [AMBER] LEaP misplaces ions
(Sat Jun 09 2012 - 23:09:44 PDT)
Re: [AMBER] LEaP misplaces ions
(Sat Jun 09 2012 - 10:36:29 PDT)
[AMBER] Fwd: LEaP misplaces ions
(Sat Jun 09 2012 - 01:48:35 PDT)
[AMBER] LEaP misplaces ions
(Sat Jun 09 2012 - 01:29:20 PDT)
[AMBER] chloride ions outside the box
(Fri Jun 01 2012 - 01:53:26 PDT)
FyD
Re: [AMBER] all_prot_nucleic10.lib file in amber12
(Wed Jun 27 2012 - 23:57:53 PDT)
Re: [AMBER] problem in the bondtype judgement step in antechamber
(Tue Jun 26 2012 - 01:27:53 PDT)
Re: [AMBER] force field library for protonated cytosine
(Tue Jun 26 2012 - 00:35:09 PDT)
Re: [AMBER] Doubt about ligand preparation in Gaussian and tleap
(Tue Jun 26 2012 - 00:03:43 PDT)
Re: [AMBER] modeling GDP
(Wed Jun 20 2012 - 00:34:42 PDT)
Re: [AMBER] modeling GDP
(Mon Jun 18 2012 - 15:31:32 PDT)
Re: [AMBER] Atom type for oxygen bound to Phosphate
(Mon Jun 18 2012 - 07:14:06 PDT)
Re: [AMBER] Atom type for oxygen bound to Phosphate
(Mon Jun 18 2012 - 05:07:07 PDT)
Re: [AMBER] chiral Sulfur atom
(Fri Jun 15 2012 - 23:51:11 PDT)
Re: [AMBER] force field library for protonated cytosine
(Fri Jun 15 2012 - 11:52:03 PDT)
Re: [AMBER] how to assign bond order for the output of RED .mol2?
(Wed Jun 13 2012 - 00:42:45 PDT)
Re: [AMBER] how to assign bond order for the output of RED .mol2?
(Wed Jun 13 2012 - 00:38:32 PDT)
Re: [AMBER] Bug in resp or respgen? using intra-molecular-charge-constraints...
(Wed Jun 13 2012 - 00:28:12 PDT)
Re: [AMBER] Bug in resp or respgen? using intra-molecular-charge-constraints...
(Mon Jun 11 2012 - 23:54:31 PDT)
Re: [AMBER] parameters and charges for R and S Configurations
(Mon Jun 11 2012 - 23:39:12 PDT)
Re: [AMBER] Problems matching atom names to PREP files
(Fri Jun 08 2012 - 07:06:34 PDT)
Re: [AMBER] No C-terminal GLH in aminoct*.in
(Wed Jun 06 2012 - 02:20:33 PDT)
Re: [AMBER] No C-terminal GLH in aminoct*.in
(Tue Jun 05 2012 - 23:22:32 PDT)
Re: [AMBER] No C-terminal GLH in aminoct*.in
(Sat Jun 02 2012 - 23:18:16 PDT)
g t
Re: [AMBER] vacuum simulation fails using pmemd
(Sat Jun 23 2012 - 10:48:44 PDT)
[AMBER] vacuum simulation fails using pmemd
(Fri Jun 22 2012 - 04:12:04 PDT)
Gabriel Jara
Re: [AMBER] am1d problem
(Fri Jun 01 2012 - 07:21:04 PDT)
gaoya
Re: [AMBER] problem with solute that breaks up
(Thu May 31 2012 - 22:20:54 PDT)
George Tzotzos
Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc.
(Thu Jun 14 2012 - 14:10:46 PDT)
Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc.
(Thu Jun 14 2012 - 13:10:04 PDT)
Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc.
(Thu Jun 14 2012 - 12:10:41 PDT)
[AMBER] Leap. Error messages on renaming ASP to AS4 etc.
(Thu Jun 14 2012 - 08:52:13 PDT)
Gerald Monard
[AMBER] FactorIX test: CUDA + MPI + ntt=2 => never ends
(Thu Jun 07 2012 - 14:06:44 PDT)
Giovanni Pavan
[AMBER] R: R: strange POPC under lipids 11 FF
(Fri Jun 15 2012 - 06:41:53 PDT)
[AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 15 2012 - 01:00:35 PDT)
Giulia
Re: [AMBER] FF param
(Mon Jun 11 2012 - 04:45:37 PDT)
Gould, Ian R
Re: [AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 22 2012 - 01:50:25 PDT)
Hai Nguyen
Re: [AMBER] REMD equilibration
(Sat Jun 09 2012 - 21:48:56 PDT)
Re: [AMBER] Effect of Temperature
(Fri Jun 01 2012 - 20:49:07 PDT)
Hannes Loeffler
Re: [AMBER] POPE lipids is too 'ordered'
(Tue Jun 19 2012 - 05:50:54 PDT)
Re: [AMBER] POPE lipids is too 'ordered'
(Tue Jun 19 2012 - 05:32:44 PDT)
Harald Lanig
[AMBER] trajectory imaging results in structural clashes in protein-ligand complexes
(Fri Jun 29 2012 - 07:42:12 PDT)
Hemant Gangwar
[AMBER] Reading velocities from netcdf file
(Tue Jun 26 2012 - 02:22:28 PDT)
[AMBER] Reading velocities from netcdf file
(Tue Jun 26 2012 - 00:31:06 PDT)
HIMANSHU JOSHI
Re: [AMBER] PMEMD CUPA MPI STOP WRITING OUTPUT IN RUNNIG STATUS
(Wed Jun 27 2012 - 10:36:22 PDT)
[AMBER] PMEMD CUPA MPI STOP WRITING OUTPUT IN RUNNIG STATUS
(Tue Jun 26 2012 - 23:55:22 PDT)
[AMBER] PTRAJ not able to read netcdf format
(Tue Jun 26 2012 - 03:25:09 PDT)
[AMBER] Fwd:
(Tue Jun 26 2012 - 03:22:00 PDT)
Re: [AMBER] Cuda performance
(Sun Jun 17 2012 - 00:29:03 PDT)
[AMBER] Cuda performance
(Sat Jun 16 2012 - 03:26:25 PDT)
houcemeddine othman
Re: [AMBER] no hydrogen added with xleap
(Fri Jun 29 2012 - 05:05:05 PDT)
[AMBER] no hydrogen added with xleap
(Fri Jun 29 2012 - 04:25:11 PDT)
[AMBER] implicit GB model for membrane simulation
(Tue Jun 26 2012 - 16:11:59 PDT)
Ilyas Yildirim
Re: [AMBER] Re [amber] north/sout energy difference
(Fri Jun 29 2012 - 10:40:33 PDT)
Re: [AMBER] Re [amber] north/sout energy difference
(Thu Jun 28 2012 - 15:25:52 PDT)
Re: [AMBER] binding energy of duplex DNA by mm-pbsa
(Mon Jun 25 2012 - 08:51:52 PDT)
Indrajit Deb
Re: [AMBER] Fwd: Mn2+ parameter and crystal water
(Tue Jun 26 2012 - 00:45:28 PDT)
[AMBER] Fwd: Mn2+ parameter and crystal water
(Sat Jun 23 2012 - 12:32:03 PDT)
[AMBER] Mn2+ parameter
(Sat Jun 23 2012 - 05:23:04 PDT)
intra\\sa175950
Re: [AMBER] Generation of ESP files
(Fri Jun 08 2012 - 01:33:03 PDT)
Ivan Ufimtsev
[AMBER] QM/MM periodic boundary conditions in Amber
(Mon Jun 11 2012 - 13:00:17 PDT)
J B
[AMBER] R: strange POPC under lipids 11 FF
(Thu Jun 21 2012 - 23:14:16 PDT)
[AMBER] R: strange POPC under lipids 11 FF
(Thu Jun 21 2012 - 15:05:40 PDT)
James Murdock
[AMBER] Low POPC area per lipid - LIPID11
(Thu Jun 28 2012 - 11:47:17 PDT)
Jan-Philip Gehrcke
[AMBER] AmberTools 12 pbsa: missing newline character in OpenDX output
(Mon Jun 25 2012 - 10:33:59 PDT)
Re: [AMBER] is the 'image' behavior of cpptraj's 'distance' command correct?
(Mon Jun 25 2012 - 02:59:06 PDT)
[AMBER] is the 'image' behavior of cpptraj's 'distance' command correct?
(Fri Jun 22 2012 - 08:07:08 PDT)
jani vinod
Re: [AMBER] Regarding running PME simulation on GPU
(Sun Jun 17 2012 - 19:29:56 PDT)
[AMBER] Regarding running PME simulation on GPU
(Thu Jun 14 2012 - 04:17:55 PDT)
[AMBER] Amber cuda test failure
(Tue Jun 12 2012 - 05:19:36 PDT)
Jason Swails
Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
(Thu Jun 28 2012 - 13:44:07 PDT)
Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop?
(Wed Jun 27 2012 - 20:39:43 PDT)
Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop?
(Wed Jun 27 2012 - 19:59:48 PDT)
Re: [AMBER] MMPBSA.py gbsa unrecognized
(Wed Jun 27 2012 - 14:14:09 PDT)
Re: [AMBER] APPEND option does not work in TRAJOUT of CPPTRAJ
(Wed Jun 27 2012 - 04:20:31 PDT)
Re: [AMBER] calculation of the average structure
(Tue Jun 26 2012 - 08:14:46 PDT)
Re: [AMBER] Can we change BUFFER_SIZE (1024) ?
(Tue Jun 26 2012 - 07:13:34 PDT)
Re: [AMBER] PTRAJ not able to read netcdf format
(Tue Jun 26 2012 - 07:08:01 PDT)
Re: [AMBER] calculation of the average structure
(Tue Jun 26 2012 - 06:55:39 PDT)
Re: [AMBER] creating a bellymask which includes residues at a given distance from a point
(Mon Jun 25 2012 - 13:15:00 PDT)
Re: [AMBER] (no subject)
(Mon Jun 25 2012 - 12:22:24 PDT)
Re: [AMBER] Problem while running MMPBSA
(Mon Jun 25 2012 - 10:09:22 PDT)
Re: [AMBER] Problem in MM-PBSA decomp module
(Sun Jun 24 2012 - 14:24:35 PDT)
Re: [AMBER] the problem of cpptraj
(Sun Jun 24 2012 - 07:43:42 PDT)
Re: [AMBER] Problem while running MMPBSA
(Fri Jun 22 2012 - 16:26:24 PDT)
Re: [AMBER] vacuum simulation fails using pmemd
(Fri Jun 22 2012 - 08:14:48 PDT)
Re: [AMBER] Solvent box specification for sander
(Thu Jun 21 2012 - 10:41:20 PDT)
Re: [AMBER] Solvent box specification for sander
(Thu Jun 21 2012 - 08:48:49 PDT)
Re: [AMBER] Solvent box specification for sander
(Thu Jun 21 2012 - 06:47:01 PDT)
Re: [AMBER] MMPBSA.py.MPI and MMPBSA.py
(Wed Jun 20 2012 - 12:53:32 PDT)
Re: [AMBER] Problem while running MMPBSA
(Wed Jun 20 2012 - 11:08:58 PDT)
Re: [AMBER] Problem while running MMPBSA
(Wed Jun 20 2012 - 10:19:53 PDT)
Re: [AMBER] Constant pH simulation at pH 7
(Wed Jun 20 2012 - 06:44:50 PDT)
Re: [AMBER] Sander output Error
(Tue Jun 19 2012 - 22:01:45 PDT)
Re: [AMBER] unfolding with iwrap=1, 500K heating is enough?
(Mon Jun 18 2012 - 06:40:04 PDT)
Re: [AMBER] C- and N-terminal amino acids in AmberTools 1.4
(Sun Jun 17 2012 - 13:59:10 PDT)
Re: [AMBER] duplicating - multiplying input files to create dimer etc.
(Sat Jun 16 2012 - 15:34:56 PDT)
Re: [AMBER] MMPBSA.py
(Fri Jun 15 2012 - 20:06:21 PDT)
Re: [AMBER] undefined reference error in compiling
(Fri Jun 15 2012 - 19:55:28 PDT)
Re: [AMBER] undefined reference error in compiling
(Fri Jun 15 2012 - 10:58:04 PDT)
Re: [AMBER] REMD equilibration
(Fri Jun 15 2012 - 06:08:21 PDT)
Re: [AMBER] The VDWAALS is huge in MMPBSA calculation.
(Fri Jun 15 2012 - 06:06:41 PDT)
Re: [AMBER] undefined reference error in compiling
(Thu Jun 14 2012 - 18:12:51 PDT)
Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc.
(Thu Jun 14 2012 - 14:37:12 PDT)
Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc.
(Thu Jun 14 2012 - 13:55:49 PDT)
Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc.
(Thu Jun 14 2012 - 12:37:19 PDT)
Re: [AMBER] force field library for protonated cytosine
(Thu Jun 14 2012 - 12:00:28 PDT)
Re: [AMBER] ptraj: combine pdb's to mdcrd
(Tue Jun 12 2012 - 19:21:32 PDT)
Re: [AMBER] mmpbsa
(Tue Jun 12 2012 - 12:59:56 PDT)
Re: [AMBER] Value of internal dielectric constant ? for per residue decomposition free energy calculation using MMGBSA method
(Tue Jun 12 2012 - 04:25:02 PDT)
Re: [AMBER] Abnormally Slow NMode entropy calculation
(Tue Jun 12 2012 - 04:16:54 PDT)
Re: [AMBER] Mac OS X Lion workaround
(Mon Jun 11 2012 - 03:35:15 PDT)
[AMBER] Mac OS X Lion workaround
(Sat Jun 09 2012 - 13:48:52 PDT)
Re: [AMBER] LEaP misplaces ions
(Sat Jun 09 2012 - 10:26:15 PDT)
Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl
(Fri Jun 08 2012 - 09:03:16 PDT)
Re: [AMBER] what version of xcode are you using?
(Fri Jun 08 2012 - 08:34:22 PDT)
Re: [AMBER] what version of xcode are you using?
(Fri Jun 08 2012 - 08:06:30 PDT)
Re: [AMBER] FIX for Mac OS X Lion with Xcode 4.3.2
(Fri Jun 08 2012 - 08:04:23 PDT)
Re: [AMBER] partial charge, charge radius and epsilon
(Fri Jun 08 2012 - 06:36:23 PDT)
Re: [AMBER] what version of xcode are you using?
(Fri Jun 08 2012 - 06:25:17 PDT)
[AMBER] FIX for Mac OS X Lion with Xcode 4.3.2
(Fri Jun 08 2012 - 05:21:26 PDT)
Re: [AMBER] what version of xcode are you using?
(Fri Jun 08 2012 - 05:01:19 PDT)
Re: [AMBER] Error in minimization
(Fri Jun 08 2012 - 04:09:54 PDT)
Re: [AMBER] Problems installing AmberTools12 on Ubuntu
(Fri Jun 08 2012 - 04:05:23 PDT)
Re: [AMBER] Problems installing AmberTools12 on Ubuntu
(Thu Jun 07 2012 - 19:16:45 PDT)
Re: [AMBER] Problems installing AmberTools12 on Ubuntu
(Thu Jun 07 2012 - 18:31:07 PDT)
Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl
(Thu Jun 07 2012 - 13:10:54 PDT)
Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl
(Thu Jun 07 2012 - 12:06:44 PDT)
Re: [AMBER] what version of xcode are you using?
(Thu Jun 07 2012 - 12:04:36 PDT)
Re: [AMBER] Problems installing AmberTools12 on Ubuntu
(Thu Jun 07 2012 - 07:40:23 PDT)
Re: [AMBER] Removing finite number of solvent particles from simulation box
(Thu Jun 07 2012 - 07:23:30 PDT)
Re: [AMBER] Removing finite number of solvent particles from simulation box
(Wed Jun 06 2012 - 19:31:25 PDT)
Re: [AMBER] Removing finite number of solvent particles from simulation box
(Wed Jun 06 2012 - 19:31:01 PDT)
Re: [AMBER] Error in minimization
(Wed Jun 06 2012 - 06:40:14 PDT)
Re: [AMBER] Error in new installation.
(Wed Jun 06 2012 - 06:39:27 PDT)
Re: [AMBER] Amber11 Installation Problem
(Wed Jun 06 2012 - 06:22:51 PDT)
Re: [AMBER] Amber11 Installation Problem
(Wed Jun 06 2012 - 04:20:42 PDT)
Re: [AMBER] No C-terminal GLH in aminoct*.in
(Tue Jun 05 2012 - 10:29:40 PDT)
Re: [AMBER] Amber11 Installation Problem
(Tue Jun 05 2012 - 06:47:10 PDT)
Re: [AMBER] compiling parallel on centOS5 - rocks with intel
(Mon Jun 04 2012 - 17:45:49 PDT)
Re: [AMBER] compiling parallel on centOS5 - rocks with intel
(Mon Jun 04 2012 - 16:16:25 PDT)
Re: [AMBER] compiling parallel on centOS5 - rocks with intel
(Mon Jun 04 2012 - 13:20:22 PDT)
Re: [AMBER] is there a batch queue app?
(Fri Jun 01 2012 - 12:22:32 PDT)
Re: [AMBER] No C-terminal GLH in aminoct*.in
(Fri Jun 01 2012 - 10:27:33 PDT)
Re: [AMBER] Configurational bias Monte Carlo
(Fri Jun 01 2012 - 10:22:25 PDT)
Re: [AMBER] cuda parallel - can't find mpi.h
(Fri Jun 01 2012 - 09:16:20 PDT)
Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0
(Fri Jun 01 2012 - 06:22:54 PDT)
Re: [AMBER] Effect of Temperature
(Fri Jun 01 2012 - 05:57:29 PDT)
Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0
(Fri Jun 01 2012 - 05:51:01 PDT)
Re: [AMBER] MMPBSA_Error: Could not find necessary program [sander]
(Fri Jun 01 2012 - 05:40:44 PDT)
Jignesh Patel
Re: [AMBER] Value of internal dielectric constant ? for per residue decomposition free energy calculation using MMGBSA method
(Tue Jun 12 2012 - 10:16:57 PDT)
[AMBER] Value of internal dielectric constant ? for per residue decomposition free energy calculation using MMGBSA method
(Tue Jun 12 2012 - 04:13:49 PDT)
Jio M
Re: [AMBER] Fw: set box problem
(Fri Jun 29 2012 - 20:29:10 PDT)
[AMBER] set box problem: not solved
(Fri Jun 29 2012 - 06:19:46 PDT)
[AMBER] Fw: set box problem
(Fri Jun 29 2012 - 06:00:23 PDT)
Re: [AMBER] force field library for protonated cytosine
(Thu Jun 28 2012 - 09:04:15 PDT)
[AMBER] set box problem
(Thu Jun 28 2012 - 08:46:55 PDT)
Re: [AMBER] gaff.dat column and preference to frcmod file params
(Wed Jun 27 2012 - 05:27:58 PDT)
[AMBER] gaff.dat column and preference to frcmod file params
(Wed Jun 27 2012 - 04:24:53 PDT)
Re: [AMBER] parameters and charges for R and S Configurations
(Tue Jun 12 2012 - 01:35:29 PDT)
[AMBER] Fw: parameters and charges for R and S Configurations
(Mon Jun 11 2012 - 14:36:08 PDT)
[AMBER] parameters and charges for R and S Configurations
(Mon Jun 11 2012 - 13:50:33 PDT)
Jiri Sponer
Re: [AMBER] Re [amber] north/sout energy difference
(Sun Jun 24 2012 - 12:39:26 PDT)
jit mukherjee
Re: [AMBER] problem in the bondtype judgement step in antechamber
(Tue Jun 26 2012 - 02:41:43 PDT)
[AMBER] problem in the bondtype judgement step in antechamber
(Tue Jun 26 2012 - 00:30:57 PDT)
[AMBER] problem in antechamber
(Mon Jun 25 2012 - 01:30:20 PDT)
Jitesh Doshi
[AMBER] Doubt about ligand preparation in Gaussian and tleap
(Mon Jun 25 2012 - 06:50:14 PDT)
Joakim Jämbeck
[AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 22 2012 - 04:10:07 PDT)
Jodi Ann Hadden
Re: [AMBER] AMBER Error: unable to achieve consistency
(Thu Jun 28 2012 - 07:06:08 PDT)
Re: [AMBER] AMBER Error: unable to achieve consistency
(Wed Jun 27 2012 - 08:32:28 PDT)
Jonathan Gough
Re: [AMBER] duplicating - multiplying input files to create dimer etc.
(Sat Jun 16 2012 - 15:41:52 PDT)
[AMBER] duplicating - multiplying input files to create dimer etc.
(Sat Jun 16 2012 - 13:45:30 PDT)
Re: [AMBER] How to get starting geometry for <10 AA peptides?
(Mon Jun 11 2012 - 03:39:18 PDT)
Re: [AMBER] FIX for Mac OS X Lion with Xcode 4.3.2
(Fri Jun 08 2012 - 12:10:47 PDT)
Re: [AMBER] what version of xcode are you using?
(Fri Jun 08 2012 - 08:36:22 PDT)
Re: [AMBER] what version of xcode are you using?
(Fri Jun 08 2012 - 08:28:04 PDT)
Re: [AMBER] what version of xcode are you using?
(Fri Jun 08 2012 - 06:59:03 PDT)
Re: [AMBER] what version of xcode are you using?
(Fri Jun 08 2012 - 05:51:06 PDT)
Re: [AMBER] what version of xcode are you using?
(Fri Jun 08 2012 - 05:05:46 PDT)
Re: [AMBER] what version of xcode are you using?
(Fri Jun 08 2012 - 04:56:01 PDT)
[AMBER] what version of xcode are you using?
(Thu Jun 07 2012 - 11:38:13 PDT)
Re: [AMBER] is there a batch queue app?
(Tue Jun 05 2012 - 14:38:42 PDT)
Re: [AMBER] compiling parallel on centOS5 - rocks with intel
(Mon Jun 04 2012 - 16:33:06 PDT)
Re: [AMBER] compiling parallel on centOS5 - rocks with intel
(Mon Jun 04 2012 - 13:38:19 PDT)
Re: [AMBER] compiling parallel on centOS5 - rocks with intel
(Mon Jun 04 2012 - 12:17:20 PDT)
[AMBER] compiling parallel on centOS5 - rocks with intel
(Mon Jun 04 2012 - 10:54:44 PDT)
Re: [AMBER] is there a batch queue app?
(Fri Jun 01 2012 - 13:56:05 PDT)
[AMBER] is there a batch queue app?
(Fri Jun 01 2012 - 11:58:12 PDT)
Re: [AMBER] cuda parallel - can't find mpi.h
(Fri Jun 01 2012 - 09:40:54 PDT)
[AMBER] cuda parallel - can't find mpi.h
(Fri Jun 01 2012 - 08:45:28 PDT)
Re: [AMBER] cuda errors
(Fri Jun 01 2012 - 08:21:24 PDT)
[AMBER] cuda errors
(Thu May 31 2012 - 21:13:22 PDT)
Junjian Miao
[AMBER] umbrella sampling -- centroid or center of mass
(Fri Jun 15 2012 - 06:24:53 PDT)
Junmei Wang
Re: [AMBER] rocks cluster: MD is much slower when using more than one node
(Sat Jun 02 2012 - 07:11:34 PDT)
[AMBER] rocks cluster: MD is much slower when using more than one node
(Fri Jun 01 2012 - 13:15:56 PDT)
Kamali Sripathi
Re: [AMBER] Ion clumping in large protein-RNA systems
(Fri Jun 22 2012 - 11:51:02 PDT)
Re: [AMBER] Ion clumping in large protein-RNA systems
(Tue Jun 19 2012 - 07:55:14 PDT)
Re: [AMBER] Ion clumping in large protein-RNA systems
(Mon Jun 18 2012 - 05:03:27 PDT)
Re: [AMBER] C- and N-terminal amino acids in AmberTools 1.4
(Sun Jun 17 2012 - 16:55:31 PDT)
[AMBER] Ion clumping in large protein-RNA systems
(Sun Jun 17 2012 - 14:28:52 PDT)
[AMBER] C- and N-terminal amino acids in AmberTools 1.4
(Sun Jun 17 2012 - 12:51:07 PDT)
Kepa K. Burusco
Re: [AMBER] Implicit solvent (GB options) with GLYCAM_06h
(Tue Jun 26 2012 - 11:27:03 PDT)
[AMBER] Implicit solvent (GB options) with GLYCAM_06h
(Tue Jun 26 2012 - 04:11:49 PDT)
Kevin Hauser
Re: [AMBER] Ion clumping in large protein-RNA systems
(Fri Jun 22 2012 - 13:38:01 PDT)
Kevin Parkes
Re: [AMBER] FF12SB + GLYCAM_06h + Fluorine
(Tue Jun 12 2012 - 03:47:47 PDT)
[AMBER] FF12SB + GLYCAM_06h + Fluorine
(Mon Jun 11 2012 - 07:18:52 PDT)
Re: [AMBER] Amber 12 on x86_64 CentOS 5 - SOLVED
(Fri Jun 01 2012 - 02:59:03 PDT)
kirtana S
Re: [AMBER] mmpbsa
(Wed Jun 13 2012 - 09:36:36 PDT)
Re: [AMBER] mmpbsa
(Tue Jun 12 2012 - 09:18:06 PDT)
[AMBER] mmpbsa
(Mon Jun 11 2012 - 12:14:39 PDT)
Kumar, Sonu
Re: [AMBER] Distance constraints not working..
(Mon Jun 04 2012 - 09:53:58 PDT)
[AMBER] Distance constraints not working..
(Mon Jun 04 2012 - 01:35:37 PDT)
kurisaki
Re: [AMBER] APPEND option does not work in TRAJOUT of CPPTRAJ
(Tue Jun 26 2012 - 23:45:00 PDT)
[AMBER] APPEND option does not work in TRAJOUT of CPPTRAJ
(Tue Jun 26 2012 - 23:36:37 PDT)
Re: [AMBER] Can we change BUFFER_SIZE (1024) ?
(Tue Jun 26 2012 - 19:42:04 PDT)
[AMBER] Can we change BUFFER_SIZE (1024) ?
(Tue Jun 26 2012 - 00:42:24 PDT)
Lachele Foley (Lists)
Re: [AMBER] parameters for Lys-sugar
(Tue Jun 26 2012 - 09:56:48 PDT)
Re: [AMBER] Implicit solvent (GB options) with GLYCAM_06h
(Tue Jun 26 2012 - 09:53:59 PDT)
Re: [AMBER] FF12SB + GLYCAM_06h + Fluorine
(Mon Jun 11 2012 - 09:00:32 PDT)
Mahendra B Thapa
[AMBER] using "append" in trajout
(Tue Jun 26 2012 - 09:46:23 PDT)
[AMBER] valence not found for for [Na+ ]
(Mon Jun 25 2012 - 12:41:26 PDT)
manikanthan bhavaraju
[AMBER] Entropy calculations with mm_pbsa.pl using amber12
(Wed Jun 20 2012 - 08:43:36 PDT)
Re: [AMBER] MMPBSA.py
(Fri Jun 15 2012 - 16:44:07 PDT)
marawan hussain
[AMBER] MMPBSA problem
(Mon Jun 18 2012 - 21:57:41 PDT)
Marc van der Kamp
Re: [AMBER] ptraj vector error
(Tue Jun 19 2012 - 02:47:36 PDT)
Re: [AMBER] ptraj vector error
(Tue Jun 19 2012 - 01:18:52 PDT)
Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc.
(Thu Jun 14 2012 - 13:28:42 PDT)
Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc.
(Thu Jun 14 2012 - 12:27:38 PDT)
Re: [AMBER] No C-terminal GLH in aminoct*.in
(Wed Jun 06 2012 - 00:29:17 PDT)
Re: [AMBER] No C-terminal GLH in aminoct*.in
(Tue Jun 05 2012 - 08:46:21 PDT)
[AMBER] No C-terminal GLH in aminoct*.in
(Fri Jun 01 2012 - 10:01:02 PDT)
Marek Maly
Re: [AMBER] R: R: strange POPC under lipids 11 FF
(Sat Jun 16 2012 - 03:19:23 PDT)
Re: [AMBER] R: R: strange POPC under lipids 11 FF
(Fri Jun 15 2012 - 07:05:22 PDT)
Maria Minakova
[AMBER] Prepgen omits information about half of the atoms
(Thu Jun 28 2012 - 14:25:15 PDT)
Mark Williamson
Re: [AMBER] Fail to read hem parameters written by P. Rydberg
(Fri Jun 15 2012 - 05:39:35 PDT)
mark94025.comcast.net
[AMBER] AMBER GPU "Success Stories"
(Fri Jun 22 2012 - 08:35:50 PDT)
Marko Wehle
Re: [AMBER] Bug in resp or respgen? using intra-molecular-charge-constraints...
(Tue Jun 12 2012 - 13:29:20 PDT)
[AMBER] Bug in resp or respgen? using intra-molecular-charge-constraints...
(Mon Jun 11 2012 - 11:39:11 PDT)
Martin Andersson
Re: [AMBER] why cut off is so small for CUDA running?
(Tue Jun 19 2012 - 04:45:45 PDT)
Matthew Zwier
Re: [AMBER] rocks cluster: MD is much slower when using more than one node
(Sun Jun 03 2012 - 06:08:09 PDT)
MD
Re: [AMBER] long range LJ correction; surface tension; trajectory
(Mon Jun 18 2012 - 03:24:36 PDT)
[AMBER] long range LJ correction; surface tension; trajectory
(Thu Jun 14 2012 - 23:53:28 PDT)
Melissa Buskes
Re: [AMBER] Sander Error
(Fri Jun 22 2012 - 01:15:20 PDT)
Michael Mayo
[AMBER] nvidia GTX 550 Ti
(Mon Jun 04 2012 - 20:52:47 PDT)
moitrayee.mbu.iisc.ernet.in
[AMBER] Problem in MM-PBSA decomp module
(Sun Jun 24 2012 - 11:57:13 PDT)
monica.imtech.res.in
[AMBER] Antechamber problem
(Mon Jun 04 2012 - 08:57:03 PDT)
Muhammad Khaled Tumbi
[AMBER] How to calculate distance between Center of Axis (DNA) to Center of Mass of Ligand in ptraj
(Sun Jun 17 2012 - 23:47:00 PDT)
Nadine.Homeyer.uni-duesseldorf.de
Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl
(Sat Jun 09 2012 - 00:58:02 PDT)
Nan Li
[AMBER] unit of energy
(Wed Jun 13 2012 - 08:41:24 PDT)
Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl
(Fri Jun 08 2012 - 09:17:21 PDT)
Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl
(Fri Jun 08 2012 - 09:01:15 PDT)
Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl
(Thu Jun 07 2012 - 12:09:52 PDT)
[AMBER] Entropy from MMPBSA.py and MM_PBSA.pl
(Thu Jun 07 2012 - 11:57:18 PDT)
Nicholus Bhattacharjee
[AMBER] Constant pH simulation at pH 7
(Wed Jun 20 2012 - 06:00:18 PDT)
Niel Henriksen
Re: [AMBER] rmsd
(Thu Jun 28 2012 - 14:33:34 PDT)
Re: [AMBER] Script error to restart MD automatically
(Mon Jun 18 2012 - 20:58:36 PDT)
Olena Dobrovolska
Re: [AMBER] calculation of the average structure
(Tue Jun 26 2012 - 08:00:24 PDT)
[AMBER] calculation of the average structure
(Tue Jun 26 2012 - 05:15:02 PDT)
panecka.icm.edu.pl
[AMBER] REMD trajectories: Ts -> replicas
(Thu Jun 28 2012 - 13:42:35 PDT)
qiao xue
Re: [AMBER] The VDWAALS is huge in MMPBSA calculation.
(Fri Jun 15 2012 - 05:25:38 PDT)
Re: [AMBER] The VDWAALS is huge in MMPBSA calculation.
(Fri Jun 15 2012 - 05:01:06 PDT)
Re: [AMBER] The VDWAALS is huge in MMPBSA calculation.
(Tue Jun 12 2012 - 23:32:08 PDT)
[AMBER] The VDWAALS is huge in MMPBSA calculation.
(Tue Jun 12 2012 - 23:03:30 PDT)
qiqi
Re: [AMBER] Problem while running MMPBSA
(Fri Jun 29 2012 - 13:08:44 PDT)
Re: [AMBER] Problem while running MMPBSA
(Thu Jun 28 2012 - 06:53:41 PDT)
Re: [AMBER] Problem while running MMPBSA
(Mon Jun 25 2012 - 08:33:43 PDT)
Re: [AMBER] Problem while running MMPBSA
(Fri Jun 22 2012 - 13:33:26 PDT)
Re: [AMBER] Problem while running MMPBSA
(Wed Jun 20 2012 - 10:32:31 PDT)
[AMBER] Problem while running MMPBSA
(Wed Jun 20 2012 - 09:08:51 PDT)
rajeevy.iitk.ac.in
[AMBER] Amber: mm_pbsa.pl
(Sat Jun 30 2012 - 03:36:00 PDT)
Rajeswari A.
Re: [AMBER] Amber11 Installation Problem
(Tue Jun 05 2012 - 03:58:14 PDT)
Ray Luo, Ph.D.
Re: [AMBER] Amber: mm_pbsa.pl
(Sat Jun 30 2012 - 07:26:43 PDT)
Re: [AMBER] implicit GB model for membrane simulation
(Tue Jun 26 2012 - 16:30:53 PDT)
[AMBER] Fwd: AmberTools 12 pbsa: missing newline character in OpenDX output
(Mon Jun 25 2012 - 10:44:07 PDT)
Re: [AMBER] PB Bomb in epsmap(): epsy out of range
(Tue Jun 19 2012 - 14:47:04 PDT)
Re: [AMBER] MMPBSA calculation reproducibility
(Mon Jun 11 2012 - 12:27:38 PDT)
Re: [AMBER] MMPBSA calculation reproducibility
(Mon Jun 11 2012 - 08:46:36 PDT)
Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11
(Thu Jun 07 2012 - 16:32:10 PDT)
Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11
(Thu Jun 07 2012 - 15:02:28 PDT)
Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11
(Thu Jun 07 2012 - 09:52:12 PDT)
Robin Betz
Re: [AMBER] Ion clumping in large protein-RNA systems
(Tue Jun 19 2012 - 08:09:59 PDT)
Re: [AMBER] LEaP misplaces ions
(Sun Jun 10 2012 - 00:11:01 PDT)
Romelia Salomon
Re: [AMBER] Problem with NAB: "Residue g not in library rna.amber94.rlb."
(Tue Jun 05 2012 - 15:07:11 PDT)
Re: [AMBER] Problem with NAB: "Residue g not in library rna.amber94.rlb."
(Tue Jun 05 2012 - 11:17:31 PDT)
[AMBER] Problem with NAB: "Residue g not in library rna.amber94.rlb."
(Tue Jun 05 2012 - 10:30:12 PDT)
Ross Walker
Re: [AMBER] sander termination upon reaching end temperature
(Fri Jun 29 2012 - 15:23:35 PDT)
Re: [AMBER] Prepgen omits information about half of the atoms
(Thu Jun 28 2012 - 14:48:44 PDT)
Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
(Thu Jun 28 2012 - 14:05:55 PDT)
Re: [AMBER] Low POPC area per lipid - LIPID11
(Thu Jun 28 2012 - 12:34:14 PDT)
Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
(Thu Jun 28 2012 - 12:28:41 PDT)
Re: [AMBER] PMEMD CUPA MPI STOP WRITING OUTPUT IN RUNNIG STATUS
(Wed Jun 27 2012 - 09:11:24 PDT)
Re: [AMBER] AMBER Error: unable to achieve consistency
(Tue Jun 26 2012 - 21:42:00 PDT)
Re: [AMBER] Problem with installing Amber 12 CUDA GPU version (NetCDF error)
(Wed Jun 20 2012 - 17:08:19 PDT)
Re: [AMBER] GPU kernel error
(Tue Jun 19 2012 - 10:02:44 PDT)
Re: [AMBER] why cut off is so small for CUDA running?
(Tue Jun 19 2012 - 09:34:58 PDT)
Re: [AMBER] Slow jobs
(Tue Jun 19 2012 - 09:22:57 PDT)
Re: [AMBER] why cut off is so small for CUDA running?
(Sun Jun 17 2012 - 21:47:47 PDT)
Re: [AMBER] GPU kernel error
(Sun Jun 17 2012 - 08:25:21 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Sat Jun 16 2012 - 09:56:02 PDT)
Re: [AMBER] Cuda performance
(Sat Jun 16 2012 - 09:29:50 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Sat Jun 16 2012 - 09:28:00 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 15 2012 - 15:56:27 PDT)
Re: [AMBER] R: R: strange POPC under lipids 11 FF
(Fri Jun 15 2012 - 15:43:30 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 15 2012 - 15:33:37 PDT)
Re: [AMBER] GPU kernel error
(Fri Jun 15 2012 - 15:33:37 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 15 2012 - 03:38:32 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 15 2012 - 03:02:54 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 15 2012 - 02:26:20 PDT)
Re: [AMBER] strange POPC under lipids 11 FF
(Thu Jun 14 2012 - 07:09:00 PDT)
Re: [AMBER] Regarding running PME simulation on GPU
(Thu Jun 14 2012 - 04:41:49 PDT)
Re: [AMBER] QM/MM periodic boundary conditions in Amber
(Mon Jun 11 2012 - 14:47:34 PDT)
Re: [AMBER] up coming workshop?
(Thu Jun 07 2012 - 13:37:01 PDT)
Re: [AMBER] cuda parallel - can't find mpi.h
(Fri Jun 01 2012 - 09:19:33 PDT)
Saaz Sakrikar
[AMBER] Making a complex
(Sat Jun 23 2012 - 05:51:40 PDT)
Sajeewa Pemasinghe
Re: [AMBER] problem in running LES calculation with a solvated shell system
(Tue Jun 26 2012 - 05:29:36 PDT)
[AMBER] Fwd: problem in running LES calculation with a solvated shell system
(Mon Jun 25 2012 - 21:08:10 PDT)
[AMBER] using bellymask and group specification together
(Mon Jun 25 2012 - 14:29:36 PDT)
[AMBER] creating a bellymask which includes residues at a given distance from a point
(Mon Jun 25 2012 - 12:56:27 PDT)
[AMBER] problem in running LES calculation with a solvated shell system
(Mon Jun 25 2012 - 09:30:37 PDT)
[AMBER] idea of RMSD calculation in AMBER
(Thu Jun 21 2012 - 15:36:36 PDT)
Re: [AMBER] problem with solvateShell command
(Tue Jun 19 2012 - 19:02:47 PDT)
[AMBER] problem with solvateShell command
(Tue Jun 19 2012 - 14:53:22 PDT)
Re: [AMBER] Fwd: Fwd: problem with running equilibration MD in an LES system
(Mon Jun 04 2012 - 10:15:21 PDT)
[AMBER] Fwd: Fwd: problem with running equilibration MD in an LES system
(Mon Jun 04 2012 - 09:25:23 PDT)
Re: [AMBER] Fwd: problem with running equilibration MD in an LES system
(Fri Jun 01 2012 - 18:51:27 PDT)
Re: [AMBER] Fwd: problem with running equilibration MD in an LES system
(Fri Jun 01 2012 - 07:43:18 PDT)
[AMBER] Fwd: problem with running equilibration MD in an LES system
(Fri Jun 01 2012 - 05:58:51 PDT)
Sangita Kachhap
Re: [AMBER] warning during nmode calulation - Not all of your snapshots minimized within tolerable limits for nmode
(Thu Jun 28 2012 - 02:28:09 PDT)
[AMBER] warning during nmode calulation - Not all of your snapshots minimized within tolerable limits for nmode
(Fri Jun 22 2012 - 03:55:28 PDT)
Re: [AMBER] MMPBSA calculation reproducibility
(Mon Jun 11 2012 - 11:56:33 PDT)
[AMBER] MMPBSA calculation reproducibility
(Mon Jun 11 2012 - 02:08:26 PDT)
Sanjib Paul
[AMBER] atom type specification for chlorine
(Fri Jun 29 2012 - 07:05:45 PDT)
Re: [AMBER] problem during heating up the system
(Wed Jun 20 2012 - 05:09:36 PDT)
[AMBER] problem during heating up the system
(Wed Jun 20 2012 - 03:13:42 PDT)
[AMBER] what is vlimit error?
(Tue Jun 12 2012 - 23:19:38 PDT)
Sarah Witzke
Re: [AMBER] update for POPE test
(Fri Jun 29 2012 - 05:55:35 PDT)
Schubert Mario
[AMBER] C-H...O hydrogen bonds?
(Thu Jun 21 2012 - 15:56:00 PDT)
Scott Brozell
Re: [AMBER] what is vlimit error?
(Thu Jun 14 2012 - 01:05:45 PDT)
Re: [AMBER] what is vlimit error?
(Wed Jun 13 2012 - 00:33:14 PDT)
Scott Le Grand
Re: [AMBER] why cut off is so small for CUDA running?
(Sun Jun 17 2012 - 18:14:55 PDT)
Re: [AMBER] GPU kernel error
(Fri Jun 15 2012 - 05:22:07 PDT)
Re: [AMBER] nvidia GTX 550 Ti
(Tue Jun 05 2012 - 08:02:38 PDT)
Re: [AMBER] is there a batch queue app?
(Fri Jun 01 2012 - 12:06:17 PDT)
shradhey gupta
[AMBER] ptraj Hbond analysis
(Fri Jun 01 2012 - 22:51:36 PDT)
[AMBER] ptraj Hbond analysis
(Thu May 31 2012 - 21:56:20 PDT)
[AMBER] ptraj Hbond analysis
(Thu May 31 2012 - 21:55:09 PDT)
Soumya Lipsa Rath
[AMBER] MMPBSA calculation of DNA solvation
(Wed Jun 27 2012 - 02:49:42 PDT)
Re: [AMBER] REMD equilibration
(Sat Jun 16 2012 - 05:05:36 PDT)
Re: [AMBER] REMD equilibration
(Fri Jun 15 2012 - 22:33:36 PDT)
Re: [AMBER] REMD equilibration
(Fri Jun 15 2012 - 07:08:20 PDT)
Re: [AMBER] REMD equilibration
(Thu Jun 14 2012 - 20:33:15 PDT)
Re: [AMBER] REMD equilibration
(Sun Jun 10 2012 - 23:15:32 PDT)
Re: [AMBER] REMD equilibration
(Fri Jun 08 2012 - 21:10:36 PDT)
[AMBER] REMD equilibration
(Thu Jun 07 2012 - 20:58:31 PDT)
Re: [AMBER] Effect of Temperature
(Fri Jun 01 2012 - 20:57:53 PDT)
Re: [AMBER] Effect of Temperature
(Fri Jun 01 2012 - 20:19:27 PDT)
[AMBER] Effect of Temperature
(Fri Jun 01 2012 - 04:15:29 PDT)
Souvik Sur
[AMBER] Sander output Error
(Tue Jun 19 2012 - 21:53:32 PDT)
[AMBER] Job running problem in sander
(Fri Jun 15 2012 - 22:34:43 PDT)
steinbrt.rci.rutgers.edu
Re: [AMBER] How to explain this phenomenon is production MD
(Sun Jun 24 2012 - 10:42:36 PDT)
Re: [AMBER] How to explain this phenomenon is production MD
(Sat Jun 23 2012 - 03:40:38 PDT)
Re: [AMBER] How to explain this phenomenon is production MD
(Fri Jun 22 2012 - 00:35:31 PDT)
Re: [AMBER] TI calculation Amber 12
(Thu Jun 21 2012 - 07:12:45 PDT)
Re: [AMBER] TI calculation Amber 12
(Thu Jun 21 2012 - 04:48:10 PDT)
Re: [AMBER] TI calculation Amber 12
(Thu Jun 21 2012 - 04:01:07 PDT)
Re: [AMBER] Switching-off the partial charges
(Wed Jun 20 2012 - 00:54:00 PDT)
Re: [AMBER] Facing problem on TUTORIAL A1
(Sun Jun 17 2012 - 07:56:10 PDT)
Re: [AMBER] Facing problem on TUTORIAL A1
(Fri Jun 15 2012 - 00:10:52 PDT)
Re: [AMBER] how to change the namme of the terminal OXT so that it can be recoginized by MOLMOL
(Mon Jun 04 2012 - 00:25:58 PDT)
Re: [AMBER] Trouble calculating free energy
(Fri Jun 01 2012 - 01:04:12 PDT)
Steven M. Graham
Re: [AMBER] Re [amber] north/sout energy difference
(Fri Jun 29 2012 - 10:03:25 PDT)
[AMBER] Re [amber] north/sout energy difference
(Thu Jun 28 2012 - 15:09:38 PDT)
[AMBER] Re [amber] north/sout energy difference
(Sun Jun 24 2012 - 10:53:23 PDT)
Subrata Paul
[AMBER] diffusion coefficient
(Tue Jun 12 2012 - 04:45:39 PDT)
[AMBER] center of mass.
(Wed Jun 06 2012 - 04:27:22 PDT)
sudipta
Re: [AMBER] Facing problem on TUTORIAL A1
(Fri Jun 15 2012 - 12:05:30 PDT)
[AMBER] Facing problem on TUTORIAL A1
(Thu Jun 14 2012 - 15:29:29 PDT)
Re: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues
(Thu Jun 14 2012 - 13:20:31 PDT)
Takeshi Baba
[AMBER] Problem of Force filed (Calculate the dihedral parameter)
(Sat Jun 16 2012 - 21:01:24 PDT)
Tales Yuan
Re: [AMBER] R: strange POPC under lipids 11 FF
(Sat Jun 16 2012 - 10:49:02 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Sat Jun 16 2012 - 10:39:22 PDT)
Thomas Cheatham
Re: [AMBER] Ion clumping in large protein-RNA systems
(Tue Jun 19 2012 - 06:16:41 PDT)
Re: [AMBER] ptraj Hbond analysis
(Mon Jun 04 2012 - 12:01:35 PDT)
tluchko
Re: [AMBER] Convergence problems with rism1d and water model other than SPC
(Wed Jun 06 2012 - 12:10:43 PDT)
Tom Patapoff
[AMBER] restraining residues with a gpu cluster
(Wed Jun 06 2012 - 17:50:18 PDT)
Tommy Yap
Re: [AMBER] Script error to restart MD automatically
(Tue Jun 19 2012 - 00:40:04 PDT)
Re: [AMBER] Script error to restart MD automatically
(Mon Jun 18 2012 - 21:49:32 PDT)
[AMBER] Script error to restart MD automatically
(Mon Jun 18 2012 - 20:06:05 PDT)
Tyler Luchko
Re: [AMBER] A small point of confusion in 3DRISM outfiles
(Wed Jun 13 2012 - 05:48:53 PDT)
Urszula Uciechowska
Re: [AMBER] parameters for Lys-sugar
(Tue Jun 26 2012 - 10:58:43 PDT)
[AMBER] hydrogen bond analysis
(Fri Jun 22 2012 - 04:48:55 PDT)
Vishal Kumar Jaiswal
Re: [AMBER] sander termination upon reaching end temperature
(Fri Jun 29 2012 - 04:43:25 PDT)
Re: [AMBER] sander termination upon reaching end temperature
(Fri Jun 29 2012 - 04:42:42 PDT)
Re: [AMBER] no hydrogen added with xleap
(Fri Jun 29 2012 - 04:30:22 PDT)
Re: [AMBER] sander termination upon reaching end temperature
(Fri Jun 29 2012 - 02:46:43 PDT)
Re: [AMBER] How does 'restraint' work in Amber?
(Sat Jun 23 2012 - 02:56:11 PDT)
Re: [AMBER] How does 'restraint' work in Amber?
(Sat Jun 23 2012 - 02:40:50 PDT)
Re: [AMBER] ptraj cannot handle large crd file
(Wed Jun 13 2012 - 11:39:32 PDT)
[AMBER] ptraj cannot handle large crd file
(Wed Jun 13 2012 - 11:01:12 PDT)
Vlad Cojocaru
Re: [AMBER] update for POPE test
(Fri Jun 29 2012 - 05:52:57 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 22 2012 - 05:44:29 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Fri Jun 22 2012 - 02:53:56 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Thu Jun 21 2012 - 22:58:13 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Thu Jun 21 2012 - 22:45:01 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Sat Jun 16 2012 - 10:19:15 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Sat Jun 16 2012 - 09:57:04 PDT)
Re: [AMBER] R: strange POPC under lipids 11 FF
(Sat Jun 16 2012 - 00:05:59 PDT)
Vítor Félix
Re: [AMBER] strange POPC under lipids 11 FF
(Fri Jun 22 2012 - 05:51:11 PDT)
William Henry BISSON
[AMBER] FF param
(Mon Jun 11 2012 - 03:48:27 PDT)
Wilson, Katie
Re: [AMBER] rmsd
(Thu Jun 28 2012 - 14:20:09 PDT)
Re: [AMBER] rmsd
(Thu Jun 28 2012 - 12:52:32 PDT)
Re: [AMBER] rmsd
(Thu Jun 28 2012 - 12:43:26 PDT)
[AMBER] rmsd
(Thu Jun 28 2012 - 12:22:12 PDT)
Xiao Ba
[AMBER] PB Bomb in epsmap(): epsy out of range
(Tue Jun 19 2012 - 14:37:12 PDT)
xiaojiong
[AMBER] the problem of cpptraj
(Sun Jun 24 2012 - 06:06:26 PDT)
[AMBER] whether it is proper to strip DPPCs
(Thu Jun 14 2012 - 05:30:26 PDT)
[AMBER] calculation the entropy of a membrane DPPC-protein-ligand complex
(Wed Jun 13 2012 - 06:37:08 PDT)
Xin Geng
Re: [AMBER] undefined reference error in compiling
(Mon Jun 18 2012 - 13:34:10 PDT)
Re: [AMBER] undefined reference error in compiling
(Fri Jun 15 2012 - 10:36:02 PDT)
[AMBER] undefined reference error in compiling
(Thu Jun 14 2012 - 17:52:18 PDT)
Xioling Chuang
[AMBER] How to estimate Tm of DNA duplex?
(Fri Jun 29 2012 - 01:19:01 PDT)
Yun Shi
[AMBER] RESP charges for single nucleic acid residue
(Mon Jun 18 2012 - 22:15:16 PDT)
[AMBER] chiral Sulfur atom
(Fri Jun 15 2012 - 15:30:00 PDT)
[AMBER] DMSO parameters
(Tue Jun 05 2012 - 15:07:38 PDT)
Åge Skjevik
Re: [AMBER] update for POPE test
(Fri Jun 29 2012 - 07:40:36 PDT)
Re: [AMBER] update for POPE test
(Fri Jun 29 2012 - 05:56:31 PDT)
Карлов Дмитрий
[AMBER] Error with box parameters
(Fri Jun 15 2012 - 03:42:11 PDT)
崔颖璐
Re: [AMBER] Fail to read hem parameters written by P. Rydberg
(Mon Jun 18 2012 - 06:13:38 PDT)
[AMBER] Fail to read hem parameters written by P. Rydberg
(Fri Jun 15 2012 - 05:08:07 PDT)
Last message date
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Sat Jun 30 2012 - 15:30:03 PDT
Archived on
: Wed Dec 25 2024 - 05:54:37 PST
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