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