Amber Archive Apr 2013 by thread
494 messages
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Starting
Mon Apr 01 2013 - 00:30:02 PDT,
Ending
Tue Apr 30 2013 - 13:30:03 PDT
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[AMBER] Problems with MMPBSA: mmphsa_py_energy could not be found
Tommy Yap
(Mon Apr 01 2013 - 00:18:54 PDT)
Re: [AMBER] Problems with MMPBSA: mmphsa_py_energy could not be found
Jason Swails
(Mon Apr 01 2013 - 05:07:22 PDT)
[AMBER] clustering based on side-chain conformations
anu chandra
(Mon Apr 01 2013 - 00:40:07 PDT)
Re: [AMBER] clustering based on side-chain conformations
Daniel Roe
(Tue Apr 02 2013 - 07:28:19 PDT)
[AMBER] Is SHAKE necessary in running an MD?V
Alan
(Mon Apr 01 2013 - 01:29:36 PDT)
Re: [AMBER] Is SHAKE necessary in running an MD?V
Gerald Monard
(Mon Apr 01 2013 - 03:08:06 PDT)
Re: [AMBER] Is SHAKE necessary in running an MD?V
Alan
(Mon Apr 01 2013 - 23:12:42 PDT)
Re: [AMBER] Is SHAKE necessary in running an MD?V
Gerald Monard
(Tue Apr 02 2013 - 00:30:34 PDT)
Re: [AMBER] Is SHAKE necessary in running an MD?V
Alan
(Tue Apr 02 2013 - 05:23:27 PDT)
Re: [AMBER] Is SHAKE necessary in running an MD?V
Adrian Roitberg
(Tue Apr 02 2013 - 05:48:48 PDT)
[AMBER] calculating diffusion constants - multiplying factor (10/6)?
Vijay Manickam Achari
(Mon Apr 01 2013 - 02:21:09 PDT)
Re: [AMBER] calculating diffusion constants - multiplying factor (10/6)?
George M Giambasu
(Mon Apr 01 2013 - 07:19:15 PDT)
[AMBER] error in perl script (mm_pbsa.pl) for binding energy
kureeckal ramesh
(Mon Apr 01 2013 - 02:42:09 PDT)
Re: [AMBER] error in perl script (mm_pbsa.pl) for binding energy
Jason Swails
(Mon Apr 01 2013 - 05:09:25 PDT)
[AMBER] Different binding energy order between ATP (GTP) and protein in Amber ff10 FF and CHARMM27 FF using MMPBSA.py script
dbaogen
(Mon Apr 01 2013 - 19:05:30 PDT)
Re: [AMBER] Different binding energy order between ATP (GTP) and protein in Amber ff10 FF and CHARMM27 FF using MMPBSA.py script
David A Case
(Tue Apr 02 2013 - 04:46:36 PDT)
[AMBER] Help with GB-OBC calculations
Kamakshi
(Tue Apr 02 2013 - 04:34:06 PDT)
Re: [AMBER] Help with GB-OBC calculations
Carlos Simmerling
(Tue Apr 02 2013 - 04:38:56 PDT)
[AMBER] need a box
Adrian Roitberg
(Tue Apr 02 2013 - 08:09:27 PDT)
[AMBER] ante-MMPBSA.py failed
Albert
(Tue Apr 02 2013 - 11:18:14 PDT)
Re: [AMBER] ante-MMPBSA.py failed
Bill Miller III
(Tue Apr 02 2013 - 11:45:27 PDT)
[AMBER] Time step of 5 fs??
HM
(Tue Apr 02 2013 - 23:59:55 PDT)
Re: [AMBER] Time step of 5 fs??
steinbrt.rci.rutgers.edu
(Wed Apr 03 2013 - 00:43:17 PDT)
Re: [AMBER] Time step of 5 fs??
Gerald Monard
(Wed Apr 03 2013 - 01:07:18 PDT)
[AMBER] MMPBSA failed
Albert
(Wed Apr 03 2013 - 00:12:10 PDT)
Re: [AMBER] MMPBSA failed
Jan-Philip Gehrcke
(Wed Apr 03 2013 - 01:30:59 PDT)
Re: [AMBER] MMPBSA failed
Albert
(Wed Apr 03 2013 - 02:05:47 PDT)
Re: [AMBER] MMPBSA failed
Jason Swails
(Wed Apr 03 2013 - 04:53:18 PDT)
Re: [AMBER] MMPBSA failed
Jan-Philip Gehrcke
(Wed Apr 03 2013 - 05:22:53 PDT)
Re: [AMBER] MMPBSA failed
Albert
(Wed Apr 03 2013 - 06:50:15 PDT)
Re: [AMBER] MMPBSA failed
Bill Miller III
(Wed Apr 03 2013 - 07:00:28 PDT)
Re: [AMBER] MMPBSA failed
Albert
(Wed Apr 03 2013 - 07:08:49 PDT)
Re: [AMBER] MMPBSA failed
Bill Miller III
(Wed Apr 03 2013 - 07:26:20 PDT)
Re: [AMBER] MMPBSA failed
Jason Swails
(Wed Apr 03 2013 - 07:30:19 PDT)
Re: [AMBER] MMPBSA failed
Albert
(Wed Apr 03 2013 - 07:40:25 PDT)
Re: [AMBER] MMPBSA failed
Albert
(Wed Apr 03 2013 - 07:56:53 PDT)
[AMBER] Regarding MD run in vacuum
Gaurao Dhoke
(Wed Apr 03 2013 - 01:56:21 PDT)
Re: [AMBER] Regarding MD run in vacuum
steinbrt.rci.rutgers.edu
(Wed Apr 03 2013 - 03:17:13 PDT)
Re: [AMBER] Regarding MD run in vacuum
Gaurao Dhoke
(Wed Apr 03 2013 - 03:26:57 PDT)
Re: [AMBER] Regarding MD run in vacuum
Aron Broom
(Wed Apr 03 2013 - 06:36:33 PDT)
Re: [AMBER] Regarding MD run in vacuum
Jason Swails
(Wed Apr 03 2013 - 06:53:28 PDT)
Re: [AMBER] Regarding MD run in vacuum
Massimiliano Porrini
(Wed Apr 03 2013 - 09:54:50 PDT)
[AMBER] vecs file
Rasha Alqus
(Wed Apr 03 2013 - 05:26:12 PDT)
Re: [AMBER] vecs file
Deák Robert
(Wed Apr 03 2013 - 05:44:43 PDT)
Re: [AMBER] vecs file
Rasha Alqus
(Wed Apr 03 2013 - 05:58:22 PDT)
Re: [AMBER] vecs file
Deák Robert
(Wed Apr 03 2013 - 06:11:25 PDT)
Re: [AMBER] vecs file
Rasha Alqus
(Wed Apr 03 2013 - 07:51:22 PDT)
Re: [AMBER] vecs file
Deák Robert
(Thu Apr 04 2013 - 05:38:30 PDT)
Re: [AMBER] vecs file
David A Case
(Wed Apr 03 2013 - 08:20:05 PDT)
[AMBER] FW: No subject
Wholly Peach
(Wed Apr 03 2013 - 06:39:22 PDT)
[AMBER] parameter problem for NVE/NPE or NPV ensemble
nguyentb.bii.a-star.edu.sg
(Thu Apr 04 2013 - 01:36:14 PDT)
Re: [AMBER] parameter problem for NVE/NPE or NPV ensemble
Jason Swails
(Thu Apr 04 2013 - 04:34:50 PDT)
Re: [AMBER] parameter problem for NVE/NPE or NPV ensemble
David A Case
(Thu Apr 04 2013 - 04:49:38 PDT)
Re: [AMBER] parameter problem for NVE/NPE or NPV ensemble
nguyentb.bii.a-star.edu.sg
(Thu Apr 04 2013 - 05:51:51 PDT)
Re: [AMBER] parameter problem for NVE/NPE or NPV ensemble
David A Case
(Thu Apr 04 2013 - 07:00:27 PDT)
[AMBER] MD Simulation of Heavy Metal(Bi or Sb) compound molecule
Yasuo Kurita
(Thu Apr 04 2013 - 02:12:34 PDT)
Re: [AMBER] MD Simulation of Heavy Metal(Bi or Sb) compound molecule
FyD
(Thu Apr 04 2013 - 02:36:15 PDT)
[AMBER] Analysis of side-chain conformational changes
anu chandra
(Thu Apr 04 2013 - 03:10:55 PDT)
[AMBER] Fwd: Analysis of side-chain conformational changes
anu chandra
(Thu Apr 04 2013 - 05:04:53 PDT)
Re: [AMBER] Analysis of side-chain conformational changes
Daniel Roe
(Fri Apr 05 2013 - 09:27:38 PDT)
Re: [AMBER] Analysis of side-chain conformational changes
anu chandra
(Fri Apr 05 2013 - 22:59:44 PDT)
[AMBER] meaning of values for dihedrals of a chromophore
Anna Marabotti
(Thu Apr 04 2013 - 03:20:15 PDT)
[AMBER] chromium in leap
marta wisniewska.
(Thu Apr 04 2013 - 15:02:44 PDT)
Re: [AMBER] chromium in leap
FyD
(Thu Apr 04 2013 - 23:25:55 PDT)
[AMBER] Out of Box in PMEMD
journal.update
(Thu Apr 04 2013 - 23:38:41 PDT)
Re: [AMBER] Out of Box in PMEMD
Daniel Roe
(Fri Apr 05 2013 - 09:15:07 PDT)
Re: [AMBER] Out of Box in PMEMD
journal.update
(Fri Apr 05 2013 - 22:03:21 PDT)
Re: [AMBER] Out of Box in PMEMD
David A Case
(Sat Apr 06 2013 - 06:10:20 PDT)
[AMBER] CalcError: sander.APBS failed with prmtop using MMPBSA.py by Amber 11 and AmberTools 12
dbaogen
(Thu Apr 04 2013 - 19:14:43 PDT)
[AMBER] Problem with order parameter calculation in PTRAJ
anu chandra
(Fri Apr 05 2013 - 00:16:00 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
Daniel Roe
(Fri Apr 05 2013 - 08:38:36 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
anu chandra
(Fri Apr 05 2013 - 22:48:33 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
Daniel Roe
(Mon Apr 08 2013 - 10:25:45 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
anu chandra
(Mon Apr 08 2013 - 23:40:45 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
Daniel Roe
(Tue Apr 09 2013 - 07:58:45 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
anu chandra
(Tue Apr 09 2013 - 22:04:27 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
anu chandra
(Tue Apr 09 2013 - 22:41:50 PDT)
Re: [AMBER] Problem with order parameter calculation in PTRAJ
anu chandra
(Tue Apr 09 2013 - 22:55:55 PDT)
[AMBER] Regarding Accelerated Molecular Dynamics
Adam Zalewski
(Fri Apr 05 2013 - 04:33:16 PDT)
Re: [AMBER] GPU job scheduling: looking for recommendations and experiences
Jan-Philip Gehrcke
(Fri Apr 05 2013 - 07:35:41 PDT)
[AMBER] Accelerated Molecular Dynamics
Diego Javier Alonso de Armiño
(Fri Apr 05 2013 - 08:44:33 PDT)
[AMBER] Fwd: Accelerated Molecular Dynamics
Diego Javier Alonso de Armiño
(Sat Apr 06 2013 - 13:40:18 PDT)
[AMBER] problem in loading 5'terminal phosphate group of tRNA
N Nandi
(Fri Apr 05 2013 - 09:49:22 PDT)
Re: [AMBER] problem in loading 5'terminal phosphate group of tRNA
FyD
(Sat Apr 06 2013 - 05:51:08 PDT)
[AMBER] How to modifie "runmd.f" to calculate force from obtained MD trajectory?
kurisaki
(Fri Apr 05 2013 - 18:50:40 PDT)
Re: [AMBER] How to modifie "runmd.f" to calculate force from obtained MD trajectory?
Jason Swails
(Fri Apr 05 2013 - 20:33:54 PDT)
Re: [AMBER] How to modifie "runmd.f" to calculate force from obtained MD trajectory?
kurisaki
(Sat Apr 06 2013 - 20:46:01 PDT)
Re: [AMBER] How to modifie "runmd.f" to calculate force from obtained MD trajectory?
kurisaki
(Sun Apr 07 2013 - 01:22:59 PDT)
Re: [AMBER] How to modifie "runmd.f" to calculate force from obtained MD trajectory?
kurisaki
(Sun Apr 07 2013 - 03:39:03 PDT)
[AMBER] Error in lmod minimization parallel test
Miguel Ortiz Lombardía
(Sat Apr 06 2013 - 06:31:21 PDT)
Re: [AMBER] Error in lmod minimization parallel test
case
(Sun Apr 07 2013 - 05:57:41 PDT)
Re: [AMBER] Error in lmod minimization parallel test
Miguel Ortiz Lombardía
(Mon Apr 08 2013 - 01:10:12 PDT)
[AMBER] Measure (and print to file) distances on the fly in pmemd.cuda
Diego Javier Alonso de Armiño
(Sat Apr 06 2013 - 13:38:11 PDT)
Re: [AMBER] Measure (and print to file) distances on the fly in pmemd.cuda
Jason Swails
(Sun Apr 07 2013 - 05:56:39 PDT)
Re: [AMBER] Measure (and print to file) distances on the fly in pmemd.cuda
Diego Javier Alonso de Armiño
(Sun Apr 07 2013 - 09:33:11 PDT)
[AMBER] minimize problem
涂志萍
(Sat Apr 06 2013 - 20:12:45 PDT)
Re: [AMBER] minimize problem
case
(Sun Apr 07 2013 - 06:02:00 PDT)
[AMBER] AMBER12 GPU performance
Neha Gandhi
(Sat Apr 06 2013 - 21:17:09 PDT)
Re: [AMBER] AMBER12 GPU performance
Aron Broom
(Sat Apr 06 2013 - 21:55:47 PDT)
[AMBER] where does sander open the output files?
kurisaki
(Sun Apr 07 2013 - 01:20:48 PDT)
Re: [AMBER] where does sander open the output files?
Jason Swails
(Sun Apr 07 2013 - 05:43:29 PDT)
Re: [AMBER] where does sander open the output files?
kurisaki
(Sun Apr 07 2013 - 05:59:23 PDT)
Re: [AMBER] where does sander open the output files?
kurisaki
(Sun Apr 07 2013 - 06:00:49 PDT)
[AMBER] =4/7/2013 3:34:47 PM=
Acoot Brett
(Sun Apr 07 2013 - 07:35:00 PDT)
[AMBER] Anyone (else) at the ACS meeting in NOLA?
Jonathan Gough
(Sun Apr 07 2013 - 19:26:03 PDT)
[AMBER] GAFFlipid forcefield
marawan hussain
(Sun Apr 07 2013 - 20:49:44 PDT)
Re: [AMBER] GAFFlipid forcefield
Dickson, Callum
(Mon Apr 08 2013 - 05:02:30 PDT)
[AMBER] problem in loading 5'terminal phosphate group of tRNA
N Nandi
(Sun Apr 07 2013 - 22:18:29 PDT)
Re: [AMBER] problem in loading 5'terminal phosphate group of tRNA
FyD
(Mon Apr 08 2013 - 00:48:41 PDT)
[AMBER] Fwd: xleap problem
suresh satpati
(Sun Apr 07 2013 - 22:52:40 PDT)
[AMBER] LINMIN FAILURE in amber12
Soumya Lipsa Rath
(Sun Apr 07 2013 - 23:00:57 PDT)
Re: [AMBER] LINMIN FAILURE in amber12
David A Case
(Mon Apr 08 2013 - 04:48:50 PDT)
Re: [AMBER] LINMIN FAILURE in amber12
Soumya Lipsa Rath
(Mon Apr 08 2013 - 05:16:30 PDT)
[AMBER] Analysis of side-chain conformational changes
anu chandra
(Mon Apr 08 2013 - 01:55:18 PDT)
[AMBER] Problem with order parameter calculation in PTRAJ
anu chandra
(Mon Apr 08 2013 - 01:56:36 PDT)
[AMBER] Problem with the amber12 compilation
James Starlight
(Mon Apr 08 2013 - 02:36:23 PDT)
Re: [AMBER] Problem with the amber12 compilation
Jan-Philip Gehrcke
(Mon Apr 08 2013 - 03:34:05 PDT)
Re: [AMBER] Problem with the amber12 compilation
James Starlight
(Mon Apr 08 2013 - 03:50:04 PDT)
[AMBER] problem in loading 5'terminal phosphate group of tRNA
N Nandi
(Mon Apr 08 2013 - 04:14:58 PDT)
Re: [AMBER] problem in loading 5'terminal phosphate group of tRNA
FyD
(Mon Apr 08 2013 - 05:33:23 PDT)
[AMBER] on the usage of Antechamber for the ligand parametrisation
James Starlight
(Mon Apr 08 2013 - 04:48:40 PDT)
Re: [AMBER] on the usage of Antechamber for the ligand parametrisation
James Starlight
(Mon Apr 08 2013 - 04:52:31 PDT)
Re: [AMBER] on the usage of Antechamber for the ligand parametrisation
FyD
(Tue Apr 09 2013 - 03:12:23 PDT)
Re: [AMBER] on the usage of Antechamber for the ligand parametrisation
James Starlight
(Tue Apr 09 2013 - 22:33:39 PDT)
Re: [AMBER] on the usage of Antechamber for the ligand parametrisation
FyD
(Tue Apr 09 2013 - 23:13:42 PDT)
Re: [AMBER] on the usage of Antechamber for the ligand parametrisation
Astrid Maaß
(Wed Apr 10 2013 - 00:06:45 PDT)
Re: [AMBER] on the usage of Antechamber for the ligand parametrisation
James Starlight
(Wed Apr 10 2013 - 00:18:26 PDT)
[AMBER] tleap problem
Odin Zeus
(Mon Apr 08 2013 - 07:54:46 PDT)
Re: [AMBER] tleap problem
steinbrt.rci.rutgers.edu
(Mon Apr 08 2013 - 08:07:06 PDT)
[AMBER] implicit solvation with periodic boundary
Syed Tarique Moin
(Mon Apr 08 2013 - 08:39:37 PDT)
Re: [AMBER] implicit solvation with periodic boundary
Nhai
(Mon Apr 08 2013 - 08:50:42 PDT)
Re: [AMBER] implicit solvation with periodic boundary
Syed Tarique Moin
(Mon Apr 08 2013 - 09:17:32 PDT)
Re: [AMBER] implicit solvation with periodic boundary
Ray Luo
(Mon Apr 08 2013 - 09:57:43 PDT)
Re: [AMBER] implicit solvation with periodic boundary
Jason Swails
(Mon Apr 08 2013 - 13:10:55 PDT)
Re: [AMBER] implicit solvation with periodic boundary
Carlos Simmerling
(Mon Apr 08 2013 - 13:28:20 PDT)
Re: [AMBER] implicit solvation with periodic boundary
Syed Tarique Moin
(Mon Apr 08 2013 - 14:27:35 PDT)
Re: [AMBER] implicit solvation with periodic boundary
Carlos Simmerling
(Mon Apr 08 2013 - 14:39:17 PDT)
Re: [AMBER] implicit solvation with periodic boundary
Syed Tarique Moin
(Mon Apr 08 2013 - 16:32:59 PDT)
[AMBER] Ligand-Receptor complex MD - ligand doesn't appear?
Sebastian Petrik
(Mon Apr 08 2013 - 18:26:30 PDT)
Re: [AMBER] Ligand-Receptor complex MD - ligand doesn't appear?
steinbrt.rci.rutgers.edu
(Tue Apr 09 2013 - 00:45:38 PDT)
Re: [AMBER] Ligand-Receptor complex MD - ligand doesn't appear?
Julio Dominguez
(Tue Apr 09 2013 - 13:13:58 PDT)
Re: [AMBER] Ligand-Receptor complex MD - ligand doesn't appear?
Sebastian Petrik
(Tue Apr 09 2013 - 16:43:24 PDT)
Re: [AMBER] Ligand-Receptor complex MD - ligand doesn't appear?
steinbrt.rci.rutgers.edu
(Wed Apr 10 2013 - 00:53:34 PDT)
Re: [AMBER] Ligand-Receptor complex MD - ligand doesn't appear?
Sebastian Petrik
(Wed Apr 10 2013 - 18:39:20 PDT)
[AMBER] About modelling the separation of the "DNA" strands
Mu Xia
(Mon Apr 08 2013 - 19:09:33 PDT)
Re: [AMBER] About modelling the separation of the "DNA" strands
Jason Swails
(Tue Apr 23 2013 - 19:02:21 PDT)
[AMBER] large difference of nonpolar solvation free energy using MMPBSA.py in AmberTools1.5 or AmberTools12
dbaogen
(Tue Apr 09 2013 - 00:24:58 PDT)
Re: [AMBER] large difference of nonpolar solvation free energy using MMPBSA.py in AmberTools1.5 or AmberTools12
Jason Swails
(Tue Apr 09 2013 - 14:56:17 PDT)
Re: [AMBER] large difference of nonpolar solvation free energy using MMPBSA.py in AmberTools1.5 or AmberTools12
dbaogen
(Tue Apr 09 2013 - 18:29:23 PDT)
Re: [AMBER] large difference of nonpolar solvation free energy using MMPBSA.py in AmberTools1.5 or AmberTools12
Jason Swails
(Tue Apr 09 2013 - 18:45:45 PDT)
[AMBER] xleap error - Created a new atom named: P within residue: .R<DG5 478>
suresh satpati
(Tue Apr 09 2013 - 01:37:39 PDT)
Re: [AMBER] xleap error - Created a new atom named: P within residue: .R<DG5 478>
Daniel Roe
(Tue Apr 09 2013 - 08:00:42 PDT)
[AMBER] The latest topology file format.
Takeshi Baba
(Tue Apr 09 2013 - 05:56:58 PDT)
Re: [AMBER] The latest topology file format.
Daniel Roe
(Tue Apr 09 2013 - 07:54:25 PDT)
Re: [AMBER] The latest topology file format.
Takeshi Baba
(Wed Apr 10 2013 - 16:38:49 PDT)
[AMBER] Constant pH calculation: calcpka
Anselm Horn
(Wed Apr 10 2013 - 23:47:18 PDT)
Re: [AMBER] Constant pH calculation: calcpka
Jason Swails
(Thu Apr 11 2013 - 07:36:39 PDT)
Re: [AMBER] Constant pH calculation: calcpka
Anselm Horn
(Thu Apr 11 2013 - 09:17:27 PDT)
[AMBER] Problem with folding simulation
moitrayee.mbu.iisc.ernet.in
(Tue Apr 09 2013 - 19:07:43 PDT)
Re: [AMBER] Problem with folding simulation
Carlos Simmerling
(Tue Apr 09 2013 - 19:41:46 PDT)
Re: [AMBER] Problem with folding simulation
Jason Swails
(Tue Apr 09 2013 - 19:51:28 PDT)
[AMBER] Extra Points support in pmemd.cuda.MPI
Thomas Evangelidis
(Wed Apr 10 2013 - 03:10:51 PDT)
Re: [AMBER] Extra Points support in pmemd.cuda.MPI
Jason Swails
(Wed Apr 10 2013 - 05:30:18 PDT)
Re: [AMBER] Extra Points support in pmemd.cuda.MPI
Thomas Evangelidis
(Wed Apr 10 2013 - 06:09:56 PDT)
Re: [AMBER] Extra Points support in pmemd.cuda.MPI
Jason Swails
(Wed Apr 10 2013 - 06:27:41 PDT)
Re: [AMBER] Extra Points support in pmemd.cuda.MPI
Ross Walker
(Wed Apr 10 2013 - 06:39:58 PDT)
Re: [AMBER] Extra Points support in pmemd.cuda.MPI
Thomas Evangelidis
(Wed Apr 10 2013 - 13:47:52 PDT)
[AMBER] Amber installation problems
Donato Pera
(Wed Apr 10 2013 - 06:48:39 PDT)
Re: [AMBER] Amber installation problems
Daniel Roe
(Wed Apr 10 2013 - 07:04:11 PDT)
Re: [AMBER] Amber installation problems
Donato Pera
(Wed Apr 10 2013 - 07:32:19 PDT)
Re: [AMBER] Amber installation problems
Jason Swails
(Wed Apr 10 2013 - 07:55:36 PDT)
Re: [AMBER] Amber installation problems
Donato Pera
(Thu Apr 11 2013 - 23:57:20 PDT)
Re: [AMBER] Amber installation problems
Donato Pera
(Fri Apr 12 2013 - 01:49:01 PDT)
Re: [AMBER] Amber installation problems
David A Case
(Fri Apr 12 2013 - 04:44:47 PDT)
Re: [AMBER] Amber installation problems
Ross Walker
(Fri Apr 12 2013 - 08:05:58 PDT)
Re: [AMBER] Amber installation problems
Igor Marques
(Fri Apr 12 2013 - 10:40:34 PDT)
Re: [AMBER] Amber installation problems
David A Case
(Fri Apr 12 2013 - 17:37:54 PDT)
Re: [AMBER] Amber installation problems
Igor Marques
(Sat Apr 13 2013 - 03:31:28 PDT)
Re: [AMBER] Amber installation problems
Tru Huynh
(Mon Apr 15 2013 - 07:40:00 PDT)
Re: [AMBER] Amber installation problems
Igor Marques
(Mon Apr 15 2013 - 08:58:01 PDT)
Re: [AMBER] Amber installation problems
Donato Pera
(Mon Apr 15 2013 - 03:16:31 PDT)
Re: [AMBER] Amber installation problems
Jason Swails
(Mon Apr 15 2013 - 04:29:10 PDT)
[AMBER] RRe: Ligand-Receptor complex MD - ligand doesn't > appear?
Julio Dominguez
(Wed Apr 10 2013 - 13:39:18 PDT)
Re: [AMBER] RRe: Ligand-Receptor complex MD - ligand doesn't > appear?
Sebastian Petrik
(Wed Apr 10 2013 - 20:14:24 PDT)
Re: [AMBER] RRe: Ligand-Receptor complex MD - ligand doesn't > appear?
steinbrt.rci.rutgers.edu
(Thu Apr 11 2013 - 02:01:52 PDT)
Re: [AMBER] bug report: tinker_to_amberfailedforsystemscontainingcounter ions
Amber Amoeba
(Wed Apr 10 2013 - 13:52:47 PDT)
[AMBER] Zero vdW parametes for HO in Amber
Morteza Chehel Amirani
(Wed Apr 10 2013 - 15:55:40 PDT)
Re: [AMBER] Zero vdW parametes for HO in Amber
Bill Ross
(Wed Apr 10 2013 - 16:41:27 PDT)
Re: [AMBER] Zero vdW parametes for HO in Amber
Lachele Foley
(Wed Apr 10 2013 - 17:22:03 PDT)
Re: [AMBER] Zero vdW parametes for HO in Amber
Yong Duan
(Wed Apr 10 2013 - 19:27:19 PDT)
Re: [AMBER] Zero vdW parametes for HO in Amber
Jason Swails
(Wed Apr 10 2013 - 21:12:24 PDT)
[AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program
dbaogen
(Wed Apr 10 2013 - 20:37:00 PDT)
Re: [AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program
Jason Swails
(Thu Apr 11 2013 - 23:07:52 PDT)
Re: [AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program
dbaogen
(Fri Apr 12 2013 - 03:23:44 PDT)
Re: [AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program
David A Case
(Fri Apr 12 2013 - 04:49:01 PDT)
Re: [AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program
dbaogen
(Sat Apr 13 2013 - 23:17:09 PDT)
[AMBER] About modelling the separation of the "DNA" strands
Mu Xia
(Thu Apr 11 2013 - 01:36:50 PDT)
[AMBER] Problem compiling AMBER12 sander.MPI with gnu
Marc van der Kamp
(Thu Apr 11 2013 - 03:19:44 PDT)
Re: [AMBER] Problem compiling AMBER12 sander.MPI with gnu
Jason Swails
(Thu Apr 11 2013 - 07:15:15 PDT)
Re: [AMBER] Problem compiling AMBER12 sander.MPI with gnu
Marc van der Kamp
(Thu Apr 11 2013 - 13:39:14 PDT)
[AMBER] large Standard Deviation of binding free energy using QM/MM-GBSA method in Amber 11 with AmberTools 12
dbaogen
(Thu Apr 11 2013 - 05:15:31 PDT)
Re: [AMBER] large Standard Deviation of binding free energy using QM/MM-GBSA method in Amber 11 with AmberTools 12
Jason Swails
(Thu Apr 11 2013 - 07:28:11 PDT)
[AMBER] Tool to parameterize the ligand molecules
Jagur Lambix
(Thu Apr 11 2013 - 16:18:14 PDT)
Re: [AMBER] Tool to parameterize the ligand molecules
Jason Swails
(Thu Apr 11 2013 - 16:45:52 PDT)
Re: [AMBER] Tool to parameterize the ligand molecules
Jagur Lambix
(Fri Apr 12 2013 - 08:05:53 PDT)
[AMBER] mopac.sh file missing in amber12/bin directory
parul sharma
(Thu Apr 11 2013 - 22:20:12 PDT)
Re: [AMBER] mopac.sh file missing in amber12/bin directory
Jason Swails
(Thu Apr 11 2013 - 22:59:44 PDT)
[AMBER] problem in loading 5'terminal phosphate group of tRNA
N Nandi
(Thu Apr 11 2013 - 22:57:07 PDT)
Re: [AMBER] problem in loading 5'terminal phosphate group of tRNA
FyD
(Fri Apr 12 2013 - 07:03:34 PDT)
[AMBER] correlation matrix of side-chain dihedral angle in PTRAJ
anu chandra
(Fri Apr 12 2013 - 04:25:42 PDT)
Re: [AMBER] correlation matrix of side-chain dihedral angle in PTRAJ
Daniel Roe
(Mon Apr 15 2013 - 07:12:09 PDT)
[AMBER] aMD simulations in amber12
Neha Gandhi
(Fri Apr 12 2013 - 05:59:07 PDT)
Re: [AMBER] aMD simulations in amber12
Carlos Simmerling
(Fri Apr 12 2013 - 06:12:35 PDT)
[AMBER] ff atom types
Urszula Uciechowska
(Fri Apr 12 2013 - 06:12:36 PDT)
Re: [AMBER] ff atom types
FyD
(Fri Apr 12 2013 - 06:46:00 PDT)
Re: [AMBER] aMD simulations in amber12
Ross Walker
(Fri Apr 12 2013 - 08:10:43 PDT)
Re: [AMBER] aMD simulations in amber12
Neha Gandhi
(Fri Apr 12 2013 - 09:20:08 PDT)
Re: [AMBER] aMD simulations in amber12
Jian Yin
(Fri Apr 12 2013 - 10:21:20 PDT)
Re: [AMBER] aMD simulations in amber12
Soumya Lipsa Rath
(Fri Apr 12 2013 - 09:28:18 PDT)
[AMBER] NPT ensemble hydrogen bond calculation
Binwu Zhao
(Fri Apr 12 2013 - 21:20:54 PDT)
Re: [AMBER] NPT ensemble hydrogen bond calculation
Daniel Roe
(Mon Apr 15 2013 - 07:21:25 PDT)
[AMBER] on the ussage of mopac with Antechamber
James Starlight
(Fri Apr 12 2013 - 22:58:56 PDT)
Re: [AMBER] on the ussage of mopac with Antechamber
David A Case
(Mon Apr 15 2013 - 10:29:59 PDT)
Re: [AMBER] on the ussage of mopac with Antechamber
James Starlight
(Mon Apr 15 2013 - 21:44:20 PDT)
Re: [AMBER] on the ussage of mopac with Antechamber
David A Case
(Tue Apr 16 2013 - 04:51:32 PDT)
Re: [AMBER] on the ussage of mopac with Antechamber
Jason Swails
(Tue Apr 16 2013 - 04:51:59 PDT)
Re: [AMBER] on the ussage of mopac with Antechamber
James Starlight
(Tue Apr 16 2013 - 08:00:53 PDT)
[AMBER] # of snapshots for force does not match that of mdcrd
kurisaki
(Sat Apr 13 2013 - 23:20:21 PDT)
Re: [AMBER] # of snapshots for force does not match that of mdcrd
kurisaki
(Sun Apr 14 2013 - 01:58:13 PDT)
[AMBER] sander not installed
Jonathan Saboury
(Mon Apr 15 2013 - 00:50:04 PDT)
Re: [AMBER] sander not installed
Anna Bauß
(Mon Apr 15 2013 - 01:34:48 PDT)
[AMBER] clustering places all frames in one cluster
Amparo Garcia Lopez
(Mon Apr 15 2013 - 01:26:00 PDT)
[AMBER] clustering places all frames in one cluster
Amparo Garcia Lopez
(Mon Apr 15 2013 - 05:44:15 PDT)
Re: [AMBER] clustering places all frames in one cluster
Daniel Roe
(Mon Apr 15 2013 - 07:09:51 PDT)
Re: [AMBER] clustering places all frames in one cluster
Amparo Garcia Lopez
(Fri Apr 19 2013 - 01:14:55 PDT)
Re: [AMBER] clustering places all frames in one cluster
Vaibhav Dixit
(Sun Apr 21 2013 - 22:20:38 PDT)
Re: [AMBER] clustering places all frames in one cluster
Miguel Ortiz Lombardía
(Mon Apr 22 2013 - 06:11:46 PDT)
Re: [AMBER] clustering places all frames in one cluster
Amparo Garcia Lopez
(Thu Apr 25 2013 - 02:20:04 PDT)
Re: [AMBER] clustering places all frames in one cluster
Daniel Roe
(Thu Apr 25 2013 - 07:32:52 PDT)
[AMBER] problem in creating circular DNA using NAB
arnab bhattacharya
(Mon Apr 15 2013 - 04:10:33 PDT)
Re: [AMBER] problem in creating circular DNA using NAB
David A Case
(Mon Apr 15 2013 - 10:58:48 PDT)
Re: [AMBER] problem in creating circular DNA using NAB
arnab bhattacharya
(Tue Apr 16 2013 - 05:30:53 PDT)
Re: [AMBER] problem in creating circular DNA using NAB
David A Case
(Wed Apr 17 2013 - 00:19:30 PDT)
[AMBER] problem in creating circular DNA with NAB
arnab bhattacharya
(Mon Apr 15 2013 - 05:00:18 PDT)
[AMBER] Hydration Free Energy by TI
Kepa K. Burusco
(Mon Apr 15 2013 - 05:09:45 PDT)
Re: [AMBER] Hydration Free Energy by TI
steinbrt.rci.rutgers.edu
(Tue Apr 23 2013 - 04:45:40 PDT)
Re: [AMBER] Hydration Free Energy by TI
Kepa K. Burusco
(Tue Apr 23 2013 - 09:33:54 PDT)
[AMBER] GAFFlipid using custom lipids
Covington, Cody Lance
(Mon Apr 15 2013 - 11:23:27 PDT)
Re: [AMBER] GAFFlipid using custom lipids
Ganesh Kamath
(Mon Apr 15 2013 - 11:32:21 PDT)
Re: [AMBER] GAFFlipid using custom lipids
Benjamin D Madej
(Mon Apr 15 2013 - 12:15:30 PDT)
Re: [AMBER] GAFFlipid using custom lipids
Covington, Cody Lance
(Mon Apr 15 2013 - 12:52:03 PDT)
[AMBER] RE : GAFFlipid using custom lipids
ABEL Stephane 175950
(Mon Apr 15 2013 - 13:29:28 PDT)
Re: [AMBER] GAFFlipid using custom lipids
Benjamin D Madej
(Mon Apr 15 2013 - 15:00:00 PDT)
Re: [AMBER] GAFFlipid using custom lipids
Covington, Cody Lance
(Mon Apr 15 2013 - 18:02:12 PDT)
Re: [AMBER] GAFFlipid using custom lipids
Benjamin D Madej
(Tue Apr 16 2013 - 12:11:30 PDT)
[AMBER] PBSA focusing
Jesper Sørensen
(Mon Apr 15 2013 - 14:06:09 PDT)
Re: [AMBER] PBSA focusing
Ray Luo, Ph.D.
(Mon Apr 15 2013 - 14:38:48 PDT)
Re: [AMBER] PBSA focusing
Jesper Sørensen
(Mon Apr 15 2013 - 16:03:50 PDT)
Re: [AMBER] PBSA focusing
Ray Luo, Ph.D.
(Mon Apr 15 2013 - 16:54:43 PDT)
Re: [AMBER] PBSA focusing
Jesper Sørensen
(Tue Apr 16 2013 - 10:33:13 PDT)
Re: [AMBER] PBSA focusing
Ray Luo, Ph.D.
(Tue Apr 16 2013 - 11:27:51 PDT)
[AMBER] Solute concentration
waleed zalloum
(Mon Apr 15 2013 - 12:45:33 PDT)
Re: [AMBER] Solute concentration
Covington, Cody Lance
(Mon Apr 15 2013 - 17:10:39 PDT)
[AMBER] tleap cannot create topology and coordinate files
javier alejandro rendon carrillo
(Mon Apr 15 2013 - 14:22:52 PDT)
Re: [AMBER] tleap cannot create topology and coordinate files
David A Case
(Wed Apr 17 2013 - 06:44:11 PDT)
[AMBER] Whirling ssDNA like a helicopter (Movie attached)
Hoshin Kim
(Mon Apr 15 2013 - 15:23:05 PDT)
Re: [AMBER] Whirling ssDNA like a helicopter (Movie attached)
David A Case
(Tue Apr 16 2013 - 04:47:35 PDT)
[AMBER] Plotting heat maps in AMBER aMD simualtions
Neha Gandhi
(Tue Apr 16 2013 - 00:19:22 PDT)
Re: [AMBER] Plotting heat maps in AMBER aMD simualtions
Jason Swails
(Tue Apr 16 2013 - 08:10:05 PDT)
Re: [AMBER] Plotting heat maps in AMBER aMD simualtions
Daniel Roe
(Tue Apr 16 2013 - 08:38:34 PDT)
Re: [AMBER] Plotting heat maps in AMBER aMD simualtions
Neha Gandhi
(Tue Apr 16 2013 - 22:28:43 PDT)
Re: [AMBER] Plotting heat maps in AMBER aMD simualtions
Levi Pierce
(Wed Apr 17 2013 - 07:52:38 PDT)
Re: [AMBER] Plotting heat maps in AMBER aMD simualtions
Jason Swails
(Thu Apr 18 2013 - 05:04:15 PDT)
Re: [AMBER] Plotting heat maps in AMBER aMD simualtions
Levi Pierce
(Thu Apr 18 2013 - 07:36:12 PDT)
[AMBER] MMPBSA result interpretation helppppp
Catein Catherine
(Thu Apr 18 2013 - 23:07:25 PDT)
Re: [AMBER] MMPBSA result interpretation helppppp
Jason Swails
(Tue Apr 23 2013 - 05:12:43 PDT)
[AMBER] Wolf2Pack Parameterization Tool
Karl N. Kirschner
(Tue Apr 16 2013 - 02:27:11 PDT)
Re: [AMBER] NPT ensemble hydrogen bond calculation (Binwu Zhao)
Binwu Zhao
(Tue Apr 16 2013 - 10:46:00 PDT)
Re: [AMBER] NPT ensemble hydrogen bond calculation (Binwu Zhao)
Daniel Roe
(Tue Apr 16 2013 - 10:52:46 PDT)
[AMBER] Newbie solvent question
Jonathan Gough
(Tue Apr 16 2013 - 10:57:55 PDT)
Re: [AMBER] Newbie solvent question
Brian Radak
(Tue Apr 16 2013 - 12:19:13 PDT)
Re: [AMBER] Newbie solvent question
Jason Swails
(Tue Apr 16 2013 - 12:31:09 PDT)
Re: [AMBER] Newbie solvent question
Jonathan Gough
(Tue Apr 16 2013 - 12:34:48 PDT)
[AMBER] Clarification on sander
George Tzotzos
(Tue Apr 16 2013 - 11:24:08 PDT)
Re: [AMBER] Clarification on sander
Jason Swails
(Tue Apr 16 2013 - 12:07:03 PDT)
Re: [AMBER] Clarification on sander
George Tzotzos
(Tue Apr 16 2013 - 13:02:31 PDT)
Re: [AMBER] Clarification on sander
Ross Walker
(Tue Apr 16 2013 - 13:13:08 PDT)
[AMBER] Problems with tleap and popc membrane with protein
Fabrício Bracht
(Tue Apr 16 2013 - 14:17:14 PDT)
Re: [AMBER] Problems with tleap and popc membrane with protein
manikanthan bhavaraju
(Tue Apr 16 2013 - 14:35:39 PDT)
[AMBER] AmberTools12 re-installation test log file
Saugata Hazra
(Tue Apr 16 2013 - 14:46:11 PDT)
Re: [AMBER] AmberTools12 re-installation test log file
Jason Swails
(Tue Apr 16 2013 - 18:27:50 PDT)
Re: [AMBER] AmberTools12 re-installation test log file
Saugata Hazra
(Tue Apr 16 2013 - 20:23:30 PDT)
[AMBER] aMD question: How to read the amd.log file
Diego Javier Alonso de Armiño
(Tue Apr 16 2013 - 14:56:54 PDT)
Re: [AMBER] aMD question: How to read the amd.log file
diego alonso
(Tue Apr 16 2013 - 16:00:12 PDT)
Re: [AMBER] aMD question: How to read the amd.log file
filip fratev
(Tue Apr 16 2013 - 18:15:50 PDT)
[AMBER] aMD reweighting and amd.log file.
Diego Javier Alonso de Armiño
(Tue Apr 16 2013 - 16:05:56 PDT)
Re: [AMBER] aMD reweighting and amd.log file.
Diego Javier Alonso de Armiño
(Wed Apr 17 2013 - 07:54:04 PDT)
[AMBER] Fwd: Problems with tleap and popc membrane with protein
Fabrício Bracht
(Tue Apr 16 2013 - 19:16:01 PDT)
Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein
manikanthan bhavaraju
(Tue Apr 16 2013 - 20:26:32 PDT)
Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein
Fabrício Bracht
(Wed Apr 17 2013 - 10:40:54 PDT)
Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein
Benjamin D Madej
(Wed Apr 17 2013 - 16:48:09 PDT)
Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein
Igor Marques
(Thu Apr 18 2013 - 06:36:43 PDT)
Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein
Fabrício Bracht
(Thu Apr 18 2013 - 11:19:56 PDT)
[AMBER] Fortran error while runnig
javier alejandro rendon carrillo
(Tue Apr 16 2013 - 22:00:03 PDT)
Re: [AMBER] Fortran error while runnig
David A Case
(Wed Apr 17 2013 - 00:34:14 PDT)
[AMBER] pmemd.cuda.MPI with npt
HIMANSHU JOSHI
(Wed Apr 17 2013 - 11:03:07 PDT)
Re: [AMBER] pmemd.cuda.MPI with npt
Gustavo Seabra
(Wed Apr 17 2013 - 11:10:43 PDT)
Re: [AMBER] pmemd.cuda.MPI with npt
HIMANSHU JOSHI
(Wed Apr 17 2013 - 11:24:37 PDT)
Re: [AMBER] pmemd.cuda.MPI with npt
Adrian Roitberg
(Wed Apr 17 2013 - 11:26:00 PDT)
Re: [AMBER] pmemd.cuda.MPI with npt
HIMANSHU JOSHI
(Wed Apr 17 2013 - 22:24:07 PDT)
Re: [AMBER] pmemd.cuda.MPI with npt
HIMANSHU JOSHI
(Thu Apr 18 2013 - 23:01:05 PDT)
Re: [AMBER] pmemd.cuda.MPI with npt
Ross Walker
(Thu Apr 18 2013 - 23:35:00 PDT)
Re: [AMBER] pmemd.cuda.MPI with npt
Gustavo Seabra
(Wed Apr 17 2013 - 11:30:40 PDT)
Re: [AMBER] pmemd.cuda.MPI with npt
Scott Le Grand
(Wed Apr 17 2013 - 17:56:42 PDT)
Re: [AMBER] pmemd.cuda.MPI with npt
HIMANSHU JOSHI
(Wed Apr 17 2013 - 22:33:11 PDT)
[AMBER] GAFFLipid parameters
Covington, Cody Lance
(Wed Apr 17 2013 - 11:45:14 PDT)
[AMBER] Print pressure tensor components of NVT ensemble by running pmemd.cuda.MPI
Wei Lin
(Wed Apr 17 2013 - 16:31:02 PDT)
[AMBER] Print pressure tensor components of NVT ensemble by running pmemd.cuda.MPI
Wei Lin
(Wed Apr 17 2013 - 16:42:18 PDT)
Re: [AMBER] Print pressure tensor components of NVT ensemble by running pmemd.cuda.MPI
Ross Walker
(Wed Apr 17 2013 - 16:48:57 PDT)
[AMBER] gaff support for iron?
Jonathan Saboury
(Thu Apr 18 2013 - 00:51:17 PDT)
Re: [AMBER] gaff support for iron?
David A Case
(Thu Apr 18 2013 - 06:14:25 PDT)
[AMBER] paramfit questions
Covington, Cody Lance
(Thu Apr 18 2013 - 10:42:24 PDT)
Re: [AMBER] paramfit questions
Robin Betz
(Thu Apr 18 2013 - 16:53:02 PDT)
Re: [AMBER] paramfit questions
Karl N. Kirschner
(Fri Apr 19 2013 - 00:26:09 PDT)
[AMBER] problems with explicit solvent MD
Niels Geudens
(Fri Apr 19 2013 - 01:09:45 PDT)
Re: [AMBER] problems with explicit solvent MD
Jason Swails
(Fri Apr 19 2013 - 03:50:11 PDT)
[AMBER] ante-MMPBSA.py problem
Chris Chris
(Fri Apr 19 2013 - 09:56:37 PDT)
Re: [AMBER] ante-MMPBSA.py problem
Jason Swails
(Fri Apr 19 2013 - 11:07:25 PDT)
Re: [AMBER] ante-MMPBSA.py problem
Chris Chris
(Fri Apr 19 2013 - 23:18:59 PDT)
[AMBER] About halogen in MMPBSA calculation in AMBER9
Wang Bo
(Fri Apr 19 2013 - 12:17:11 PDT)
[AMBER] Using 3D-RISM to compute solvation free energy
Abhishek Mukhopadhyay
(Fri Apr 19 2013 - 13:36:05 PDT)
Re: [AMBER] Using 3D-RISM to compute solvation free energy
tluchko
(Fri Apr 19 2013 - 14:02:06 PDT)
Re: [AMBER] Using 3D-RISM to compute solvation free energy
Abhishek Mukhopadhyay
(Fri Apr 19 2013 - 15:10:14 PDT)
Re: [AMBER] Using 3D-RISM to compute solvation free energy
tluchko
(Fri Apr 19 2013 - 15:34:19 PDT)
Re: [AMBER] Using 3D-RISM to compute solvation free energy
Abhishek Mukhopadhyay
(Sat Apr 20 2013 - 15:00:37 PDT)
Re: [AMBER] Using 3D-RISM to compute solvation free energy
Tyler Luchko
(Sat Apr 20 2013 - 15:23:57 PDT)
[AMBER] Leap: Setting the bounding box manually
Anselm Horn
(Sun Apr 21 2013 - 09:04:06 PDT)
Re: [AMBER] Leap: Setting the bounding box manually
Jason Swails
(Sun Apr 21 2013 - 20:05:19 PDT)
[AMBER] Using MTKPP to turn a nonstandard organometallic compound in pdb format into AMBER inpcrd and prmtop files
Jonathan Saboury
(Fri Apr 19 2013 - 13:50:37 PDT)
Re: [AMBER] Using MTKPP to turn a nonstandard organometallic compound in pdb format into AMBER inpcrd and prmtop files
David A Case
(Sat Apr 20 2013 - 05:43:39 PDT)
Re: [AMBER] Using MTKPP to turn a nonstandard organometallic compound in pdb format into AMBER inpcrd and prmtop files
FyD
(Sun Apr 21 2013 - 07:42:29 PDT)
[AMBER] About halogen in MMPBSA calculation in AMBER9
Wang Bo
(Fri Apr 19 2013 - 14:43:50 PDT)
Re: [AMBER] About halogen in MMPBSA calculation in AMBER9
Ray Luo, Ph.D.
(Fri Apr 19 2013 - 14:52:09 PDT)
[AMBER] Changing vdW parameters for HO-type atom
Morteza Chehel Amirani
(Fri Apr 19 2013 - 15:17:25 PDT)
Re: [AMBER] Changing vdW parameters for HO-type atom
Brian Radak
(Mon Apr 22 2013 - 06:09:59 PDT)
[AMBER] protein-ligand docking
James Starlight
(Fri Apr 19 2013 - 23:57:37 PDT)
Re: [AMBER] protein-ligand docking
David A Case
(Sat Apr 20 2013 - 05:48:27 PDT)
[AMBER] segmentation fault in tleap
Jonathan Gough
(Sun Apr 21 2013 - 20:09:37 PDT)
Re: [AMBER] segmentation fault in tleap
Robin Betz
(Sun Apr 21 2013 - 21:05:33 PDT)
Re: [AMBER] segmentation fault in tleap
Jonathan Gough
(Sun Apr 21 2013 - 21:39:32 PDT)
[AMBER] Input file for NVT simulation
Vaibhav Dixit
(Mon Apr 22 2013 - 00:43:16 PDT)
[AMBER] Fwd: Input file for NVT simulation
Vaibhav Dixit
(Mon Apr 22 2013 - 00:46:53 PDT)
Re: [AMBER] Fwd: Input file for NVT simulation
kurisaki
(Mon Apr 22 2013 - 00:59:49 PDT)
Re: [AMBER] Input file for NVT simulation
Brian Radak
(Mon Apr 22 2013 - 05:51:22 PDT)
[AMBER] Amber MPI CPU number problem
Donato Pera
(Mon Apr 22 2013 - 02:34:43 PDT)
Re: [AMBER] Amber MPI CPU number problem
Jason Swails
(Mon Apr 22 2013 - 19:15:37 PDT)
[AMBER] amber tutorial13 :constructing and simulating crystals with amber12
Yongxiu Li
(Mon Apr 22 2013 - 05:16:14 PDT)
Re: [AMBER] amber tutorial13 :constructing and simulating crystals with amber12
David A Case
(Thu Apr 25 2013 - 16:48:03 PDT)
[AMBER] parameters for single amino acid MD
Rilei Yu
(Mon Apr 22 2013 - 05:49:47 PDT)
Re: [AMBER] parameters for single amino acid MD
David A Case
(Mon Apr 22 2013 - 08:03:04 PDT)
[AMBER] dihedral term for furan and thiophene molecules
Chang Woon Jang
(Mon Apr 22 2013 - 07:17:00 PDT)
Re: [AMBER] dihedral term for furan and thiophene molecules
David A Case
(Mon Apr 22 2013 - 08:04:18 PDT)
Re: [AMBER] dihedral term for furan and thiophene molecules
Chang Woon Jang
(Mon Apr 22 2013 - 08:21:29 PDT)
Re: [AMBER] dihedral term for furan and thiophene molecules
Karl N. Kirschner
(Tue Apr 23 2013 - 04:31:29 PDT)
[AMBER] VMD shows an atom stretched waaaay out
Jonathan Gough
(Mon Apr 22 2013 - 08:50:10 PDT)
Re: [AMBER] VMD shows an atom stretched waaaay out
Hai Nguyen
(Mon Apr 22 2013 - 12:15:02 PDT)
Re: [AMBER] VMD shows an atom stretched waaaay out
Jonathan Gough
(Mon Apr 22 2013 - 12:50:05 PDT)
Re: [AMBER] VMD shows an atom stretched waaaay out
Daniel Roe
(Mon Apr 22 2013 - 14:20:24 PDT)
Re: [AMBER] VMD shows an atom stretched waaaay out
Jonathan Gough
(Mon Apr 22 2013 - 14:27:57 PDT)
[AMBER] carbohydrate-GLYCAM 06-cellulose Iβ
Rasha Alqus
(Mon Apr 22 2013 - 09:14:49 PDT)
Re: [AMBER] carbohydrate-GLYCAM 06-cellulose Iβ
Lachele Foley
(Mon Apr 22 2013 - 09:59:58 PDT)
Re: [AMBER] carbohydrate-GLYCAM 06-cellulose Iβ
David A Case
(Mon Apr 22 2013 - 17:56:33 PDT)
Re: [AMBER] carbohydrate-GLYCAM 06-cellulose Iβ
Rasha Alqus
(Fri Apr 26 2013 - 06:19:53 PDT)
[AMBER] Reducing positional restraint gradually
Rahul Banerjee
(Mon Apr 22 2013 - 12:11:44 PDT)
Re: [AMBER] Reducing positional restraint gradually
Brian Radak
(Mon Apr 22 2013 - 13:12:56 PDT)
Re: [AMBER] Reducing positional restraint gradually
Jan-Philip Gehrcke
(Mon Apr 22 2013 - 14:11:07 PDT)
Re: [AMBER] Reducing positional restraint gradually
Rahul Banerjee
(Tue Apr 23 2013 - 06:32:14 PDT)
Re: [AMBER] Reducing positional restraint gradually
Jason Swails
(Tue Apr 23 2013 - 07:05:06 PDT)
Re: [AMBER] Reducing positional restraint gradually
Jan-Philip Gehrcke
(Tue Apr 23 2013 - 07:17:44 PDT)
Re: [AMBER] Reducing positional restraint gradually
David A Case
(Tue Apr 23 2013 - 09:02:30 PDT)
Re: [AMBER] Reducing positional restraint gradually
Jan-Philip Gehrcke
(Wed Apr 24 2013 - 01:46:24 PDT)
[AMBER] AMBER Training Workshop - Recife, Brazil - Save the Date
Ross Walker
(Mon Apr 22 2013 - 12:53:01 PDT)
[AMBER] Release of AmberTools13
David A Case
(Mon Apr 22 2013 - 13:33:11 PDT)
[AMBER] ambertools13 fails to update
Jonathan Gough
(Mon Apr 22 2013 - 15:32:22 PDT)
Re: [AMBER] ambertools13 fails to update
Jason Swails
(Mon Apr 22 2013 - 15:39:04 PDT)
Re: [AMBER] ambertools13 fails to update
Jonathan Gough
(Mon Apr 22 2013 - 15:45:18 PDT)
Re: [AMBER] ambertools13 fails to update
Jason Swails
(Mon Apr 22 2013 - 15:59:40 PDT)
Re: [AMBER] ambertools13 fails to update
Jonathan Gough
(Mon Apr 22 2013 - 17:09:08 PDT)
Re: [AMBER] ambertools13 fails to update
M. L. Dodson
(Mon Apr 22 2013 - 17:25:21 PDT)
[AMBER] Problem with cluster analysis in ptraj
nicolai petelski
(Mon Apr 22 2013 - 18:12:41 PDT)
Re: [AMBER] Problem with cluster analysis in ptraj
Daniel Roe
(Tue Apr 23 2013 - 07:18:22 PDT)
[AMBER] Is there a trick to fix a poor structural feature?
Jonathan Gough
(Tue Apr 23 2013 - 11:47:19 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
Jason Swails
(Tue Apr 23 2013 - 18:01:54 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
Bill Ross
(Tue Apr 23 2013 - 21:26:26 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
Jonathan Gough
(Wed Apr 24 2013 - 10:54:18 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
David A Case
(Wed Apr 24 2013 - 11:20:21 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
Jonathan Gough
(Wed Apr 24 2013 - 13:32:21 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
Jonathan Gough
(Wed Apr 24 2013 - 14:13:00 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
tec3.utah.edu
(Wed Apr 24 2013 - 19:51:23 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
Bill Ross
(Wed Apr 24 2013 - 21:40:14 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
Thomas Evangelidis
(Wed Apr 24 2013 - 23:02:23 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
Symon Gathiaka
(Thu Apr 25 2013 - 08:04:22 PDT)
Re: [AMBER] Is there a trick to fix a poor structural feature?
Jonathan Gough
(Sat Apr 27 2013 - 17:39:08 PDT)
[AMBER] ig=-1 in NVE simulation
Subrata Paul
(Tue Apr 23 2013 - 23:02:11 PDT)
Re: [AMBER] ig=-1 in NVE simulation
Ross Walker
(Tue Apr 23 2013 - 23:33:10 PDT)
[AMBER] Cyclic peptide problem
Changqing Yan
(Wed Apr 24 2013 - 07:20:59 PDT)
Re: [AMBER] Cyclic peptide problem
Jason Swails
(Wed Apr 24 2013 - 08:34:50 PDT)
Re: [AMBER] Cyclic peptide problem
Changqing Yan
(Thu Apr 25 2013 - 00:55:18 PDT)
Re: [AMBER] Cyclic peptide problem
David A Case
(Thu Apr 25 2013 - 04:30:23 PDT)
Re: [AMBER] Cyclic peptide problem
Changqing Yan
(Thu Apr 25 2013 - 00:56:02 PDT)
[AMBER] Question for AMBER input files
陶晓芳
(Wed Apr 24 2013 - 18:19:01 PDT)
Re: [AMBER] Question for AMBER input files
Daniel Roe
(Thu Apr 25 2013 - 07:33:55 PDT)
[AMBER] Question for AMBER input files (inpcrd file)
陶晓芳
(Wed Apr 24 2013 - 19:00:07 PDT)
[AMBER] pmemd: time-dependent distance restraint (as with jar=1) + torsional restraints
Jan-Philip Gehrcke
(Thu Apr 25 2013 - 05:08:06 PDT)
Re: [AMBER] pmemd: time-dependent distance restraint (as with jar=1) + torsional restraints
Jan-Philip Gehrcke
(Thu Apr 25 2013 - 05:22:58 PDT)
Re: [AMBER] pmemd: time-dependent distance restraint (as with jar=1) + torsional restraints
Jan-Philip Gehrcke
(Thu Apr 25 2013 - 07:35:12 PDT)
[AMBER] Compilation errors for AmberTools 13 with OpenMP
Eugene Yedvabny
(Thu Apr 25 2013 - 18:32:34 PDT)
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
Jason Swails
(Sat Apr 27 2013 - 06:53:51 PDT)
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
M. L. Dodson
(Sat Apr 27 2013 - 07:21:34 PDT)
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
Jason Swails
(Sat Apr 27 2013 - 14:43:14 PDT)
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
Eugene Yedvabny
(Sat Apr 27 2013 - 15:26:15 PDT)
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
M. L. Dodson
(Sat Apr 27 2013 - 17:05:15 PDT)
Re: [AMBER-Developers] [AMBER] Compilation errors for AmberTools 13 with OpenMP
David A Case
(Sun Apr 28 2013 - 04:10:11 PDT)
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
M. L. Dodson
(Sun Apr 28 2013 - 05:55:56 PDT)
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
David A Case
(Sun Apr 28 2013 - 13:34:08 PDT)
Re: [AMBER-Developers] [AMBER] Compilation errors for AmberTools 13 with OpenMP
Scott Brozell
(Sun Apr 28 2013 - 15:29:57 PDT)
Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP
M. L. Dodson
(Sun Apr 28 2013 - 15:38:45 PDT)
Re: [AMBER-Developers] [AMBER] Compilation errors for AmberTools 13 with OpenMP
Ross Walker
(Sun Apr 28 2013 - 13:18:21 PDT)
Re: [AMBER] [AMBER-Developers] Compilation errors for AmberTools 13 with OpenMP
M. L. Dodson
(Sun Apr 28 2013 - 14:07:32 PDT)
[AMBER] Gradually reduce the restraint within one step
crazylyf
(Thu Apr 25 2013 - 20:28:45 PDT)
Re: [AMBER] Gradually reduce the restraint within one step
David A Case
(Fri Apr 26 2013 - 12:08:33 PDT)
Re: [AMBER] Gradually reduce the restraint within one step
crazylyf.126.com
(Fri Apr 26 2013 - 17:51:32 PDT)
[AMBER] Gradually reduce the restraint within one step
Jian Yin
(Fri Apr 26 2013 - 20:24:56 PDT)
Re: [AMBER] Gradually reduce the restraint within one step
crazylyf.126.com
(Fri Apr 26 2013 - 20:40:51 PDT)
Re: [AMBER] Gradually reduce the restraint within one step
Jian Yin
(Fri Apr 26 2013 - 21:08:50 PDT)
Re: [AMBER] Gradually reduce the restraint within one step
crazylyf.126.com
(Fri Apr 26 2013 - 21:29:53 PDT)
Re: [AMBER] Gradually reduce the restraint within one step
David A Case
(Sat Apr 27 2013 - 03:57:13 PDT)
Re: [AMBER] Gradually reduce the restraint within one step
crazylyf.126.com
(Sat Apr 27 2013 - 17:27:07 PDT)
Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to Sim failed for K20x using JAC and Cellulose benchmarks
Chinh Su Tran To
(Thu Apr 25 2013 - 21:00:30 PDT)
Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to Sim failed for K20x using JAC and Cellulose benchmarks
Ross Walker
(Thu Apr 25 2013 - 21:10:22 PDT)
Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to Sim failed for K20x using JAC and Cellulose benchmarks
Chinh Su Tran To
(Thu Apr 25 2013 - 22:46:46 PDT)
[AMBER] the role of surface charge
Sun
(Fri Apr 26 2013 - 01:13:53 PDT)
Re: [AMBER] the role of surface charge
David A Case
(Fri Apr 26 2013 - 17:28:28 PDT)
Re: [AMBER] Query about checking of convergence in REMD
gargi borgohai
(Fri Apr 26 2013 - 06:14:58 PDT)
Re: [AMBER] Query about checking of convergence in REMD
Carlos Simmerling
(Fri Apr 26 2013 - 06:20:01 PDT)
Re: [AMBER] Query about checking of convergence in REMD
Daniel Roe
(Fri Apr 26 2013 - 09:47:38 PDT)
[AMBER] RMD with selected NMR restraints
Krisztina Feher
(Fri Apr 26 2013 - 06:32:40 PDT)
Re: [AMBER] RMD with selected NMR restraints
David A Case
(Fri Apr 26 2013 - 17:24:49 PDT)
[AMBER] list of (dihedral and angle) parameters (GAFF)
Vedat Durmaz
(Fri Apr 26 2013 - 09:14:24 PDT)
Re: [AMBER] list of (dihedral and angle) parameters (GAFF)
Ilyas Yildirim
(Fri Apr 26 2013 - 09:41:48 PDT)
Re: [AMBER] list of (dihedral and angle) parameters (GAFF)
Daniel Roe
(Fri Apr 26 2013 - 09:42:30 PDT)
[AMBER] distance restraint
Sangita Kachhap
(Fri Apr 26 2013 - 10:54:38 PDT)
Re: [AMBER] distance restraint
David A Case
(Fri Apr 26 2013 - 17:22:29 PDT)
[AMBER] Compiling problems with -openmp
David A Case
(Fri Apr 26 2013 - 12:51:28 PDT)
Re: [AMBER] Compiling problems with -openmp
Eugene Yedvabny
(Fri Apr 26 2013 - 17:22:00 PDT)
Re: [AMBER] Compiling problems with -openmp
David A Case
(Sun Apr 28 2013 - 03:57:37 PDT)
[AMBER] paramfit question
Covington, Cody Lance
(Fri Apr 26 2013 - 15:20:08 PDT)
Re: [AMBER] paramfit question
Robin Betz
(Fri Apr 26 2013 - 17:16:29 PDT)
[AMBER] how to get force information through MD run
kurisaki
(Sat Apr 27 2013 - 01:06:54 PDT)
Re: [AMBER] how to get force information through MD run
David A Case
(Sat Apr 27 2013 - 04:02:38 PDT)
[AMBER] hbond print option equivalent in cpptraj from AmberTools13?
miguel
(Sat Apr 27 2013 - 08:01:54 PDT)
Re: [AMBER] hbond print option equivalent in cpptraj from AmberTools13?
Daniel Roe
(Sat Apr 27 2013 - 10:01:42 PDT)
Re: [AMBER] hbond print option equivalent in cpptraj from AmberTools13?
miguel
(Sun Apr 28 2013 - 00:48:07 PDT)
[AMBER] Problem in parameter file generation
Kshatresh Dutta Dubey
(Sat Apr 27 2013 - 13:41:34 PDT)
Re: [AMBER] Problem in parameter file generation
Bill Ross
(Sat Apr 27 2013 - 14:03:09 PDT)
Re: [AMBER] Problem in parameter file generation
Kshatresh Dutta Dubey
(Sat Apr 27 2013 - 14:28:23 PDT)
Re: [AMBER] Problem in parameter file generation
Jason Swails
(Sat Apr 27 2013 - 21:58:54 PDT)
Re: [AMBER] Problem in parameter file generation
Kshatresh Dutta Dubey
(Sun Apr 28 2013 - 00:23:31 PDT)
[AMBER] Sander/PMEMD doesn't understand line - corrupted RST output?
Sebastian Petrik
(Sun Apr 28 2013 - 17:17:26 PDT)
Re: [AMBER] Sander/PMEMD doesn't understand line - corrupted RST output?
Jason Swails
(Sun Apr 28 2013 - 17:59:48 PDT)
Re: [AMBER] Sander/PMEMD doesn't understand line - corrupted RST output?
Sebastian Petrik
(Sun Apr 28 2013 - 18:49:56 PDT)
[AMBER] Prepare PRMTOP file for off-SHAKE simulation
kurisaki
(Sun Apr 28 2013 - 20:18:56 PDT)
Re: [AMBER] Prepare PRMTOP file for off-SHAKE simulation
kurisaki
(Sun Apr 28 2013 - 21:14:20 PDT)
[AMBER] Palladium complex parametrization in antechamber
Alexey Zeifman
(Sun Apr 28 2013 - 23:43:14 PDT)
Re: [AMBER] Palladium complex parametrization in antechamber
David A Case
(Mon Apr 29 2013 - 04:53:16 PDT)
Re: [AMBER] Palladium complex parametrization in antechamber
Alexey Zeifman
(Mon Apr 29 2013 - 04:58:02 PDT)
[AMBER] Paper detailing GPU Simulations Compared to CPU code
ET
(Mon Apr 29 2013 - 08:15:02 PDT)
Re: [AMBER] Paper detailing GPU Simulations Compared to CPU code
Ross Walker
(Mon Apr 29 2013 - 09:19:46 PDT)
[AMBER] bug in impose command in amber tleap
sandeep singh
(Mon Apr 29 2013 - 11:21:19 PDT)
Re: [AMBER] bug in impose command in amber tleap
David A Case
(Mon Apr 29 2013 - 11:42:11 PDT)
[AMBER] antechamber espgen error for molybdenum complex:fitting values are missing
Sergio R Aragon
(Mon Apr 29 2013 - 17:57:49 PDT)
Re: [AMBER] antechamber espgen error for molybdenum complex:fitting values are missing
Sergio R Aragon
(Mon Apr 29 2013 - 19:52:56 PDT)
[AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
Jan-Philip Gehrcke
(Tue Apr 30 2013 - 03:06:56 PDT)
Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
Jan-Philip Gehrcke
(Tue Apr 30 2013 - 03:51:27 PDT)
Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
Jason Swails
(Tue Apr 30 2013 - 05:07:27 PDT)
Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
Jan-Philip Gehrcke
(Tue Apr 30 2013 - 06:05:09 PDT)
Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
Jason Swails
(Tue Apr 30 2013 - 06:32:20 PDT)
Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
Jan-Philip Gehrcke
(Tue Apr 30 2013 - 06:37:27 PDT)
[AMBER] DNA basestep stacking energy/interaction energy
BERGY
(Tue Apr 30 2013 - 03:27:03 PDT)
Re: [AMBER] DNA basestep stacking energy/interaction energy
David A Case
(Tue Apr 30 2013 - 06:20:49 PDT)
[AMBER] pb_read.F90: minor issue // AmberTools . GitHub?
Jan-Philip Gehrcke
(Tue Apr 30 2013 - 06:27:51 PDT)
[AMBER] AMBER CUDA Installation
Kanin Wichapong
(Tue Apr 30 2013 - 09:17:59 PDT)
Re: [AMBER] AMBER CUDA Installation
Scott Le Grand
(Tue Apr 30 2013 - 11:13:26 PDT)
[AMBER] improper Dihedral Specification
Covington, Cody Lance
(Tue Apr 30 2013 - 13:06:35 PDT)
Last message date
:
Tue Apr 30 2013 - 13:30:03 PDT
Archived on
: Fri Dec 20 2024 - 05:54:47 PST
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