Amber Archive Mar 2013 by author
569 messages
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Starting
Thu Feb 28 2013 - 20:30:02 PST,
Ending
Sat Mar 30 2013 - 12:30:02 PDT
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. mirage
Re: [AMBER] angle between two plan
(Sat Mar 16 2013 - 04:04:11 PDT)
Re: [AMBER] angle between two plan
(Thu Mar 14 2013 - 10:34:34 PDT)
[AMBER] angle between two plan
(Thu Mar 14 2013 - 02:10:50 PDT)
ABEL Stephane 175950
[AMBER] RE : problems in parameters calculated with AMBER
(Mon Mar 25 2013 - 05:30:35 PDT)
[AMBER] RE : PMEMD in amber12
(Thu Mar 14 2013 - 08:34:16 PDT)
[AMBER] N-Carboxymethionine charges and parameters for AMBER
(Sat Mar 09 2013 - 02:46:58 PST)
Adrian Roitberg
Re: [AMBER] COM support with GPU
(Mon Mar 18 2013 - 12:17:15 PDT)
Ahmed Ayoub
[AMBER] Cofactor GDP Atom Types
(Thu Mar 14 2013 - 12:22:40 PDT)
Albert
[AMBER] strange output information
(Thu Mar 28 2013 - 03:02:53 PDT)
Re: [AMBER] aMD job failed
(Wed Mar 27 2013 - 08:37:21 PDT)
[AMBER] aMD job failed
(Wed Mar 27 2013 - 00:21:05 PDT)
Re: [AMBER] how can we calculate average dihedral for aMD?
(Sun Mar 24 2013 - 09:45:57 PDT)
Re: [AMBER] how can we calculate average dihedral for aMD?
(Sun Mar 24 2013 - 09:30:52 PDT)
[AMBER] how to plot CA matrix?
(Sun Mar 24 2013 - 05:14:00 PDT)
[AMBER] how can we calculate average dihedral for aMD?
(Sun Mar 24 2013 - 04:41:17 PDT)
Re: [AMBER] NVT stacked at GPU running
(Sat Mar 23 2013 - 01:45:30 PDT)
[AMBER] can we calculate them together?
(Fri Mar 22 2013 - 07:44:32 PDT)
[AMBER] how can we plot energy profile for REMD?
(Thu Mar 21 2013 - 01:51:11 PDT)
Re: [AMBER] why no periodic information?
(Tue Mar 19 2013 - 07:48:29 PDT)
[AMBER] why no periodic information?
(Tue Mar 19 2013 - 07:00:52 PDT)
Re: [AMBER] can we specify mpi path in ./configure?
(Tue Mar 19 2013 - 03:40:17 PDT)
Re: [AMBER] can we specify mpi path in ./configure?
(Tue Mar 19 2013 - 00:38:52 PDT)
[AMBER] can we specify mpi path in ./configure?
(Mon Mar 18 2013 - 13:30:28 PDT)
Re: [AMBER] NVT stacked at GPU running
(Mon Mar 18 2013 - 13:17:42 PDT)
Re: [AMBER] GTX Titan was finally released
(Mon Mar 18 2013 - 11:29:09 PDT)
Re: [AMBER] NVT stacked at GPU running
(Mon Mar 18 2013 - 11:10:24 PDT)
Re: [AMBER] NVT stacked at GPU running
(Mon Mar 18 2013 - 11:09:05 PDT)
[AMBER] NVT stacked at GPU running
(Mon Mar 18 2013 - 08:51:44 PDT)
Re: [AMBER] no restrains?
(Mon Mar 18 2013 - 07:44:10 PDT)
[AMBER] no restrains?
(Mon Mar 18 2013 - 06:43:30 PDT)
Alessandro Orro
[AMBER] Fwd: cudaMemcpy GpuBuffer::Download failed
(Mon Mar 25 2013 - 05:06:13 PDT)
Amber Amoeba
Re: [AMBER] bug report: tinker_to_amber failedforsystemscontainingcounter ions
(Mon Mar 11 2013 - 11:18:08 PDT)
Re: [AMBER] bug report: tinker_to_amber failed forsystemscontainingcounter ions
(Thu Mar 07 2013 - 08:03:28 PST)
Re: [AMBER] bug report: tinker_to_amber failed for systemscontainingcounter ions
(Wed Mar 06 2013 - 22:53:46 PST)
Re: [AMBER] bug report: tinker_to_amber failed for systems containingcounter ions
(Wed Mar 06 2013 - 10:27:27 PST)
[AMBER] test
(Tue Mar 05 2013 - 14:27:01 PST)
[AMBER] bug report: tinker_to_amber failed for systems containing counter ions
(Tue Mar 05 2013 - 12:33:21 PST)
Amy Davenport
Re: [AMBER] Trouble with MM-PBSA calculations in large complex
(Thu Mar 21 2013 - 12:05:12 PDT)
Re: [AMBER] AMBER Digest, Vol 457, Issue 1
(Wed Mar 20 2013 - 12:48:36 PDT)
[AMBER] Trouble with MM-PBSA calculations in large complex
(Tue Mar 19 2013 - 17:27:19 PDT)
aneesh cna
Re: [AMBER] Generating PDB files with atom radii information
(Thu Mar 28 2013 - 22:20:40 PDT)
Re: [AMBER] Generating PDB files with atom radii information
(Thu Mar 28 2013 - 02:25:50 PDT)
[AMBER] Generating PDB files with atom radii information
(Wed Mar 27 2013 - 22:01:18 PDT)
[AMBER] residue-wise SASA calculation in CPPTRAJ
(Tue Mar 26 2013 - 03:08:48 PDT)
Anna Marabotti
Re: [AMBER] problems in parameters calculated with AMBER
(Tue Mar 26 2013 - 02:41:00 PDT)
[AMBER] problems in parameters calculated with AMBER
(Mon Mar 25 2013 - 05:12:09 PDT)
Anselm Horn
Re: [AMBER] disulfide bonds
(Fri Mar 08 2013 - 06:17:00 PST)
Anshuman Dixit
[AMBER] problem in running antechamber
(Tue Mar 26 2013 - 00:39:08 PDT)
Aron Broom
Re: [AMBER] Histidine problem
(Wed Mar 27 2013 - 20:41:57 PDT)
Re: [AMBER] RMSD with ptraj fit vs unfit
(Wed Mar 27 2013 - 10:22:35 PDT)
Re: [AMBER] Which memory of GTX580 should I choose in 30, 000-50, 000 atoms system
(Thu Mar 21 2013 - 20:32:40 PDT)
Re: [AMBER] GTX Titan was finally released
(Thu Mar 14 2013 - 10:42:22 PDT)
Re: [AMBER] GTX 460 ?
(Wed Mar 13 2013 - 07:35:28 PDT)
Re: [AMBER] GTX 460 ?
(Tue Mar 12 2013 - 13:39:24 PDT)
Re: [AMBER] PCI-E 2.0 vs 3.0 (AMD vs INTEL?)
(Thu Feb 28 2013 - 21:24:10 PST)
Asmita Gupta
Re: [AMBER] conformational sampling in non helical RNA structures
(Sat Mar 30 2013 - 11:27:27 PDT)
[AMBER] conformational sampling in non helical RNA structures
(Sat Mar 30 2013 - 08:44:39 PDT)
[AMBER] amber12 configure error
(Fri Mar 01 2013 - 00:09:27 PST)
Attilio Vittorio Vargiu
[AMBER] Restart SMD simulation
(Tue Mar 12 2013 - 08:35:59 PDT)
Baldoni Hector Armando
Re: [AMBER] GTX 460 ?
(Mon Mar 11 2013 - 06:59:26 PDT)
[AMBER] GPU overload
(Fri Mar 01 2013 - 05:42:04 PST)
Bayse, Craig A.
[AMBER] mapping problem with makeDIST_RST
(Mon Mar 11 2013 - 11:14:05 PDT)
Benjamin D Madej
Re: [AMBER] membrane protein modeling
(Sun Mar 24 2013 - 22:15:34 PDT)
Re: [AMBER] how to save a snapshot from the trajectory
(Tue Mar 19 2013 - 10:46:48 PDT)
Re: [AMBER] PCI-E 2.0 vs 3.0 (AMD vs INTEL?)
(Thu Feb 28 2013 - 22:05:38 PST)
Re: [AMBER] PCI-E 2.0 vs 3.0 (AMD vs INTEL?)
(Thu Feb 28 2013 - 22:00:21 PST)
Bill Ross
Re: [AMBER] Generating PDB files with atom radii information
(Fri Mar 29 2013 - 16:07:45 PDT)
Re: [AMBER] Generating PDB files with atom radii information
(Fri Mar 29 2013 - 16:03:13 PDT)
Re: [AMBER] Generating PDB files with atom radii information
(Wed Mar 27 2013 - 22:32:23 PDT)
Re: [AMBER] angle between two plan
(Sat Mar 16 2013 - 11:14:49 PDT)
Re: [AMBER] REMD simulation
(Thu Mar 14 2013 - 16:47:55 PDT)
Re: [AMBER] REMD simulation
(Thu Mar 14 2013 - 16:12:20 PDT)
Re: [AMBER] WG: tleap output of mol2 format with incorrect bond order
(Thu Mar 07 2013 - 15:36:22 PST)
Brian Radak
Re: [AMBER] problems in parameters calculated with AMBER
(Tue Mar 26 2013 - 09:14:09 PDT)
Re: [AMBER] why no periodic information?
(Tue Mar 19 2013 - 10:11:13 PDT)
Re: [AMBER] QM/MM restart problem
(Thu Mar 14 2013 - 09:26:29 PDT)
Re: [AMBER] Fwd: failed to run sander ....
(Thu Mar 07 2013 - 12:03:28 PST)
Re: [AMBER] TIP5P water simulation
(Wed Mar 06 2013 - 10:29:32 PST)
Re: [AMBER] TIP5P water simulation
(Wed Mar 06 2013 - 06:34:41 PST)
Re: [AMBER] temperature fluctuation amber ntp ensemble
(Mon Mar 04 2013 - 08:35:50 PST)
Browning, Nicholas
[AMBER] Number Excluded Atoms List Generation
(Thu Mar 07 2013 - 08:53:40 PST)
Carlos Simmerling
Re: [AMBER] REMD simulation
(Fri Mar 15 2013 - 09:03:05 PDT)
[AMBER] March 15 deadline for ACS COMP division awards for Fall 2013 Indianapolis national meeting
(Sat Mar 02 2013 - 05:04:05 PST)
Re: [AMBER] RMSD Fluctuation
(Thu Mar 07 2013 - 03:24:01 PST)
Cenk \(Jenk\) Andac
[AMBER] NVIDIA GTX-675
(Tue Mar 12 2013 - 07:49:54 PDT)
CHAMI F.
[AMBER] Charge relocation Amber 12
(Tue Mar 05 2013 - 05:54:03 PST)
Changqing Yan
[AMBER] Histidine problem
(Wed Mar 27 2013 - 20:18:15 PDT)
[AMBER] Is there a way to keep ions fixed in a amber MD?
(Thu Mar 07 2013 - 05:39:51 PST)
Chiara Pallara
[AMBER] MMPBSA ATP-Mg
(Wed Mar 13 2013 - 10:54:38 PDT)
Chinthaka Ratnaweera
Re: [AMBER] MMPBSA calculations
(Wed Mar 27 2013 - 14:01:10 PDT)
Re: [AMBER] MMPBSA calculations
(Wed Mar 27 2013 - 10:46:39 PDT)
[AMBER] MMPBSA calculations
(Wed Mar 27 2013 - 09:08:20 PDT)
cieplak.cgl.ucsf.edu
Re: [AMBER] Number Excluded Atoms List Generation
(Thu Mar 07 2013 - 09:04:56 PST)
Cuiyl
Re: [AMBER] Bad atom type: fe in MMPBSA calculations
(Mon Mar 18 2013 - 01:50:13 PDT)
Re: [AMBER] Bad atom type: fe in MMPBSA calculations
(Thu Mar 14 2013 - 01:57:55 PDT)
Re: [AMBER] Bad atom type: fe in MMPBSA calculations
(Thu Mar 14 2013 - 00:38:10 PDT)
[AMBER] Bad atom type: fe in MMPBSA calculations
(Wed Mar 13 2013 - 22:03:59 PDT)
Daniel Roe
Re: [AMBER] Problem reading a psf file in cpptraj
(Fri Mar 29 2013 - 13:44:17 PDT)
Re: [AMBER] Problem reading a psf file in cpptraj
(Fri Mar 29 2013 - 12:57:41 PDT)
Re: [AMBER] Generating PDB files with atom radii information
(Thu Mar 28 2013 - 07:12:32 PDT)
Re: [AMBER] strange output information
(Thu Mar 28 2013 - 06:02:19 PDT)
Re: [AMBER] RMSD with ptraj fit vs unfit
(Wed Mar 27 2013 - 10:22:11 PDT)
Re: [AMBER] problem combining trajectories with diff. number of residues
(Tue Mar 26 2013 - 07:55:08 PDT)
Re: [AMBER] cpptraj
(Tue Mar 26 2013 - 07:48:00 PDT)
Re: [AMBER] residue-wise SASA calculation in CPPTRAJ
(Tue Mar 26 2013 - 07:40:20 PDT)
Re: [AMBER] cpptraj
(Tue Mar 26 2013 - 07:34:29 PDT)
Re: [AMBER] leap - removing terminals problem
(Fri Mar 22 2013 - 09:15:45 PDT)
Re: [AMBER] aMD simulations in AMBER 12 (GPU version)
(Thu Mar 21 2013 - 09:42:27 PDT)
Re: [AMBER] problem combining trajectories with diff. number of residues
(Thu Mar 21 2013 - 07:35:12 PDT)
Re: [AMBER] pmemd.cuda compilation problems on Ubuntu 12.4
(Wed Mar 20 2013 - 12:15:31 PDT)
Re: [AMBER] problem combining trajectories with diff. number of residues
(Wed Mar 20 2013 - 07:59:59 PDT)
Re: [AMBER] solvating and neutralizing a lipid bilayer
(Wed Mar 20 2013 - 07:40:35 PDT)
Re: [AMBER] Error while generating B factor Graph
(Tue Mar 19 2013 - 13:16:44 PDT)
Re: [AMBER] how to save a snapshot from the trajectory
(Tue Mar 19 2013 - 13:00:58 PDT)
Re: [AMBER] can we specify mpi path in ./configure?
(Mon Mar 18 2013 - 14:39:30 PDT)
Re: [AMBER] ptraj skipping frames depending on the computer OS?
(Fri Mar 15 2013 - 08:49:55 PDT)
Re: [AMBER] Amber 11 and Amber 12
(Fri Mar 15 2013 - 08:42:30 PDT)
Re: [AMBER] Regarding MSD calculations in ptraj
(Fri Mar 15 2013 - 08:16:17 PDT)
Re: [AMBER] Cofactor GDP Atom Types
(Fri Mar 15 2013 - 08:07:40 PDT)
Re: [AMBER] Amber 11 and Amber 12
(Wed Mar 13 2013 - 11:57:57 PDT)
Re: [AMBER] trajin: command not found
(Tue Mar 12 2013 - 07:41:25 PDT)
Re: [AMBER] frcmod problem
(Tue Mar 12 2013 - 06:59:21 PDT)
Re: [AMBER] Regarding centering a tetrameric molecule
(Mon Mar 11 2013 - 05:12:08 PDT)
Re: [AMBER] Imaging issues with ptraj
(Sat Mar 09 2013 - 19:50:46 PST)
Re: [AMBER] RMSD Fluctuation
(Tue Mar 05 2013 - 21:01:46 PST)
Re: [AMBER] ptraj action command
(Sun Mar 03 2013 - 20:46:03 PST)
Re: [AMBER] Problem in Arsenite parameterisation
(Sat Mar 02 2013 - 12:47:22 PST)
Re: [AMBER] Problem in Arsenite parameterisation
(Fri Mar 01 2013 - 06:44:16 PST)
Re: [AMBER] GPU overload
(Fri Mar 01 2013 - 06:43:08 PST)
David A Case
Re: [AMBER] Generating PDB files with atom radii information
(Sat Mar 30 2013 - 07:52:51 PDT)
Re: [AMBER] IED web link to essential dynamics is broken
(Mon Mar 25 2013 - 04:55:14 PDT)
Re: [AMBER] '.' follows exponent in NUMBER-like thing
(Mon Mar 25 2013 - 04:48:49 PDT)
Re: [AMBER] the prpblem in constructing the close circular DNA
(Mon Mar 25 2013 - 04:47:29 PDT)
Re: [AMBER] Amber release time table
(Sun Mar 24 2013 - 13:10:17 PDT)
Re: [AMBER] how can we calculate average dihedral for aMD?
(Sun Mar 24 2013 - 08:17:11 PDT)
Re: [AMBER] IED web link to essential dynamics is broken
(Sat Mar 23 2013 - 07:11:11 PDT)
Re: [AMBER] Langevin Dynamics
(Fri Mar 22 2013 - 13:06:51 PDT)
Re: [AMBER] How to use AMBER parameters for modified amino acids
(Thu Mar 21 2013 - 05:29:14 PDT)
Re: [AMBER] Problem to save a particular snapshot from the trajectory
(Tue Mar 19 2013 - 07:39:32 PDT)
Re: [AMBER] leap insert missing atoms in aminoacids according to ...
(Tue Mar 19 2013 - 07:36:52 PDT)
Re: [AMBER] ions (salt concentration) and deep energetics problem
(Tue Mar 19 2013 - 05:11:05 PDT)
Re: [AMBER] leap insert missing atoms in aminoacids according to ...
(Tue Mar 19 2013 - 05:06:54 PDT)
Re: [AMBER] Antechamber: AM1-BCC charges from MOPAC output
(Tue Mar 19 2013 - 05:01:59 PDT)
Re: [AMBER] problem combining trajectories with diff. number of residues
(Tue Mar 19 2013 - 04:56:21 PDT)
Re: [AMBER] can we specify mpi path in ./configure?
(Mon Mar 18 2013 - 18:09:11 PDT)
Re: [AMBER] no restrains?
(Mon Mar 18 2013 - 07:40:21 PDT)
Re: [AMBER] RESP charges for iron-sulfur cluster
(Fri Mar 15 2013 - 08:24:03 PDT)
Re: [AMBER] mapping problem with makeDIST_RST
(Fri Mar 15 2013 - 08:20:35 PDT)
Re: [AMBER] RESP charges for iron-sulfur cluster
(Fri Mar 15 2013 - 05:13:31 PDT)
Re: [AMBER] mapping problem with makeDIST_RST
(Fri Mar 15 2013 - 05:02:04 PDT)
Re: [AMBER] the protein was crashed
(Fri Mar 15 2013 - 04:52:37 PDT)
Re: [AMBER] charge problem
(Wed Mar 13 2013 - 06:34:45 PDT)
Re: [AMBER] Amber12 MPI OK on one node but not across nodes
(Tue Mar 12 2013 - 17:29:26 PDT)
Re: [AMBER] Thermodynamic Integration
(Tue Mar 12 2013 - 05:48:01 PDT)
Re: [AMBER] generate prepin from mol2 which has charges/atom types for Heme
(Sun Mar 10 2013 - 09:24:03 PDT)
Re: [AMBER] WG: tleap output of mol2 format with incorrect bond order
(Fri Mar 08 2013 - 14:57:25 PST)
Re: [AMBER] Fwd: failed to run sander ....
(Thu Mar 07 2013 - 12:15:36 PST)
Re: [AMBER] WG: tleap output of mol2 format with incorrect bond order
(Thu Mar 07 2013 - 12:04:44 PST)
Re: [AMBER] xleap_the hydrogen atom in C-terminus of peptides
(Wed Mar 06 2013 - 17:53:46 PST)
Re: [AMBER] TIP5P water simulation
(Wed Mar 06 2013 - 17:49:09 PST)
Re: [AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA
(Tue Mar 05 2013 - 07:55:58 PST)
Re: [AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA
(Tue Mar 05 2013 - 04:36:05 PST)
David Winogradoff
Re: [AMBER] Amber 11 and Amber 12
(Wed Mar 13 2013 - 16:30:36 PDT)
Re: [AMBER] Amber 11 and Amber 12
(Wed Mar 13 2013 - 10:25:40 PDT)
[AMBER] Amber 11 and Amber 12
(Mon Mar 11 2013 - 15:34:31 PDT)
dbaogen
[AMBER] How to implement QM/MM-PBSA method in Amber 11 with AmberTools 12
(Wed Mar 27 2013 - 23:36:58 PDT)
Re: [AMBER] Problem parsing PB output using MMPBSA.py in AMBER11 and AmberTools 1.5
(Mon Mar 04 2013 - 19:10:55 PST)
[AMBER] Problem parsing PB output using MMPBSA.py in AMBER11 and AmberTools 1.5
(Mon Mar 04 2013 - 04:27:08 PST)
DEBOSTUTI GHOSHDASTIDAR
Re: [AMBER] Regarding MSD calculations in ptraj
(Fri Mar 15 2013 - 22:56:15 PDT)
[AMBER] Regarding MSD calculations in ptraj
(Fri Mar 15 2013 - 03:32:32 PDT)
dilrajl.bii.a-star.edu.sg
Re: [AMBER] Regarding centering a tetrameric molecule
(Sun Mar 10 2013 - 23:50:16 PDT)
[AMBER] Regarding centering a tetrameric molecule
(Fri Mar 08 2013 - 04:51:00 PST)
Dmitry Nilov
Re: [AMBER] Query On Steered Molecular Dynamics
(Tue Mar 05 2013 - 05:24:02 PST)
Elise Duboué-Dijon
[AMBER] Segmentation fault with EVB calculations on multiple cores for a system with more than 60 atom types
(Mon Mar 04 2013 - 15:19:05 PST)
Emilio Angelina
[AMBER] how to restart a molecular dynamics simulation
(Tue Mar 05 2013 - 11:46:52 PST)
Fabrício Bracht
[AMBER] COM support with GPU
(Mon Mar 18 2013 - 12:04:27 PDT)
[AMBER] Softcore selection
(Thu Feb 28 2013 - 20:19:24 PST)
Fenley, Andrew
Re: [AMBER] GPU overload
(Fri Mar 01 2013 - 06:54:04 PST)
filip fratev
Re: [AMBER] GTX Titan was finally released
(Mon Mar 18 2013 - 10:58:13 PDT)
Re: [AMBER] GTX Titan was finally released
(Sun Mar 17 2013 - 06:53:32 PDT)
Re: [AMBER] GTX Titan was finally released
(Thu Mar 14 2013 - 12:48:45 PDT)
Re: [AMBER] GTX Titan was finally released
(Thu Mar 14 2013 - 09:33:40 PDT)
Re: [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3
(Wed Mar 13 2013 - 15:44:46 PDT)
Re: [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3
(Wed Mar 13 2013 - 14:55:58 PDT)
francesco oteri
Re: [AMBER] RESP charges for iron-sulfur cluster
(Mon Mar 11 2013 - 03:29:50 PDT)
FyD
Re: [AMBER] urea frcmod file
(Tue Mar 19 2013 - 05:50:56 PDT)
Re: [AMBER] N-Carboxymethionine charges and parameters for AMBER
(Sat Mar 09 2013 - 23:23:10 PST)
Re: [AMBER] antechamber dCTP
(Fri Mar 08 2013 - 23:09:19 PST)
Re: [AMBER] impose for improper torsion: from I. Kurisaki
(Fri Mar 08 2013 - 03:36:35 PST)
Re: [AMBER] Can IMPOSE apply to improper angle?
(Thu Mar 07 2013 - 23:11:25 PST)
Re: [AMBER] tleap output of mol2 format with incorrect bond order
(Thu Mar 07 2013 - 12:50:57 PST)
Re: [AMBER] antechamber dCTP
(Thu Mar 07 2013 - 12:45:38 PST)
Re: [AMBER] antechamber dCTP
(Thu Mar 07 2013 - 02:55:59 PST)
Re: [AMBER] xleap_the hydrogen atom in C-terminus of peptides
(Wed Mar 06 2013 - 22:54:45 PST)
Re: [AMBER] antechamber dCTP
(Wed Mar 06 2013 - 22:30:52 PST)
Re: [AMBER] force field file
(Thu Feb 28 2013 - 22:32:25 PST)
Re: [AMBER] Modified amino acid parameter generation
(Thu Feb 28 2013 - 22:13:51 PST)
Ganesh Kamath
Re: [AMBER] Problem reading a psf file in cpptraj
(Fri Mar 29 2013 - 13:35:50 PDT)
[AMBER] Problem reading a psf file in cpptraj
(Fri Mar 29 2013 - 11:43:15 PDT)
gargi borgohai
[AMBER] urea frcmod file
(Tue Mar 19 2013 - 00:17:29 PDT)
George M Giambasu
Re: [AMBER] rotational diffusion via cpptraj
(Fri Mar 29 2013 - 06:14:03 PDT)
George Tzotzos
[AMBER] SMD centre of the restraint
(Sat Mar 23 2013 - 14:51:21 PDT)
Re: [AMBER] Langevin Dynamics
(Fri Mar 22 2013 - 13:56:54 PDT)
[AMBER] Langevin Dynamics
(Fri Mar 22 2013 - 12:00:27 PDT)
Gerald Monard
Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure
(Sun Mar 17 2013 - 14:12:47 PDT)
Giulia
[AMBER] R: mmpbsa calculations for a ternary protein/dna/ligand complex
(Fri Mar 22 2013 - 02:18:26 PDT)
[AMBER] mmpbsa calculations for a ternary protein/dna/ligand complex in presence of cocrystalized Mg ions
(Thu Mar 21 2013 - 08:26:00 PDT)
Re: [AMBER] mmpbsa calculations on a PROTEIN/DNA/LIGAND ternary complex
(Thu Mar 21 2013 - 02:14:13 PDT)
Giulia Palermo
[AMBER] R: mmpbsa calculations on a PROTEIN/DNA/LIGAND ternary complex
(Thu Mar 21 2013 - 07:08:02 PDT)
[AMBER] mmpbsa calculations on a PROTEIN/DNA/LIGAND ternary complex
(Wed Mar 20 2013 - 10:33:11 PDT)
Guillermo Mulliert Carlín
[AMBER] amber12 remd problem and solution recompiling sander.MPI with AMBERBUILDFLAGS -DVERBOSE_REM
(Fri Mar 22 2013 - 00:21:01 PDT)
Gustavo Seabra
Re: [AMBER] QM/MM restart problem
(Thu Mar 14 2013 - 13:45:30 PDT)
Re: [AMBER] GTX Titan was finally released
(Thu Mar 14 2013 - 10:49:07 PDT)
Re: [AMBER] GTX Titan was finally released
(Thu Mar 14 2013 - 10:31:43 PDT)
Re: [AMBER] QM/MM restart problem
(Thu Mar 14 2013 - 10:29:55 PDT)
Re: [AMBER] Implicit membrane models
(Fri Mar 01 2013 - 12:34:04 PST)
[AMBER] Implicit membrane models
(Fri Mar 01 2013 - 10:32:02 PST)
Hai Nguyen
Re: [AMBER] igb=8 available for MMPBSA.py ?
(Thu Mar 07 2013 - 11:00:15 PST)
Hector A. Baldoni
Re: [AMBER] GTX 460 ?
(Tue Mar 12 2013 - 12:20:57 PDT)
Re: [AMBER] how to restart a molecular dynamics simulation
(Tue Mar 05 2013 - 12:22:49 PST)
Re: [AMBER] GPU overload
(Fri Mar 01 2013 - 11:57:10 PST)
HIMANSHU JOSHI
Re: [AMBER] RMSD with ptraj fit vs unfit
(Wed Mar 27 2013 - 23:07:31 PDT)
[AMBER] RMSD with ptraj fit vs unfit
(Wed Mar 27 2013 - 10:17:38 PDT)
[AMBER] VLIMIT problem with Folic acid (gaff parm)
(Wed Mar 06 2013 - 21:19:07 PST)
Ignacio J. General
Re: [AMBER] cpptraj
(Tue Mar 26 2013 - 07:38:39 PDT)
[AMBER] cpptraj
(Tue Mar 26 2013 - 07:25:58 PDT)
Re: [AMBER] leap - removing terminals problem
(Fri Mar 22 2013 - 09:59:08 PDT)
[AMBER] leap - removing terminals problem
(Fri Mar 22 2013 - 08:59:32 PDT)
Re: [AMBER] Hydration Free Enery by TI
(Mon Mar 18 2013 - 10:07:36 PDT)
Indrajit Deb
[AMBER] Cross correlation calculation
(Wed Mar 06 2013 - 01:33:12 PST)
Ismail, Mohd F.
Re: [AMBER] Question about 'sequence' command
(Tue Mar 26 2013 - 22:57:16 PDT)
[AMBER] Question about 'sequence' command
(Tue Mar 26 2013 - 22:47:34 PDT)
[AMBER] Question about AM1BCC
(Thu Mar 14 2013 - 00:15:59 PDT)
Re: [AMBER] Kepler and Amber11?
(Sat Mar 02 2013 - 12:14:35 PST)
[AMBER] Kepler and Amber11?
(Fri Mar 01 2013 - 00:16:16 PST)
Itamar Kass (Med)
Re: [AMBER] Cyclic peptide
(Sun Mar 24 2013 - 03:47:17 PDT)
[AMBER] Cyclic peptide
(Mon Mar 11 2013 - 03:34:59 PDT)
Jan Fredin
[AMBER] Amber12 MPI OK on one node but not across nodes
(Tue Mar 12 2013 - 09:38:46 PDT)
Jan-Philip Gehrcke
[AMBER] minor development note: make symbolic link to pmemd.cuda relative instead of absolute
(Wed Mar 27 2013 - 05:26:40 PDT)
Re: [AMBER] patching unsuccessful even after modifying patch_amber.py
(Mon Mar 25 2013 - 06:31:46 PDT)
Re: [AMBER] patching unsuccessful even after modifying patch_amber.py
(Mon Mar 25 2013 - 04:05:20 PDT)
Re: [AMBER] patching unsuccessful even after modifying patch_amber.py
(Mon Mar 25 2013 - 03:32:06 PDT)
Re: [AMBER] pmemd.cuda compilation problems on Ubuntu 12.4
(Wed Mar 20 2013 - 11:38:40 PDT)
Re: [AMBER] can we specify mpi path in ./configure?
(Tue Mar 19 2013 - 03:28:51 PDT)
[AMBER] GPU job scheduling: looking for recommendations and experiences
(Mon Mar 18 2013 - 06:35:07 PDT)
Jason Swails
Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 530 C5' CI
(Thu Mar 28 2013 - 10:01:58 PDT)
Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 530 C5' CI
(Thu Mar 28 2013 - 08:37:30 PDT)
Re: [AMBER] MM PBSA tutorial
(Thu Mar 28 2013 - 06:37:04 PDT)
Re: [AMBER] MM PBSA tutorial
(Thu Mar 28 2013 - 05:54:14 PDT)
Re: [AMBER] Generating PDB files with atom radii information
(Thu Mar 28 2013 - 05:46:51 PDT)
Re: [AMBER] How to implement QM/MM-PBSA method in Amber 11 with AmberTools 12
(Thu Mar 28 2013 - 05:32:01 PDT)
Re: [AMBER] ff10 with ILDN + Best&Hummer modifications
(Thu Mar 28 2013 - 05:20:02 PDT)
Re: [AMBER] MMPBSA calculations
(Wed Mar 27 2013 - 11:31:50 PDT)
Re: [AMBER] MMPBSA calculations
(Wed Mar 27 2013 - 09:48:43 PDT)
Re: [AMBER] aMD job failed
(Wed Mar 27 2013 - 07:32:56 PDT)
Re: [AMBER] cpptraj
(Tue Mar 26 2013 - 07:50:39 PDT)
Re: [AMBER] residue-wise SASA calculation in CPPTRAJ
(Tue Mar 26 2013 - 04:54:31 PDT)
Re: [AMBER] patching unsuccessful even after modifying patch_amber.py
(Mon Mar 25 2013 - 06:24:16 PDT)
Re: [AMBER] problems in parameters calculated with AMBER
(Mon Mar 25 2013 - 05:27:59 PDT)
Re: [AMBER] patching unsuccessful even after modifying patch_amber.py
(Mon Mar 25 2013 - 04:21:00 PDT)
Re: [AMBER] patching unsuccessful even after modifying patch_amber.py
(Mon Mar 25 2013 - 03:03:44 PDT)
Re: [AMBER] patching unsuccessful even after modifying patch_amber.py
(Sun Mar 24 2013 - 17:19:17 PDT)
Re: [AMBER] patching unsuccessful even after modifying patch_amber.py
(Sun Mar 24 2013 - 17:12:25 PDT)
Re: [AMBER] SMD centre of the restraint
(Sat Mar 23 2013 - 19:24:37 PDT)
Re: [AMBER] RXSGLD Simulation Error
(Fri Mar 22 2013 - 15:51:14 PDT)
Re: [AMBER] leap - removing terminals problem
(Fri Mar 22 2013 - 10:05:09 PDT)
Re: [AMBER] aMD simulations in AMBER 12 (GPU version) update
(Thu Mar 21 2013 - 17:55:56 PDT)
Re: [AMBER] mmpbsa calculations for a ternary protein/dna/ligand complex in presence of cocrystalized Mg ions
(Thu Mar 21 2013 - 15:37:54 PDT)
Re: [AMBER] Trouble with MM-PBSA calculations in large complex
(Thu Mar 21 2013 - 15:34:45 PDT)
Re: [AMBER] mmpbsa calculations for a ternary protein/dna/ligand complex in presence of cocrystalized Mg ions
(Thu Mar 21 2013 - 08:36:19 PDT)
Re: [AMBER] Meaning of electrostatic pairwise interaction in GB/PBSA
(Wed Mar 20 2013 - 07:05:05 PDT)
Re: [AMBER] Meaning of electrostatic pairwise interaction in GB/PBSA
(Wed Mar 20 2013 - 07:03:35 PDT)
Re: [AMBER] Trouble with MM-PBSA calculations in large complex
(Wed Mar 20 2013 - 06:04:41 PDT)
Re: [AMBER] Ante-mmpbsa.py error
(Tue Mar 19 2013 - 13:01:14 PDT)
Re: [AMBER] Problem with Alanine Scanning using MMPBSA.py with Terminal Residues
(Tue Mar 19 2013 - 07:31:28 PDT)
Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure
(Sat Mar 16 2013 - 08:46:56 PDT)
Re: [AMBER] Amber 9
(Sat Mar 16 2013 - 07:25:04 PDT)
Re: [AMBER] angle between two plan
(Sat Mar 16 2013 - 05:34:19 PDT)
Re: [AMBER] Amber 11 and Amber 12
(Fri Mar 15 2013 - 10:11:12 PDT)
Re: [AMBER] modified dna
(Fri Mar 15 2013 - 06:50:18 PDT)
Re: [AMBER] PMEMD in amber12
(Fri Mar 15 2013 - 06:49:11 PDT)
Re: [AMBER] REMD simulation
(Thu Mar 14 2013 - 16:43:06 PDT)
Re: [AMBER] angle between two plan
(Thu Mar 14 2013 - 11:03:17 PDT)
Re: [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3
(Thu Mar 14 2013 - 09:56:37 PDT)
Re: [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3
(Wed Mar 13 2013 - 14:19:14 PDT)
Re: [AMBER] MMPBSA ATP-Mg
(Wed Mar 13 2013 - 14:13:24 PDT)
Re: [AMBER] Query on Steered Molecular Dynamics
(Wed Mar 13 2013 - 06:44:12 PDT)
Re: [AMBER] Restart SMD simulation
(Tue Mar 12 2013 - 15:23:49 PDT)
Re: [AMBER] frcmod file problem
(Tue Mar 12 2013 - 13:41:49 PDT)
Re: [AMBER] Problem in parallel installation of Amber 12
(Tue Mar 12 2013 - 12:17:28 PDT)
Re: [AMBER] Amber 11 and Amber 12
(Mon Mar 11 2013 - 15:56:58 PDT)
Re: [AMBER] Cyclic peptide
(Mon Mar 11 2013 - 06:21:35 PDT)
Re: [AMBER] ligand molecule problem
(Mon Mar 11 2013 - 06:18:14 PDT)
Re: [AMBER] GTX 460 ?
(Mon Mar 11 2013 - 06:13:47 PDT)
Re: [AMBER] generate prepin from mol2 which has charges/atom types for Heme
(Mon Mar 11 2013 - 06:09:29 PDT)
Re: [AMBER] generate prepin from mol2 which has charges/atom types for Heme
(Sun Mar 10 2013 - 08:25:28 PDT)
Re: [AMBER] Does MMPBSA.py actually make a file called _MMPBSA_nmode.in?
(Sun Mar 10 2013 - 08:20:51 PDT)
Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure
(Sun Mar 10 2013 - 08:17:41 PDT)
Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure
(Fri Mar 08 2013 - 05:20:12 PST)
Re: [AMBER] Regarding centering a tetrameric molecule
(Fri Mar 08 2013 - 05:15:20 PST)
Re: [AMBER] impose for improper torsion: from I. Kurisaki
(Fri Mar 08 2013 - 05:08:23 PST)
Re: [AMBER] WG: tleap output of mol2 format with incorrect bond order
(Thu Mar 07 2013 - 12:01:16 PST)
Re: [AMBER] Number Excluded Atoms List Generation
(Thu Mar 07 2013 - 10:52:41 PST)
Re: [AMBER] Is there a way to keep ions fixed in a amber MD?
(Thu Mar 07 2013 - 05:48:42 PST)
Re: [AMBER] MMPBSA jobs on a cluster Calcerror:
(Wed Mar 06 2013 - 15:19:04 PST)
Re: [AMBER] MMPBSA jobs on a cluster Calcerror:
(Wed Mar 06 2013 - 15:16:59 PST)
Re: [AMBER] Error in MMPBSA
(Wed Mar 06 2013 - 15:15:33 PST)
Re: [AMBER] MMPBSA jobs on a cluster Calcerror:
(Wed Mar 06 2013 - 14:13:29 PST)
Re: [AMBER] Error in MMPBSA
(Wed Mar 06 2013 - 14:12:43 PST)
Re: [AMBER] MMPBSA jobs on a cluster Calcerror:
(Wed Mar 06 2013 - 13:47:18 PST)
Re: [AMBER] MMPBSA jobs on a cluster Calcerror:
(Wed Mar 06 2013 - 12:25:39 PST)
Re: [AMBER] how to restart a molecular dynamics simulation
(Tue Mar 05 2013 - 11:59:33 PST)
Re: [AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA
(Tue Mar 05 2013 - 05:38:10 PST)
Re: [AMBER] Problem parsing PB output using MMPBSA.py in AMBER11 and AmberTools 1.5
(Tue Mar 05 2013 - 04:36:38 PST)
Re: [AMBER] Problem parsing PB output using MMPBSA.py in AMBER11 and AmberTools 1.5
(Mon Mar 04 2013 - 04:37:14 PST)
Re: [AMBER] Problem in Arsenite parameterisation
(Sat Mar 02 2013 - 10:22:42 PST)
Re: [AMBER] Kepler and Amber11?
(Fri Mar 01 2013 - 06:16:54 PST)
Re: [AMBER] amber12 configure error
(Fri Mar 01 2013 - 06:15:58 PST)
javacfish
Re: [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3
(Thu Mar 14 2013 - 08:51:21 PDT)
Re: [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3
(Thu Mar 14 2013 - 02:05:54 PDT)
[AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3
(Wed Mar 13 2013 - 10:54:21 PDT)
Jiri Sponer
Re: [AMBER] conformational sampling in non helical RNA structures
(Sat Mar 30 2013 - 12:16:57 PDT)
Re: [AMBER] conformational sampling in non helical RNA structures
(Sat Mar 30 2013 - 09:11:07 PDT)
Joel Dockray
Re: [AMBER] Does MMPBSA.py actually make a file called _MMPBSA_nmode.in?
(Sun Mar 10 2013 - 09:31:15 PDT)
[AMBER] Does MMPBSA.py actually make a file called _MMPBSA_nmode.in?
(Sun Mar 10 2013 - 05:33:20 PDT)
John Gehman
Re: [AMBER] solvating and neutralizing a lipid bilayer
(Wed Mar 20 2013 - 08:28:00 PDT)
[AMBER] solvating and neutralizing a lipid bilayer
(Wed Mar 20 2013 - 07:16:11 PDT)
Re: [AMBER] GTX 460 ?
(Wed Mar 13 2013 - 06:40:47 PDT)
Re: [AMBER] GTX 460 ?
(Mon Mar 11 2013 - 18:56:30 PDT)
[AMBER] GTX 460 ?
(Sun Mar 10 2013 - 23:54:31 PDT)
Jonathan Gough
[AMBER] Amber release time table
(Sun Mar 24 2013 - 12:11:01 PDT)
Re: [AMBER] GPU job scheduling: looking for recommendations and experiences
(Mon Mar 18 2013 - 09:10:16 PDT)
Re: [AMBER] PCI-E 2.0 vs 3.0 (AMD vs INTEL?)
(Fri Mar 01 2013 - 04:24:14 PST)
Josep Maria Campanera Alsina
[AMBER] Meaning of electrostatic pairwise interaction in GB/PBSA
(Tue Mar 19 2013 - 08:00:55 PDT)
Kepa K. Burusco
Re: [AMBER] Hydration Free Enery by TI
(Wed Mar 20 2013 - 04:50:32 PDT)
Re: [AMBER] Hydration Free Enery by TI
(Tue Mar 19 2013 - 12:27:18 PDT)
Re: [AMBER] Hydration Free Enery by TI
(Mon Mar 18 2013 - 09:28:18 PDT)
Re: [AMBER] Hydration Free Enery by TI
(Mon Mar 18 2013 - 09:11:32 PDT)
[AMBER] Hydration Free Enery by TI
(Fri Mar 15 2013 - 10:06:25 PDT)
Kira Armacost
Re: [AMBER] Imaging issues with ptraj
(Mon Mar 11 2013 - 07:05:06 PDT)
[AMBER] Imaging issues with ptraj
(Sat Mar 09 2013 - 17:55:06 PST)
Kong, Ren
[AMBER] membrane protein modeling
(Sun Mar 24 2013 - 16:55:38 PDT)
Kshatresh Dutta Dubey
Re: [AMBER] why no periodic information?
(Tue Mar 19 2013 - 07:21:10 PDT)
Re: [AMBER] Problem in parallel installation of Amber 12
(Wed Mar 13 2013 - 04:21:37 PDT)
Re: [AMBER] Problem in parallel installation of Amber 12
(Tue Mar 12 2013 - 08:59:03 PDT)
[AMBER] Problem in parallel installation of Amber 12
(Tue Mar 12 2013 - 08:41:49 PDT)
Re: [AMBER] Problem in Arsenite parameterisation
(Sat Mar 02 2013 - 10:39:05 PST)
Re: [AMBER] Problem in Arsenite parameterisation
(Sat Mar 02 2013 - 10:28:31 PST)
Re: [AMBER] Problem in Arsenite parameterisation
(Sat Mar 02 2013 - 01:03:09 PST)
[AMBER] Problem in Arsenite parameterisation
(Fri Mar 01 2013 - 05:28:00 PST)
kurisaki
Re: [AMBER] ions (salt concentration) and deep energetics problem
(Mon Mar 18 2013 - 17:40:59 PDT)
Re: [AMBER] impose for improper torsion: from I. Kurisaki
(Fri Mar 08 2013 - 05:37:20 PST)
Re: [AMBER] impose for improper torsion: from I. Kurisaki
(Fri Mar 08 2013 - 03:46:14 PST)
[AMBER] Can IMPOSE apply to improper angle?
(Thu Mar 07 2013 - 21:05:04 PST)
Re: [AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA
(Tue Mar 05 2013 - 16:37:19 PST)
Re: [AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA
(Tue Mar 05 2013 - 05:24:40 PST)
Re: [AMBER] Wrong Annotation of PREPIN generated by RESIDUEGEN
(Tue Mar 05 2013 - 01:42:02 PST)
[AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA
(Tue Mar 05 2013 - 01:38:00 PST)
Lachele Foley
[AMBER] GLYCAM-Web server disruptions
(Thu Mar 21 2013 - 07:17:38 PDT)
llduan
[AMBER] the prpblem in constructing the close circular DNA
(Sun Mar 24 2013 - 18:02:42 PDT)
M. L. Dodson
Re: [AMBER] problem in running antechamber
(Tue Mar 26 2013 - 02:22:14 PDT)
Re: [AMBER] angle between two plan
(Sat Mar 16 2013 - 06:37:57 PDT)
Re: [AMBER] angle between two plan
(Fri Mar 15 2013 - 17:42:47 PDT)
Re: [AMBER] QM/MM restart problem
(Thu Mar 14 2013 - 12:49:54 PDT)
Re: [AMBER] angle between two plan
(Thu Mar 14 2013 - 11:26:21 PDT)
Mark Healey
[AMBER] RXSGLD Simulation Error
(Fri Mar 22 2013 - 13:05:49 PDT)
[AMBER] RXSGLD Simulation Error
(Thu Mar 21 2013 - 12:53:27 PDT)
mark94025.comcast.net
[AMBER] March 5, 2013 Webinar: AMBER and Kepler GPUs
(Thu Feb 28 2013 - 21:00:11 PST)
Marko Wehle
Re: [AMBER] WG: tleap output of mol2 format with incorrect bond order
(Fri Mar 08 2013 - 08:51:45 PST)
[AMBER] WG: tleap output of mol2 format with incorrect bond order
(Thu Mar 07 2013 - 10:44:28 PST)
[AMBER] tleap output of mol2 format with incorrect bond order
(Thu Mar 07 2013 - 09:08:23 PST)
Marta Perez
Re: [AMBER] leap insert missing atoms in aminoacids according to ...
(Tue Mar 19 2013 - 05:34:18 PDT)
Re: [AMBER] leap insert missing atoms in aminoacids according to ...
(Tue Mar 19 2013 - 03:25:51 PDT)
Mary Varughese
Re: [AMBER] PMEMD in amber12
(Mon Mar 18 2013 - 22:31:27 PDT)
Re: [AMBER] PMEMD in amber12
(Mon Mar 18 2013 - 10:58:36 PDT)
Re: [AMBER] PMEMD in amber12
(Fri Mar 15 2013 - 10:01:20 PDT)
Re: [AMBER] PMEMD in amber12
(Fri Mar 15 2013 - 09:23:53 PDT)
[AMBER] modified dna
(Fri Mar 15 2013 - 02:45:49 PDT)
Re: [AMBER] PMEMD in amber12
(Thu Mar 14 2013 - 20:20:54 PDT)
[AMBER] PMEMD in amber12
(Thu Mar 14 2013 - 08:04:05 PDT)
Massimiliano Porrini
Re: [AMBER] Amber MD using NAMD
(Fri Mar 01 2013 - 01:58:01 PST)
Matthew Zwier
Re: [AMBER] QM/MM restart problem
(Thu Mar 14 2013 - 11:54:59 PDT)
Miguel Ortiz Lombardia
Re: [AMBER] mmpbsa calculations on a PROTEIN/DNA/LIGAND ternary complex
(Wed Mar 20 2013 - 10:52:29 PDT)
Miguel Ortiz Lombardía
Re: [AMBER] R: mmpbsa calculations for a ternary protein/dna/ligand complex
(Fri Mar 22 2013 - 03:32:02 PDT)
Re: [AMBER] mmpbsa calculations for a ternary protein/dna/ligand complex in presence of cocrystalized Mg ions
(Thu Mar 21 2013 - 08:52:58 PDT)
Re: [AMBER] R: mmpbsa calculations on a PROTEIN/DNA/LIGAND ternary complex
(Thu Mar 21 2013 - 07:44:20 PDT)
Re: [AMBER] mmpbsa calculations on a PROTEIN/DNA/LIGAND ternary complex
(Thu Mar 21 2013 - 03:18:57 PDT)
Re: [AMBER] ptraj skipping frames depending on the computer OS?
(Fri Mar 15 2013 - 03:08:35 PDT)
[AMBER] ptraj skipping frames depending on the computer OS?
(Thu Mar 14 2013 - 08:31:59 PDT)
Miro Moman
[AMBER] Antechamber: AM1-BCC charges from MOPAC output
(Tue Mar 19 2013 - 02:05:03 PDT)
Mu Xia
[AMBER] Which memory of GTX580 should I choose in 30, 000-50, 000 atoms system
(Thu Mar 21 2013 - 20:24:55 PDT)
N Nandi
[AMBER] problem in generating pbsa.phi file using PBSA
(Thu Mar 28 2013 - 22:06:09 PDT)
[AMBER] problem in generating pbsa.phi file using PBSA
(Fri Mar 22 2013 - 01:57:55 PDT)
[AMBER] problem in generating pbsa.phi file using PBSA
(Sun Mar 17 2013 - 22:15:37 PDT)
[AMBER] problem to generate pbsa.phi file using PBSA
(Thu Mar 07 2013 - 23:38:13 PST)
[AMBER] Fw: problem in calculating electrostatic potential using PBSA
(Thu Mar 07 2013 - 20:56:53 PST)
[AMBER] problem in calculating electrostatic potential using PBSA
(Sun Mar 03 2013 - 21:52:11 PST)
Nan Li
[AMBER] xleap_the hydrogen atom in C-terminus of peptides
(Wed Mar 06 2013 - 11:02:14 PST)
Neha Gandhi
Re: [AMBER] aMD simulations in AMBER 12 (GPU version) update
(Thu Mar 21 2013 - 17:20:26 PDT)
[AMBER] aMD simulations in AMBER 12 (GPU version)
(Thu Mar 21 2013 - 03:26:44 PDT)
[AMBER] ions (salt concentration) and deep energetics problem
(Mon Mar 18 2013 - 07:04:24 PDT)
[AMBER] temperature fluctuation amber ntp ensemble
(Mon Mar 04 2013 - 06:50:53 PST)
Niel Henriksen
Re: [AMBER] REMD simulation
(Thu Mar 14 2013 - 18:39:13 PDT)
Re: [AMBER] REMD simulation
(Thu Mar 14 2013 - 15:51:42 PDT)
Paul Mortenson
Re: [AMBER] Bad atom type: fe in MMPBSA calculations
(Thu Mar 14 2013 - 03:02:58 PDT)
pooja chahal
[AMBER] Amber 9
(Fri Mar 15 2013 - 20:54:22 PDT)
psu4.uic.edu
Re: [AMBER] Amber 2013 workshop
(Fri Mar 08 2013 - 09:30:28 PST)
[AMBER] Amber 2013 workshop
(Wed Mar 06 2013 - 09:31:50 PST)
R. Xiong
Re: [AMBER] QM/MM restart problem
(Thu Mar 14 2013 - 14:01:18 PDT)
Re: [AMBER] QM/MM restart problem
(Thu Mar 14 2013 - 13:13:57 PDT)
Re: [AMBER] QM/MM restart problem
(Thu Mar 14 2013 - 12:23:00 PDT)
Re: [AMBER] QM/MM restart problem
(Thu Mar 14 2013 - 11:14:09 PDT)
Re: [AMBER] QM/MM restart problem
(Thu Mar 14 2013 - 10:53:09 PDT)
[AMBER] QM/MM restart problem
(Thu Mar 14 2013 - 07:42:56 PDT)
rajith bhaskaran
Re: [AMBER] MM PBSA tutorial
(Thu Mar 28 2013 - 06:26:16 PDT)
Re: [AMBER] MM PBSA tutorial
(Thu Mar 28 2013 - 06:03:12 PDT)
Re: [AMBER] MM PBSA tutorial
(Thu Mar 28 2013 - 05:55:43 PDT)
[AMBER] MM PBSA tutorial
(Thu Mar 28 2013 - 05:42:42 PDT)
Ray Luo, Ph.D.
Re: [AMBER] problem in generating pbsa.phi file using PBSA
(Fri Mar 29 2013 - 16:39:24 PDT)
Re: [AMBER] MMPBSA calculations
(Wed Mar 27 2013 - 14:11:30 PDT)
Re: [AMBER] MMPBSA calculations
(Wed Mar 27 2013 - 11:02:45 PDT)
Re: [AMBER] problem in generating pbsa.phi file using PBSA
(Tue Mar 19 2013 - 15:10:19 PDT)
Re: [AMBER] problem in generating pbsa.phi file using PBSA
(Mon Mar 18 2013 - 14:38:31 PDT)
Re: [AMBER] Error in MMPBSA
(Wed Mar 06 2013 - 12:41:56 PST)
Re: [AMBER] Implicit membrane models
(Fri Mar 01 2013 - 12:07:11 PST)
Ross Walker
Re: [AMBER] minor development note: make symbolic link to pmemd.cuda relative instead of absolute
(Wed Mar 27 2013 - 11:07:10 PDT)
Re: [AMBER] Fwd: cudaMemcpy GpuBuffer::Download failed
(Mon Mar 25 2013 - 10:35:11 PDT)
Re: [AMBER] Fwd: cudaMemcpy GpuBuffer::Download failed
(Mon Mar 25 2013 - 10:22:05 PDT)
Re: [AMBER] NVT stacked at GPU running
(Sat Mar 23 2013 - 10:18:01 PDT)
Re: [AMBER] Which memory of GTX580 should I choose in 30, 000-50, 000 atoms system
(Fri Mar 22 2013 - 11:14:35 PDT)
Re: [AMBER] PMEMD in amber12
(Mon Mar 18 2013 - 16:34:09 PDT)
Re: [AMBER] GTX Titan was finally released
(Mon Mar 18 2013 - 15:53:11 PDT)
Re: [AMBER] NVT stacked at GPU running
(Mon Mar 18 2013 - 15:49:24 PDT)
Re: [AMBER] NVT stacked at GPU running
(Mon Mar 18 2013 - 09:17:51 PDT)
Re: [AMBER] GPU job scheduling: looking for recommendations and experiences
(Mon Mar 18 2013 - 08:04:03 PDT)
Re: [AMBER] GTX Titan was finally released
(Sat Mar 16 2013 - 18:08:47 PDT)
Re: [AMBER] PMEMD in amber12
(Fri Mar 15 2013 - 09:27:31 PDT)
Re: [AMBER] PMEMD in amber12
(Fri Mar 15 2013 - 08:27:42 PDT)
Re: [AMBER] GTX Titan was finally released
(Thu Mar 14 2013 - 11:54:28 PDT)
Re: [AMBER] PMEMD in amber12
(Thu Mar 14 2013 - 08:46:16 PDT)
Re: [AMBER] Problem in parallel installation of Amber 12
(Tue Mar 12 2013 - 09:55:51 PDT)
Re: [AMBER] Amber12 MPI OK on one node but not across nodes
(Tue Mar 12 2013 - 09:50:58 PDT)
Re: [AMBER] Problem in parallel installation of Amber 12
(Tue Mar 12 2013 - 08:53:56 PDT)
Re: [AMBER] NVIDIA GTX-675
(Tue Mar 12 2013 - 07:57:48 PDT)
Re: [AMBER] GTX 460 ?
(Mon Mar 11 2013 - 08:20:22 PDT)
Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure
(Thu Mar 07 2013 - 21:02:19 PST)
Re: [AMBER] temperature fluctuation amber ntp ensemble
(Thu Mar 07 2013 - 20:09:46 PST)
Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure
(Thu Mar 07 2013 - 19:53:33 PST)
Re: [AMBER] Amber 2013 workshop
(Wed Mar 06 2013 - 10:31:28 PST)
safwat abdel-azeim
Re: [AMBER] RESP charges for iron-sulfur cluster
(Fri Mar 15 2013 - 10:51:21 PDT)
Re: [AMBER] RESP charges for iron-sulfur cluster
(Fri Mar 15 2013 - 05:33:28 PDT)
Re: [AMBER] RESP charges for iron-sulfur cluster
(Mon Mar 11 2013 - 04:57:59 PDT)
[AMBER] RESP charges for iron-sulfur cluster
(Mon Mar 11 2013 - 02:42:45 PDT)
Saugata Hazra
Re: [AMBER] Error in MMPBSA
(Wed Mar 06 2013 - 15:30:12 PST)
Re: [AMBER] Error in MMPBSA
(Wed Mar 06 2013 - 14:52:22 PST)
Re: [AMBER] Error in MMPBSA
(Wed Mar 06 2013 - 12:50:15 PST)
[AMBER] Error in MMPBSA
(Wed Mar 06 2013 - 12:30:00 PST)
Scott Le Grand
Re: [AMBER] Fwd: cudaMemcpy GpuBuffer::Download failed
(Mon Mar 25 2013 - 10:32:07 PDT)
Re: [AMBER] NVT stacked at GPU running
(Mon Mar 18 2013 - 09:22:34 PDT)
Re: [AMBER] GTX Titan was finally released
(Thu Mar 14 2013 - 12:14:57 PDT)
Re: [AMBER] GTX 460 ?
(Tue Mar 12 2013 - 10:39:58 PDT)
Re: [AMBER] GPU overload
(Mon Mar 04 2013 - 16:43:11 PST)
Shashidhar Rao
[AMBER] Fwd: failed to run sander ....
(Thu Mar 07 2013 - 11:13:58 PST)
Shruti Koulgi
[AMBER] tutorial on thermodynamic integration
(Tue Mar 19 2013 - 04:44:53 PDT)
[AMBER] Thermodynamic Integration
(Tue Mar 12 2013 - 05:25:47 PDT)
siddharth kesharwani
Re: [AMBER] Bad atom type: fe in MMPBSA calculations
(Thu Mar 14 2013 - 02:18:30 PDT)
Re: [AMBER] Bad atom type: fe in MMPBSA calculations
(Wed Mar 13 2013 - 22:57:26 PDT)
[AMBER] Query on Steered Molecular Dynamics
(Wed Mar 13 2013 - 04:29:51 PDT)
[AMBER] Query On Steered Molecular Dynamics
(Tue Mar 05 2013 - 05:01:34 PST)
Sindrila Dutta banik
[AMBER] Problem to save a particular snapshot from the trajectory
(Tue Mar 19 2013 - 05:56:01 PDT)
[AMBER] how to save a snapshot from the trajectory
(Mon Mar 18 2013 - 23:25:07 PDT)
somedatta pal
[AMBER] How protein-water electrostatic interaction can be turned off keeping protein-protein vdw, protein-protein (vdw+elect) and water-water (vdw+elect) intact
(Wed Mar 20 2013 - 03:28:42 PDT)
steinbrt.rci.rutgers.edu
Re: [AMBER] MM PBSA tutorial
(Thu Mar 28 2013 - 08:05:40 PDT)
Re: [AMBER] MM PBSA tutorial
(Thu Mar 28 2013 - 06:16:56 PDT)
Re: [AMBER] MM PBSA tutorial
(Thu Mar 28 2013 - 05:46:31 PDT)
Re: [AMBER] Meaning of electrostatic pairwise interaction in GB/PBSA
(Wed Mar 20 2013 - 07:20:35 PDT)
Re: [AMBER] How protein-water electrostatic interaction can be turned off keeping protein-protein vdw, protein-protein (vdw+elect) and water-water (vdw+elect) intact
(Wed Mar 20 2013 - 03:34:02 PDT)
Re: [AMBER] Hydration Free Enery by TI
(Wed Mar 20 2013 - 02:36:19 PDT)
Re: [AMBER] Hydration Free Enery by TI
(Tue Mar 19 2013 - 04:07:27 PDT)
Re: [AMBER] Hydration Free Enery by TI
(Tue Mar 19 2013 - 04:00:39 PDT)
Re: [AMBER] Hydration Free Enery by TI
(Fri Mar 15 2013 - 17:28:29 PDT)
Re: [AMBER] angle between two plan
(Fri Mar 15 2013 - 17:17:52 PDT)
Re: [AMBER] Question about AM1BCC
(Thu Mar 14 2013 - 09:40:49 PDT)
Re: [AMBER] Softcore selection
(Fri Mar 01 2013 - 00:41:48 PST)
Steven M. Graham
Re: [AMBER] [AMBER: gauche effect in OS-CT-CT-F
(Sat Mar 09 2013 - 13:42:14 PST)
sudipta
Re: [AMBER] REMD simulation
(Fri Mar 15 2013 - 09:25:31 PDT)
Re: [AMBER] REMD simulation
(Fri Mar 15 2013 - 09:24:35 PDT)
Re: [AMBER] REMD simulation
(Thu Mar 14 2013 - 16:51:42 PDT)
Re: [AMBER] REMD simulation
(Thu Mar 14 2013 - 16:28:52 PDT)
Re: [AMBER] REMD simulation
(Thu Mar 14 2013 - 16:07:41 PDT)
[AMBER] REMD simulation
(Thu Mar 14 2013 - 10:06:51 PDT)
Sumra Wajid Abbasi 30-FBAS/MSBI/F09
[AMBER] Error while generating B factor Graph
(Tue Mar 19 2013 - 02:55:10 PDT)
Sun
[AMBER] ptraj action command
(Sun Mar 03 2013 - 18:57:49 PST)
Symon Gathiaka
Re: [AMBER] How to use AMBER parameters for modified amino acids
(Sat Mar 23 2013 - 10:38:43 PDT)
[AMBER] How to use AMBER parameters for modified amino acids
(Wed Mar 20 2013 - 14:27:37 PDT)
Terry
Re: [AMBER] Build DNA structure based on squence
(Fri Mar 01 2013 - 01:51:52 PST)
Theodosia Teo
[AMBER] RMSD Fluctuation
(Tue Mar 05 2013 - 19:28:40 PST)
Thomas Evangelidis
Re: [AMBER] Estimating time in AMD
(Sat Mar 02 2013 - 05:48:07 PST)
tianchuan881
[AMBER] problem
(Thu Mar 14 2013 - 00:13:54 PDT)
[AMBER] charge problem
(Wed Mar 13 2013 - 04:13:18 PDT)
[AMBER] frcmod problem
(Tue Mar 12 2013 - 06:50:03 PDT)
[AMBER] frcmod file problem
(Tue Mar 12 2013 - 06:09:22 PDT)
[AMBER] ligand molecule problem
(Sun Mar 10 2013 - 20:08:09 PDT)
Tong ZHU
[AMBER] Build DNA structure based on squence
(Fri Mar 01 2013 - 01:48:25 PST)
Tu Zhiping
[AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure
(Thu Mar 07 2013 - 19:12:38 PST)
uday spike
Re: [AMBER] trajin: command not found
(Thu Mar 14 2013 - 05:22:41 PDT)
[AMBER] trajin: command not found
(Tue Mar 12 2013 - 07:31:45 PDT)
Urszula Uciechowska
[AMBER] disulfide bonds
(Fri Mar 08 2013 - 06:03:42 PST)
Vaibhav Dixit
Re: [AMBER] one sided connection warning HEM P450 MD input files
(Thu Mar 28 2013 - 22:17:19 PDT)
Re: [AMBER] cpptraj
(Tue Mar 26 2013 - 20:33:11 PDT)
Re: [AMBER] problem combining trajectories with diff. number of residues
(Tue Mar 26 2013 - 20:20:01 PDT)
Re: [AMBER] problem combining trajectories with diff. number of residues
(Tue Mar 26 2013 - 04:11:28 PDT)
Re: [AMBER] patching unsuccessful even after modifying patch_amber.py
(Mon Mar 25 2013 - 06:26:41 PDT)
Re: [AMBER] patching unsuccessful even after modifying patch_amber.py
(Mon Mar 25 2013 - 06:16:53 PDT)
Re: [AMBER] patching unsuccessful even after modifying patch_amber.py
(Mon Mar 25 2013 - 03:49:36 PDT)
Re: [AMBER] patching unsuccessful even after modifying patch_amber.py
(Mon Mar 25 2013 - 03:17:05 PDT)
Re: [AMBER] patching unsuccessful even after modifying patch_amber.py
(Sun Mar 24 2013 - 23:04:02 PDT)
Re: [AMBER] patching unsuccessful even after modifying patch_amber.py
(Sun Mar 24 2013 - 22:43:41 PDT)
[AMBER] patching unsuccessful even after modifying patch_amber.py
(Sun Mar 24 2013 - 05:17:50 PDT)
[AMBER] one sided connection warning HEM P450 MD input files
(Sat Mar 23 2013 - 22:53:15 PDT)
Re: [AMBER] IED web link to essential dynamics is broken
(Sat Mar 23 2013 - 21:34:50 PDT)
Re: [AMBER] problem combining trajectories with diff. number of residues
(Wed Mar 20 2013 - 22:07:03 PDT)
Re: [AMBER] problem combining trajectories with diff. number of residues
(Tue Mar 19 2013 - 21:33:36 PDT)
[AMBER] IED web link to essential dynamics is broken
(Tue Mar 19 2013 - 05:20:49 PDT)
[AMBER] problem combining trajectories with diff. number of residues
(Tue Mar 19 2013 - 00:28:12 PDT)
Re: [AMBER] generate prepin from mol2 which has charges/atom types for Heme
(Mon Mar 11 2013 - 08:24:57 PDT)
Re: [AMBER] generate prepin from mol2 which has charges/atom types for Heme
(Sun Mar 10 2013 - 21:37:45 PDT)
[AMBER] generate prepin from mol2 which has charges/atom types for Heme
(Sun Mar 10 2013 - 03:23:17 PDT)
Vijay Manickam Achari
[AMBER] rotational diffusion via cpptraj
(Fri Mar 29 2013 - 04:11:12 PDT)
Vishal Maingi
Re: [AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA
(Tue Mar 05 2013 - 05:10:21 PST)
Re: [AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA
(Tue Mar 05 2013 - 04:54:21 PST)
Vivek Shankar Bharadwaj
[AMBER] Ante-mmpbsa.py error
(Tue Mar 19 2013 - 10:22:57 PDT)
Re: [AMBER] MMPBSA jobs on a cluster Calcerror:
(Wed Mar 06 2013 - 14:26:53 PST)
Re: [AMBER] MMPBSA jobs on a cluster Calcerror:
(Wed Mar 06 2013 - 14:00:14 PST)
Re: [AMBER] MMPBSA jobs on a cluster Calcerror:
(Wed Mar 06 2013 - 12:36:30 PST)
[AMBER] MMPBSA jobs on a cluster Calcerror:
(Wed Mar 06 2013 - 12:05:01 PST)
Vlad Cojocaru
Re: [AMBER] ff10 with ILDN + Best&Hummer modifications
(Thu Mar 28 2013 - 07:17:39 PDT)
[AMBER] ff10 with ILDN + Best&Hummer modifications
(Thu Mar 28 2013 - 03:56:59 PDT)
Re: [AMBER] IED web link to essential dynamics is broken
(Tue Mar 19 2013 - 06:40:49 PDT)
Re: [AMBER] angle between two plan
(Sat Mar 16 2013 - 05:59:11 PDT)
Weinzierl, Robert O J
Re: [AMBER] Amber Digest, Vol. 458, Issue 1, Topic 1 pmemd.cuda compilation problems on Ubuntu 12.4 (Daniel Roe)
(Mon Mar 25 2013 - 04:01:10 PDT)
[AMBER] pmemd.cuda compilation problems on Ubuntu 12.4
(Wed Mar 20 2013 - 10:56:51 PDT)
Xioling Chuang
Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 530 C5' CI
(Thu Mar 28 2013 - 08:56:21 PDT)
[AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 530 C5' CI
(Thu Mar 28 2013 - 08:25:51 PDT)
Ye MEI
Re: [AMBER] bug report: tinker_to_amberfailedforsystemscontainingcounter ions
(Thu Mar 14 2013 - 09:43:58 PDT)
Re: [AMBER] bug report: tinker_to_amberfailedforsystemscontainingcounter ions
(Wed Mar 13 2013 - 07:48:07 PDT)
Re: [AMBER] bug report: tinker_to_amber failedforsystemscontainingcounter ions
(Fri Mar 08 2013 - 07:35:35 PST)
Re: [AMBER] bug report: tinker_to_amber failed forsystemscontainingcounter ions
(Thu Mar 07 2013 - 02:31:24 PST)
Re: [AMBER] bug report: tinker_to_amber failed for systemscontainingcounter ions
(Wed Mar 06 2013 - 18:23:58 PST)
Re: [AMBER] bug report: tinker_to_amber failed for systems containingcounter ions
(Wed Mar 06 2013 - 00:19:25 PST)
[AMBER] bug report: tinker_to_amber failed for systems containing counter ions
(Mon Mar 04 2013 - 20:54:51 PST)
Yew Mun Yip
[AMBER] Problem with Alanine Scanning using MMPBSA.py with Terminal Residues
(Mon Mar 18 2013 - 20:54:52 PDT)
Yun Shi
[AMBER] '.' follows exponent in NUMBER-like thing
(Sun Mar 24 2013 - 12:15:15 PDT)
YZ Qin
Re: [AMBER] antechamber dCTP
(Fri Mar 08 2013 - 08:01:32 PST)
Re: [AMBER] antechamber dCTP
(Thu Mar 07 2013 - 06:35:02 PST)
Re: [AMBER] antechamber dCTP
(Thu Mar 07 2013 - 01:17:47 PST)
Re: [AMBER] antechamber dCTP
(Thu Mar 07 2013 - 01:13:16 PST)
[AMBER] antechamber dCTP
(Wed Mar 06 2013 - 17:56:44 PST)
zhenquan hu
[AMBER] restraint domains
(Fri Mar 01 2013 - 08:42:15 PST)
涂志萍
Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure
(Sun Mar 17 2013 - 20:14:58 PDT)
Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure
(Sat Mar 16 2013 - 02:49:57 PDT)
Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure
(Sun Mar 10 2013 - 07:20:16 PDT)
Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure
(Thu Mar 07 2013 - 20:51:01 PST)
纪晓峰
Re: [AMBER] the protein was crashed
(Mon Mar 25 2013 - 19:24:25 PDT)
Re: [AMBER] the protein was crashed
(Mon Mar 25 2013 - 19:23:24 PDT)
[AMBER] the protein was crashed
(Fri Mar 15 2013 - 00:44:55 PDT)
[AMBER] organic
(Fri Mar 15 2013 - 00:37:47 PDT)
강현아
Re: [AMBER] TIP5P water simulation
(Wed Mar 06 2013 - 07:32:59 PST)
[AMBER] TIP5P water simulation
(Wed Mar 06 2013 - 03:31:48 PST)
Last message date
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Sat Mar 30 2013 - 12:30:02 PDT
Archived on
: Fri Dec 20 2024 - 05:54:47 PST
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