Amber Archive Apr 2014 by author
545 messages
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Starting
Mon Mar 31 2014 - 10:00:04 PDT,
Ending
Wed Apr 30 2014 - 11:00:02 PDT
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ABEL Stephane 175950
Re: [AMBER] 【AMBER12】Including water when using General Amber Force Field leaprc.gaff
(Sat Apr 19 2014 - 03:47:50 PDT)
[AMBER] SDS parameters in AMBER
(Tue Apr 15 2014 - 05:39:10 PDT)
Re: [AMBER] SDS parameters in AMBER
(Tue Apr 15 2014 - 05:36:32 PDT)
Adrian Roitberg
Re: [AMBER] SHAWKTRAJ, a new trajectory analysis tool
(Tue Apr 01 2014 - 07:02:55 PDT)
Ahmed Ayoub
[AMBER] Normal mode for truncated system
(Wed Apr 02 2014 - 11:45:19 PDT)
Ahmet Yıldırım
Re: [AMBER] Calculation of charges, force constanst, bonds, angles of a ligand using antechamber and gaussian
(Sat Apr 26 2014 - 05:22:51 PDT)
Re: [AMBER] Calculation of charges, force constanst, bonds, angles of a ligand using antechamber and gaussian
(Fri Apr 25 2014 - 23:57:41 PDT)
[AMBER] Calculation of charges, force constanst, bonds, angles of a ligand using antechamber and gaussian
(Fri Apr 25 2014 - 01:07:26 PDT)
Re: [AMBER] RESP procedure
(Mon Apr 21 2014 - 21:13:30 PDT)
[AMBER] RESP procedure
(Mon Apr 21 2014 - 08:51:47 PDT)
Re: [AMBER] updates for amber12 bugfix18
(Mon Apr 21 2014 - 05:43:04 PDT)
Re: [AMBER] updates for amber12 bugfix18
(Mon Apr 21 2014 - 04:49:29 PDT)
[AMBER] updates for amber12 bugfix18
(Mon Apr 21 2014 - 03:43:14 PDT)
amr hamed
[AMBER] WHAM Analysis Histograms
(Tue Apr 01 2014 - 21:33:50 PDT)
Andre C. Stiel
Re: [AMBER] PCA analysis
(Tue Apr 29 2014 - 08:55:22 PDT)
Arun Kumar Somavarapu
Re: [AMBER] MMPBSA calculation with entropy
(Wed Apr 02 2014 - 02:11:07 PDT)
arundhati dutta
[AMBER] About Clustering
(Thu Apr 24 2014 - 15:05:10 PDT)
Arunima Shilpi
[AMBER] MMPBSA query
(Thu Apr 24 2014 - 23:07:32 PDT)
[AMBER] positive value of delta G in MMPBSA calculation
(Wed Apr 23 2014 - 20:08:09 PDT)
[AMBER] error in running entropy
(Sat Apr 19 2014 - 21:55:36 PDT)
[AMBER] error in loading protein
(Mon Apr 07 2014 - 23:05:11 PDT)
[AMBER] error in reading protein file
(Mon Apr 07 2014 - 22:58:18 PDT)
[AMBER] entropy calculation mmpbsa_nm
(Mon Apr 07 2014 - 04:35:15 PDT)
[AMBER] Protein-ligand interaction
(Sun Apr 06 2014 - 09:05:28 PDT)
[AMBER] protein-ligand interaction
(Sat Apr 05 2014 - 21:07:04 PDT)
[AMBER] ligand residue interaction
(Sat Apr 05 2014 - 20:37:53 PDT)
[AMBER] ligand residue interaction
(Sat Apr 05 2014 - 20:00:39 PDT)
[AMBER] Ligand-residue interaction plot
(Sat Apr 05 2014 - 04:39:54 PDT)
[AMBER] Ligand-residue interaction plot
(Sat Apr 05 2014 - 00:08:37 PDT)
Asaminew Haile
Re: [AMBER] strip some atoms to compute RMSD
(Tue Apr 22 2014 - 08:50:47 PDT)
Re: [AMBER] strip some atoms to compute RMSD
(Tue Apr 22 2014 - 05:12:19 PDT)
Re: [AMBER] error in input file /nmropt=1
(Wed Apr 09 2014 - 03:46:27 PDT)
Re: [AMBER] error in input file /nmropt=1
(Tue Apr 08 2014 - 06:03:31 PDT)
ASFARINA AMIR HASSAN
Re: [AMBER] Error: invalid argument launching kernel kNLGenerateSpatialHash
(Sun Apr 27 2014 - 22:51:54 PDT)
[AMBER] Error: invalid argument launching kernel kNLGenerateSpatialHash
(Thu Apr 24 2014 - 02:01:44 PDT)
Ashutosh Shandilya
Re: [AMBER] REMD with pmemd.cuda
(Tue Apr 08 2014 - 05:45:09 PDT)
Re: [AMBER] REMD with pmemd.cuda
(Tue Apr 08 2014 - 04:54:23 PDT)
Ayesha Fatima
Re: [AMBER] MM-PBSA for two drug molecules
(Thu Apr 24 2014 - 05:18:18 PDT)
Re: [AMBER] GPU not being recognised
(Mon Mar 31 2014 - 09:52:05 PDT)
Bill Ross
Re: [AMBER] truncatiing water molecules
(Mon Apr 21 2014 - 21:13:08 PDT)
Re: [AMBER] Generate a pdb with unique atom names
(Sun Apr 13 2014 - 13:30:24 PDT)
Re: [AMBER] Bad atom type: C0
(Fri Apr 04 2014 - 12:00:29 PDT)
Re: [AMBER] SHAWKTRAJ, a new trajectory analysis tool
(Tue Apr 01 2014 - 18:04:43 PDT)
Re: [AMBER] Possible bug in xleap
(Tue Apr 01 2014 - 16:44:23 PDT)
Brian Radak
Re: [AMBER] How to extract each frame of a trajectory as individual .mdcrd files?
(Wed Apr 30 2014 - 06:43:51 PDT)
Re: [AMBER] making test not successful in ambertool14
(Thu Apr 17 2014 - 06:24:42 PDT)
Re: [AMBER] Nonbond Energy for Single Water Molecule ?
(Mon Apr 14 2014 - 08:08:41 PDT)
[AMBER] rism1d error
(Fri Apr 11 2014 - 17:19:08 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Wed Apr 09 2014 - 10:29:48 PDT)
Re: [AMBER] error in input file /nmropt=1
(Tue Apr 08 2014 - 06:49:49 PDT)
Brown, Kyle
[AMBER] Hofmeister Effects
(Fri Apr 25 2014 - 09:47:38 PDT)
Carlos Romero
Re: [AMBER] antechamber problem
(Wed Apr 23 2014 - 09:23:36 PDT)
Re: [AMBER] antechamber problem
(Tue Apr 22 2014 - 11:23:22 PDT)
Re: [AMBER] antechamber problem
(Tue Apr 22 2014 - 10:17:52 PDT)
[AMBER] antechamber problem
(Mon Apr 21 2014 - 21:51:02 PDT)
Carlos Simmerling
Re: [AMBER] Quantification of alpha helix
(Tue Apr 29 2014 - 08:34:46 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Wed Apr 09 2014 - 10:47:23 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Mon Apr 07 2014 - 12:48:18 PDT)
Re: [AMBER] igb=1
(Fri Apr 04 2014 - 04:40:38 PDT)
Cenk \(Jenk\) Andac
Re: [AMBER] pmemd.cuda.mpi installation
(Sun Apr 06 2014 - 10:47:04 PDT)
Re: [AMBER] pmemd.cuda.mpi installation
(Thu Apr 03 2014 - 11:47:33 PDT)
[AMBER] pmemd.cuda.mpi installation
(Thu Apr 03 2014 - 10:28:34 PDT)
[AMBER] pmemd.cuda.mpi installation
(Thu Apr 03 2014 - 09:29:01 PDT)
[AMBER] pmemd.cuda.mpi installation
(Thu Apr 03 2014 - 09:03:27 PDT)
Christina Bergonzo
Re: [AMBER] Really Weird Problem with Replica Exchange
(Tue Apr 08 2014 - 07:46:33 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Mon Apr 07 2014 - 13:08:28 PDT)
Christopher A Thiebaut
Re: [AMBER] diferent results
(Tue Apr 22 2014 - 08:03:43 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Wed Apr 09 2014 - 11:19:32 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Wed Apr 09 2014 - 10:36:23 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Wed Apr 09 2014 - 10:32:46 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Wed Apr 09 2014 - 10:20:32 PDT)
Re: [AMBER] I make box with solvatebox complex TIP3PBOX 15.0 and unfilled gap remains near wall
(Wed Apr 09 2014 - 10:13:00 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Wed Apr 09 2014 - 10:05:06 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Mon Apr 07 2014 - 13:21:54 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Mon Apr 07 2014 - 13:02:28 PDT)
[AMBER] Really Weird Problem with Replica Exchange
(Mon Apr 07 2014 - 11:58:26 PDT)
CHRISTOPHER PATRICK MCNARY
[AMBER] Why do I get an error in antechamber when a metal is involved?
(Fri Apr 04 2014 - 12:24:10 PDT)
[AMBER] Why do I get an error in antechamber when a metal is involved?
(Fri Apr 04 2014 - 12:01:43 PDT)
Daniel Roe
Re: [AMBER] PCA analysis
(Tue Apr 29 2014 - 09:05:39 PDT)
Re: [AMBER] Minimization with (0, 0, 0) coordinates
(Tue Apr 29 2014 - 08:30:08 PDT)
Re: [AMBER] Native Contact Help
(Mon Apr 28 2014 - 12:28:18 PDT)
Re: [AMBER] Native Contact Help
(Mon Apr 28 2014 - 12:22:56 PDT)
Re: [AMBER] Accelerated MD
(Sun Apr 27 2014 - 17:26:08 PDT)
Re: [AMBER] Corresponding PDB and snapshot PDB
(Sun Apr 27 2014 - 12:59:49 PDT)
Re: [AMBER] Native Contact Help
(Sat Apr 26 2014 - 09:44:45 PDT)
Re: [AMBER] problem with installation amber12 and ambertools13 in ubuntu
(Sat Apr 26 2014 - 09:28:50 PDT)
Re: [AMBER] problems with Amber12 installation - cuda and mpi
(Fri Apr 25 2014 - 21:03:45 PDT)
Re: [AMBER] average problem........
(Fri Apr 25 2014 - 06:53:11 PDT)
Re: [AMBER] OpenMP and MKL
(Thu Apr 24 2014 - 07:15:35 PDT)
Re: [AMBER] Error with quasi-harmonic MMPBSA.py calculations
(Tue Apr 22 2014 - 17:10:49 PDT)
Re: [AMBER] Native Contact Help
(Tue Apr 22 2014 - 08:18:12 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Tue Apr 22 2014 - 07:31:11 PDT)
Re: [AMBER] strip some atoms to compute RMSD
(Tue Apr 22 2014 - 07:10:32 PDT)
Re: [AMBER] Can I do PCA on simply a particular domain of the whole protein?
(Mon Apr 21 2014 - 07:34:15 PDT)
Re: [AMBER] PCA analysis and histogram
(Mon Apr 21 2014 - 07:30:14 PDT)
Re: [AMBER] FW: How to use "divergence" command
(Mon Apr 21 2014 - 07:24:06 PDT)
Re: [AMBER] Combining trajectories with velocities
(Sat Apr 19 2014 - 15:57:44 PDT)
Re: [AMBER] Combining trajectories with velocities
(Sat Apr 19 2014 - 14:59:01 PDT)
Re: [AMBER] How to use "divergence" command
(Fri Apr 18 2014 - 13:05:56 PDT)
Re: [AMBER] rdf averaging problem
(Tue Apr 15 2014 - 13:43:13 PDT)
Re: [AMBER] rdf averaging problem
(Mon Apr 14 2014 - 12:12:26 PDT)
Re: [AMBER] PCA analysis and histogram
(Mon Apr 14 2014 - 08:20:46 PDT)
Re: [AMBER] rdf averaging problem
(Fri Apr 11 2014 - 12:57:42 PDT)
Re: [AMBER] rdf averaging problem
(Fri Apr 11 2014 - 11:33:49 PDT)
Re: [AMBER] comparing RDF plots
(Wed Apr 09 2014 - 12:20:15 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Wed Apr 09 2014 - 10:27:10 PDT)
Re: [AMBER] number of ions (integral) too much in RDF plot
(Wed Apr 09 2014 - 07:28:19 PDT)
Re: [AMBER] comparing RDF plots
(Wed Apr 09 2014 - 07:22:01 PDT)
Re: [AMBER] KShake problem with GPU
(Wed Apr 09 2014 - 07:11:15 PDT)
Re: [AMBER] averaged NMR distance
(Mon Apr 07 2014 - 07:49:45 PDT)
Re: [AMBER] Principal component analysis
(Sat Apr 05 2014 - 08:02:07 PDT)
Re: [AMBER] Error: Could not parse mask [(:1]: radial calculation
(Thu Apr 03 2014 - 15:48:11 PDT)
Re: [AMBER] distance in one plane
(Thu Apr 03 2014 - 13:08:51 PDT)
Re: [AMBER] leap error
(Thu Apr 03 2014 - 09:06:06 PDT)
Re: [AMBER] leap error
(Thu Apr 03 2014 - 08:58:42 PDT)
Re: [AMBER] Asking about using Vector Analysis: Thermo
(Thu Apr 03 2014 - 07:31:21 PDT)
David A Case
Re: [AMBER] Extract velocity from the restart file
(Tue Apr 29 2014 - 17:54:30 PDT)
Re: [AMBER] Simulation of protein- cyclic nucleotide complex
(Tue Apr 29 2014 - 10:12:38 PDT)
Re: [AMBER] Simulation of protein- cyclic nucleotide complex
(Tue Apr 29 2014 - 04:54:12 PDT)
Re: [AMBER] negative dihedral energy with ff14ipq
(Mon Apr 28 2014 - 04:39:01 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Mon Apr 28 2014 - 04:36:50 PDT)
Re: [AMBER] Corresponding PDB and snapshot PDB
(Sun Apr 27 2014 - 05:33:50 PDT)
Re: [AMBER] problem with installation amber12 and ambertools13 in ubuntu
(Sat Apr 26 2014 - 06:13:48 PDT)
Re: [AMBER] simulated annelaing of protein ligand complex
(Fri Apr 25 2014 - 12:18:18 PDT)
Re: [AMBER] Question about volume when switching from NPT to NVE ensemble
(Thu Apr 24 2014 - 12:31:35 PDT)
Re: [AMBER] installation error
(Thu Apr 24 2014 - 11:37:20 PDT)
Re: [AMBER] MM-PBSA for two drug molecules
(Thu Apr 24 2014 - 06:29:54 PDT)
Re: [AMBER] MM-PBSA for two drug molecules
(Thu Apr 24 2014 - 05:07:49 PDT)
Re: [AMBER] AMBER minimization problem
(Thu Apr 24 2014 - 05:00:56 PDT)
Re: [AMBER] modified residues
(Thu Apr 24 2014 - 04:56:05 PDT)
Re: [AMBER] temperature increments
(Thu Apr 24 2014 - 04:50:09 PDT)
Re: [AMBER] AMBER minimization problem
(Wed Apr 23 2014 - 10:27:07 PDT)
Re: [AMBER] xmin
(Wed Apr 23 2014 - 04:44:40 PDT)
Re: [AMBER] antechamber problem
(Tue Apr 22 2014 - 11:05:34 PDT)
Re: [AMBER] making test not successful in ambertool14
(Thu Apr 17 2014 - 09:44:27 PDT)
[AMBER] Announcement: Release of Amber14 and AmberTools14
(Tue Apr 15 2014 - 13:35:18 PDT)
Re: [AMBER] distance restraint
(Mon Apr 14 2014 - 05:05:46 PDT)
[AMBER] Mailing list problems
(Fri Apr 11 2014 - 08:02:26 PDT)
Re: [AMBER] antechamber
(Thu Apr 10 2014 - 09:34:38 PDT)
Re: [AMBER] I make box with solvatebox complex TIP3PBOX 15.0 and unfilled gap remains near wall
(Wed Apr 09 2014 - 05:59:57 PDT)
Re: [AMBER] Asking about using Vector Analysis: Thermo
(Tue Apr 08 2014 - 09:08:44 PDT)
Re: [AMBER] error in input file /nmropt=1
(Tue Apr 08 2014 - 09:02:30 PDT)
Re: [AMBER] Karplus J-coupling
(Tue Apr 08 2014 - 05:24:27 PDT)
Re: [AMBER] antechamber
(Mon Apr 07 2014 - 12:12:13 PDT)
Re: [AMBER] averaged NMR distance
(Mon Apr 07 2014 - 04:52:05 PDT)
Re: [AMBER] pmemd.cuda.mpi installation
(Sun Apr 06 2014 - 10:55:19 PDT)
Re: [AMBER] ATOMIC NUMBER section in prmtop file - Sustiva example:potential bug
(Sat Apr 05 2014 - 10:59:34 PDT)
Re: [AMBER] Why do I get an error in antechamber when a metal is involved?
(Fri Apr 04 2014 - 12:56:00 PDT)
Re: [AMBER] antechamber
(Thu Apr 03 2014 - 09:26:56 PDT)
Re: [AMBER] Fw: loading multiple prepin file in xleap - gives warning
(Thu Apr 03 2014 - 04:45:20 PDT)
Re: [AMBER] Asking about using Vector Analysis: Thermo
(Thu Apr 03 2014 - 04:41:13 PDT)
de Waal, Parker
Re: [AMBER] Simulation of protein- cyclic nucleotide complex
(Mon Apr 28 2014 - 05:19:55 PDT)
Re: [AMBER] new error
(Fri Apr 04 2014 - 06:28:41 PDT)
Re: [AMBER] new error
(Fri Apr 04 2014 - 05:58:39 PDT)
Eugene Yedvabny
[AMBER] OpenMP and MKL
(Wed Apr 23 2014 - 16:21:23 PDT)
Re: [AMBER] Combining trajectories with velocities
(Sat Apr 19 2014 - 15:43:02 PDT)
[AMBER] Combining trajectories with velocities
(Sat Apr 19 2014 - 11:01:29 PDT)
Fabian Glaser
Re: [AMBER] MM-PBSA for two drug molecules
(Tue Apr 29 2014 - 23:41:28 PDT)
Re: [AMBER] MM-PBSA for two drug molecules
(Sun Apr 27 2014 - 21:38:11 PDT)
Re: [AMBER] MM-PBSA for two drug molecules
(Thu Apr 24 2014 - 05:34:24 PDT)
Re: [AMBER] MM-PBSA for two drug molecules
(Thu Apr 24 2014 - 04:48:05 PDT)
[AMBER] MM-PBSA for two drug molecules
(Thu Apr 24 2014 - 03:46:58 PDT)
[AMBER] small molecules
(Mon Apr 07 2014 - 05:14:14 PDT)
[AMBER] simulating small molecules systems
(Mon Apr 07 2014 - 05:10:59 PDT)
Re: [AMBER] SHAWKTRAJ, a new trajectory analysis tool
(Tue Apr 01 2014 - 04:20:10 PDT)
Fabiana Caporuscio
Re: [AMBER] xmin
(Wed Apr 23 2014 - 08:23:23 PDT)
[AMBER] xmin
(Wed Apr 23 2014 - 03:15:18 PDT)
filip fratev
Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure."
(Thu Apr 17 2014 - 09:14:31 PDT)
Filip Lankas
Re: [AMBER] reg: the charges for methylated cytosine atoms
(Wed Apr 02 2014 - 02:25:24 PDT)
FyD
Re: [AMBER] Calculation of charges, force constanst, bonds, angles of a ligand using antechamber and gaussian
(Sat Apr 26 2014 - 06:46:33 PDT)
Re: [AMBER] Calculation of charges, force constanst, bonds, angles of a ligand using antechamber and gaussian
(Sat Apr 26 2014 - 04:31:12 PDT)
Re: [AMBER] modified residues
(Wed Apr 23 2014 - 23:27:48 PDT)
Re: [AMBER] modified residues
(Wed Apr 23 2014 - 22:45:57 PDT)
Re: [AMBER] modified residues
(Wed Apr 23 2014 - 21:38:26 PDT)
Re: [AMBER] RESP procedure
(Tue Apr 22 2014 - 23:41:20 PDT)
Re: [AMBER] antechamber problem
(Tue Apr 22 2014 - 23:37:58 PDT)
Re: [AMBER] Generate a pdb with unique atom names
(Tue Apr 15 2014 - 07:06:39 PDT)
Re: [AMBER] Generate a pdb with unique atom names
(Tue Apr 15 2014 - 05:51:15 PDT)
Re: [AMBER] Generate a pdb with unique atom names
(Mon Apr 14 2014 - 22:31:31 PDT)
Re: [AMBER] Generate a pdb with unique atom names
(Mon Apr 14 2014 - 12:20:12 PDT)
Re: [AMBER] Generate a pdb with unique atom names
(Sun Apr 13 2014 - 22:08:46 PDT)
Geoffrey Gray
Re: [AMBER] Umbrella Slice module
(Mon Apr 21 2014 - 10:42:29 PDT)
[AMBER] Umbrella Slice module
(Mon Apr 21 2014 - 06:29:16 PDT)
Gustavo Seabra
Re: [AMBER] MM-PBSA for two drug molecules
(Fri Apr 25 2014 - 13:27:27 PDT)
Hamed S. Hayatshahi
Re: [AMBER] WHAM Analysis Histograms
(Wed Apr 02 2014 - 21:28:41 PDT)
Him Shweta
[AMBER] LIPID14 force field for DPPC gel phase simulation
(Fri Apr 25 2014 - 00:52:14 PDT)
HM
[AMBER] velocity information in restart file
(Mon Apr 28 2014 - 04:54:29 PDT)
Ibrahim Said
[AMBER] PCA analysis
(Tue Apr 29 2014 - 08:40:05 PDT)
[AMBER] Principal component analysis
(Fri Apr 04 2014 - 13:19:45 PDT)
Ilyas Yildirim
Re: [AMBER] MM-PBSA for two drug molecules
(Thu Apr 24 2014 - 06:12:35 PDT)
Re: [AMBER] modified residues
(Thu Apr 24 2014 - 06:00:06 PDT)
JAIME RUBIO MARTINEZ
Re: [AMBER] antechamber problem
(Tue Apr 22 2014 - 11:18:15 PDT)
Re: [AMBER] antechamber problem
(Tue Apr 22 2014 - 01:33:21 PDT)
James Starlight
Re: [AMBER] Simulation of protein- cyclic nucleotide complex
(Wed Apr 30 2014 - 06:59:00 PDT)
Re: [AMBER] Simulation of protein- cyclic nucleotide complex
(Wed Apr 30 2014 - 03:27:55 PDT)
Re: [AMBER] Simulation of protein- cyclic nucleotide complex
(Tue Apr 29 2014 - 23:53:19 PDT)
Re: [AMBER] Simulation of protein- cyclic nucleotide complex
(Tue Apr 29 2014 - 23:52:23 PDT)
Re: [AMBER] Simulation of protein- cyclic nucleotide complex
(Tue Apr 29 2014 - 23:33:49 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Tue Apr 29 2014 - 22:58:12 PDT)
Re: [AMBER] Simulation of protein- cyclic nucleotide complex
(Tue Apr 29 2014 - 11:48:11 PDT)
Re: [AMBER] Simulation of protein- cyclic nucleotide complex
(Tue Apr 29 2014 - 09:54:26 PDT)
Re: [AMBER] Simulation of protein- cyclic nucleotide complex
(Tue Apr 29 2014 - 08:34:53 PDT)
Re: [AMBER] Simulation of protein- cyclic nucleotide complex
(Tue Apr 29 2014 - 02:48:49 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Mon Apr 28 2014 - 23:20:34 PDT)
[AMBER] Simulation of protein- cyclic nucleotide complex
(Mon Apr 28 2014 - 05:02:21 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Mon Apr 28 2014 - 00:17:45 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Sun Apr 27 2014 - 23:58:58 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Sat Apr 26 2014 - 07:12:03 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Sat Apr 26 2014 - 05:35:28 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Sat Apr 26 2014 - 05:12:41 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Fri Apr 25 2014 - 07:17:19 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Fri Apr 25 2014 - 00:55:19 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Fri Apr 25 2014 - 00:27:47 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Wed Apr 23 2014 - 00:57:13 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Wed Apr 23 2014 - 03:14:20 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Tue Apr 22 2014 - 03:43:26 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Tue Apr 22 2014 - 02:49:40 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Tue Apr 22 2014 - 01:54:20 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Mon Apr 21 2014 - 07:32:12 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Mon Apr 21 2014 - 03:37:39 PDT)
[AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Mon Apr 21 2014 - 02:43:15 PDT)
Jason Swails
Re: [AMBER] ptraj in parallel
(Wed Apr 30 2014 - 10:43:18 PDT)
Re: [AMBER] How to extract each frame of a trajectory as individual .mdcrd files?
(Wed Apr 30 2014 - 08:55:26 PDT)
Re: [AMBER] Extract velocity from the restart file
(Wed Apr 30 2014 - 08:32:54 PDT)
Re: [AMBER] Minimization with restraints
(Wed Apr 30 2014 - 04:51:44 PDT)
Re: [AMBER] Simulation of protein- cyclic nucleotide complex
(Wed Apr 30 2014 - 04:43:10 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Wed Apr 30 2014 - 04:22:46 PDT)
Re: [AMBER] Simulation of protein- cyclic nucleotide complex
(Tue Apr 29 2014 - 12:38:50 PDT)
Re: [AMBER] Regarding simulation of alanine molecules in water box
(Tue Apr 29 2014 - 04:21:33 PDT)
Re: [AMBER] pmemd.cuda error amber14
(Mon Apr 28 2014 - 09:34:43 PDT)
Re: [AMBER] velocity information in restart file
(Mon Apr 28 2014 - 05:16:36 PDT)
Re: [AMBER] negative dihedral energy with ff14ipq
(Mon Apr 28 2014 - 05:13:13 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Mon Apr 28 2014 - 04:54:41 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Mon Apr 28 2014 - 04:44:45 PDT)
Re: [AMBER] negative dihedral energy with ff14ipq
(Sun Apr 27 2014 - 14:34:46 PDT)
Re: [AMBER] Accelerated MD
(Sun Apr 27 2014 - 07:01:31 PDT)
Re: [AMBER] Corresponding PDB and snapshot PDB
(Sun Apr 27 2014 - 06:50:37 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Sat Apr 26 2014 - 07:24:44 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Sat Apr 26 2014 - 05:48:25 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Sat Apr 26 2014 - 05:26:08 PDT)
Re: [AMBER] How to use Divalent ion parameters in tleap
(Fri Apr 25 2014 - 08:15:26 PDT)
Re: [AMBER] MD run
(Fri Apr 25 2014 - 08:11:44 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Fri Apr 25 2014 - 08:10:25 PDT)
Re: [AMBER] MMPBSA query
(Fri Apr 25 2014 - 04:25:41 PDT)
Re: [AMBER] MMPBSA query
(Fri Apr 25 2014 - 04:18:38 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Fri Apr 25 2014 - 04:10:38 PDT)
Re: [AMBER] AMBER minimization problem
(Thu Apr 24 2014 - 07:47:14 PDT)
Re: [AMBER] MMPBSA error
(Thu Apr 24 2014 - 07:30:40 PDT)
Re: [AMBER] could not extend the MD simulation
(Thu Apr 24 2014 - 05:44:01 PDT)
Re: [AMBER] MM-PBSA for two drug molecules
(Thu Apr 24 2014 - 04:38:45 PDT)
Re: [AMBER] Corresponding dry trajectory and PDB
(Thu Apr 24 2014 - 04:32:01 PDT)
Re: [AMBER] distance restraints
(Thu Apr 24 2014 - 04:29:08 PDT)
Re: [AMBER] Error: invalid argument launching kernel kNLGenerateSpatialHash
(Thu Apr 24 2014 - 04:26:33 PDT)
Re: [AMBER] strip some atoms to compute RMSD
(Thu Apr 24 2014 - 04:23:32 PDT)
Re: [AMBER] positive value of delta G in MMPBSA calculation
(Thu Apr 24 2014 - 04:19:25 PDT)
Re: [AMBER] OpenMP and MKL
(Wed Apr 23 2014 - 19:29:34 PDT)
Re: [AMBER] FFTW3 related error when compiling AmberTools13 on Fedora20
(Wed Apr 23 2014 - 19:02:27 PDT)
Re: [AMBER] FFTW3 related error when compiling AmberTools13 on Fedora20
(Wed Apr 23 2014 - 14:27:50 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Wed Apr 23 2014 - 04:18:49 PDT)
Re: [AMBER] xmin
(Wed Apr 23 2014 - 04:27:03 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Tue Apr 22 2014 - 04:16:47 PDT)
Re: [AMBER] Umbrella Slice module
(Mon Apr 21 2014 - 10:50:51 PDT)
Re: [AMBER] Umbrella Slice module
(Mon Apr 21 2014 - 09:58:19 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Mon Apr 21 2014 - 07:36:54 PDT)
Re: [AMBER] updates for amber12 bugfix18
(Mon Apr 21 2014 - 05:52:48 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Mon Apr 21 2014 - 04:47:33 PDT)
Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
(Mon Apr 21 2014 - 04:44:24 PDT)
Re: [AMBER] updates for amber12 bugfix18
(Mon Apr 21 2014 - 04:38:06 PDT)
Re: [AMBER] simulated annelaing condtions and requiremnets
(Sun Apr 20 2014 - 08:06:24 PDT)
Re: [AMBER] error in running entropy
(Sat Apr 19 2014 - 23:19:11 PDT)
Re: [AMBER] Running parallel simulations on different no of cores
(Sat Apr 19 2014 - 14:48:12 PDT)
Re: [AMBER] 【AMBER12】Including water when using General Amber Force Field leaprc.gaff
(Sat Apr 19 2014 - 04:44:10 PDT)
Re: [AMBER] How to use "divergence" command
(Fri Apr 18 2014 - 11:02:44 PDT)
Re: [AMBER] Regarding Interaction energy calculation
(Thu Apr 17 2014 - 07:14:12 PDT)
Re: [AMBER] Nonbond Energy for Single Water Molecule ?
(Wed Apr 16 2014 - 08:10:18 PDT)
Re: [AMBER] Regarding Interaction energy calculation
(Wed Apr 16 2014 - 05:42:31 PDT)
Re: [AMBER] Generate a pdb with unique atom names
(Mon Apr 14 2014 - 12:24:13 PDT)
Re: [AMBER] Nonbond Energy for Single Water Molecule ?
(Mon Apr 14 2014 - 08:37:58 PDT)
Re: [AMBER] Generate a pdb with unique atom names
(Mon Apr 14 2014 - 06:01:44 PDT)
Re: [AMBER] Generate a pdb with unique atom names
(Mon Apr 14 2014 - 05:10:25 PDT)
Re: [AMBER] distance restraint
(Mon Apr 14 2014 - 05:04:06 PDT)
Re: [AMBER] MMPBSA
(Mon Apr 14 2014 - 04:56:57 PDT)
Re: [AMBER] MMPBSA
(Sun Apr 13 2014 - 08:20:52 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Wed Apr 09 2014 - 11:26:59 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Wed Apr 09 2014 - 11:05:40 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Wed Apr 09 2014 - 10:50:32 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Wed Apr 09 2014 - 10:42:35 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Wed Apr 09 2014 - 10:37:11 PDT)
Re: [AMBER] I make box with solvatebox complex TIP3PBOX 15.0 and unfilled gap remains near wall
(Wed Apr 09 2014 - 10:29:52 PDT)
Re: [AMBER] Really Weird Problem with Replica Exchange
(Wed Apr 09 2014 - 10:20:34 PDT)
Re: [AMBER] Fwd: MMPBSA.py PrmtopError: Complex natom != receptor natom + ligand natom
(Wed Apr 09 2014 - 03:23:59 PDT)
Re: [AMBER] Questions about the energy of H3O+
(Tue Apr 08 2014 - 08:52:12 PDT)
Re: [AMBER] REMD with pmemd.cuda
(Tue Apr 08 2014 - 07:59:20 PDT)
Re: [AMBER] REMD with pmemd.cuda
(Tue Apr 08 2014 - 05:40:55 PDT)
Re: [AMBER] REMD with pmemd.cuda
(Tue Apr 08 2014 - 04:45:18 PDT)
Re: [AMBER] error in reading protein file
(Tue Apr 08 2014 - 04:42:09 PDT)
Re: [AMBER] When I run the pmemd.cuda, sometimes computer will be rebooted.
(Tue Apr 08 2014 - 04:35:45 PDT)
Re: [AMBER] About the error "Unable to correctly identify element CU" in QMMM simulation
(Tue Apr 08 2014 - 04:29:14 PDT)
Re: [AMBER] antechamber
(Mon Apr 07 2014 - 15:00:15 PDT)
Re: [AMBER] entropy calculation mmpbsa_nm
(Mon Apr 07 2014 - 05:07:51 PDT)
Re: [AMBER] Regarding Interaction energy calculation
(Sun Apr 06 2014 - 06:38:36 PDT)
Re: [AMBER] Ligand-residue interaction plot
(Sat Apr 05 2014 - 05:39:31 PDT)
Re: [AMBER] Bad atom type: C0
(Fri Apr 04 2014 - 16:26:31 PDT)
Re: [AMBER] Bad atom type: C0
(Fri Apr 04 2014 - 16:25:54 PDT)
Re: [AMBER] Bad atom type: C0
(Fri Apr 04 2014 - 10:25:59 PDT)
Re: [AMBER] new error
(Fri Apr 04 2014 - 05:53:45 PDT)
Re: [AMBER] leap error
(Fri Apr 04 2014 - 04:59:08 PDT)
Re: [AMBER] Error using MMPBSA.py
(Fri Apr 04 2014 - 04:35:01 PDT)
Re: [AMBER] igb=1
(Fri Apr 04 2014 - 04:30:08 PDT)
Re: [AMBER] Error: Could not parse mask [(:1]: radial calculation
(Thu Apr 03 2014 - 15:27:42 PDT)
Re: [AMBER] pmemd.cuda.mpi installation
(Thu Apr 03 2014 - 12:03:50 PDT)
Re: [AMBER] pmemd.cuda.mpi installation
(Thu Apr 03 2014 - 11:05:24 PDT)
Re: [AMBER] leap error
(Thu Apr 03 2014 - 08:57:22 PDT)
Re: [AMBER] Fw: loading multiple prepin file in xleap - gives warning
(Thu Apr 03 2014 - 04:29:14 PDT)
Re: [AMBER] truncatiing water molecules
(Wed Apr 02 2014 - 08:21:39 PDT)
Re: [AMBER] truncatiing water molecules
(Wed Apr 02 2014 - 06:52:13 PDT)
Re: [AMBER] Distance constraints
(Wed Apr 02 2014 - 06:45:17 PDT)
Re: [AMBER] truncatiing water molecules
(Wed Apr 02 2014 - 04:54:15 PDT)
Re: [AMBER] loading multiple prepin file in xleap - gives warning
(Wed Apr 02 2014 - 04:50:56 PDT)
Re: [AMBER] MMPBSA calculation with entropy
(Wed Apr 02 2014 - 04:44:43 PDT)
Re: [AMBER] SHAWKTRAJ, a new trajectory analysis tool
(Tue Apr 01 2014 - 10:30:23 PDT)
[AMBER] SHAWKTRAJ, a new trajectory analysis tool
(Tue Apr 01 2014 - 04:03:25 PDT)
Javier Alejandro Rendon Carrillo
[AMBER] MMPBSA.py PrmtopError: Complex natom != receptor natom + ligand natom
(Tue Apr 08 2014 - 21:54:12 PDT)
[AMBER] Fwd: MMPBSA.py PrmtopError: Complex natom != receptor natom + ligand natom
(Tue Apr 08 2014 - 20:47:14 PDT)
Jean-Patrick Francoia
Re: [AMBER] Minimization with (0, 0, 0) coordinates
(Tue Apr 29 2014 - 08:44:09 PDT)
[AMBER] Minimization with (0, 0, 0) coordinates
(Tue Apr 29 2014 - 08:19:45 PDT)
Re: [AMBER] Generate a pdb with unique atom names
(Tue Apr 15 2014 - 06:35:49 PDT)
Re: [AMBER] Generate a pdb with unique atom names
(Tue Apr 15 2014 - 00:52:37 PDT)
Re: [AMBER] Generate a pdb with unique atom names
(Mon Apr 14 2014 - 11:57:44 PDT)
Re: [AMBER] Generate a pdb with unique atom names
(Mon Apr 14 2014 - 05:50:35 PDT)
Re: [AMBER] Generate a pdb with unique atom names
(Mon Apr 14 2014 - 00:18:54 PDT)
Re: [AMBER] Generate a pdb with unique atom names
(Sun Apr 13 2014 - 15:06:00 PDT)
[AMBER] Generate a pdb with unique atom names
(Sun Apr 13 2014 - 12:40:18 PDT)
[AMBER] Generate a pdb with unique atom names
(Sun Apr 13 2014 - 12:38:37 PDT)
Jeff Wereszczynski
Re: [AMBER] Accelerated MD
(Sun Apr 27 2014 - 12:16:34 PDT)
Jinfeng Huang
Re: [AMBER] Nonbond Energy for Single Water Molecule ?
(Tue Apr 15 2014 - 21:11:25 PDT)
jinfenghuang
[AMBER] Fw:Problems with the gas energy of H3O+ and H2O
(Thu Apr 10 2014 - 20:06:53 PDT)
Re: [AMBER] AMBER Digest, Vol 818, Issue 1
(Thu Apr 10 2014 - 19:18:48 PDT)
[AMBER] Questions about the energy of H3O+
(Tue Apr 08 2014 - 07:26:22 PDT)
Jio M
Re: [AMBER] comparing RDF plots
(Tue Apr 08 2014 - 19:38:33 PDT)
[AMBER] comparing RDF plots
(Tue Apr 08 2014 - 19:12:17 PDT)
[AMBER] number of ions (integral) too much in RDF plot
(Tue Apr 08 2014 - 05:44:35 PDT)
[AMBER] number of ions (integral) too much in RDF plot
(Mon Apr 07 2014 - 19:33:01 PDT)
Re: [AMBER] Error: Could not parse mask [(:1]: radial calculation
(Thu Apr 03 2014 - 17:44:15 PDT)
[AMBER] Error: Could not parse mask [(:1]: radial calculation
(Thu Apr 03 2014 - 14:57:31 PDT)
Re: [AMBER] distance in one plane
(Thu Apr 03 2014 - 13:33:36 PDT)
[AMBER] distance in one plane
(Thu Apr 03 2014 - 12:35:37 PDT)
[AMBER] coordinates for replicating truncated octahedron
(Wed Apr 02 2014 - 13:51:45 PDT)
KangMooseok
[AMBER] When I run the pmemd.cuda, sometimes computer will be rebooted.
(Mon Apr 07 2014 - 23:01:45 PDT)
[AMBER] When I run the pmemd.cuda, sometimes computer will be rebooted.
(Mon Apr 07 2014 - 22:34:26 PDT)
kara tuong vi
[AMBER] Native Contact Help
(Mon Apr 21 2014 - 22:59:38 PDT)
kara tuong vi ngo
Re: [AMBER] Native Contact Help
(Thu Apr 24 2014 - 16:48:31 PDT)
Karl Kirschner
Re: [AMBER] Calculation of charges, force constanst, bonds, angles of a ligand using antechamber and gaussian
(Fri Apr 25 2014 - 01:26:08 PDT)
Keiran Rowell
[AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure."
(Tue Apr 15 2014 - 23:14:58 PDT)
Kipp Johnson
[AMBER] Error with quasi-harmonic MMPBSA.py calculations
(Tue Apr 22 2014 - 16:21:42 PDT)
Lara rajam
Re: [AMBER] MD run
(Fri Apr 25 2014 - 08:23:33 PDT)
[AMBER] MD run
(Fri Apr 25 2014 - 07:32:58 PDT)
Re: [AMBER] modified residues
(Wed Apr 23 2014 - 23:03:43 PDT)
Re: [AMBER] modified residues
(Wed Apr 23 2014 - 22:16:10 PDT)
[AMBER] modified residues
(Wed Apr 23 2014 - 20:32:45 PDT)
Re: [AMBER] antechamber
(Thu Apr 10 2014 - 11:07:31 PDT)
[AMBER] antechamber
(Thu Apr 10 2014 - 06:39:41 PDT)
Re: [AMBER] antechamber
(Tue Apr 08 2014 - 07:57:40 PDT)
Re: [AMBER] antechamber
(Mon Apr 07 2014 - 13:24:34 PDT)
Re: [AMBER] antechamber
(Mon Apr 07 2014 - 10:08:13 PDT)
[AMBER] antechamber_error
(Thu Apr 03 2014 - 08:38:19 PDT)
[AMBER] antechamber
(Thu Apr 03 2014 - 08:29:13 PDT)
Lists
Re: [AMBER] rism1d error
(Mon Apr 14 2014 - 09:37:10 PDT)
Re: [AMBER] rism1d error
(Sun Apr 13 2014 - 14:52:23 PDT)
Lorenzo Gontrani
Re: [AMBER] KShake problem with GPU
(Wed Apr 09 2014 - 08:00:31 PDT)
[AMBER] KShake problem with GPU
(Wed Apr 09 2014 - 07:05:33 PDT)
Mahendra B Thapa
Re: [AMBER] FW: How to use "divergence" command
(Mon Apr 21 2014 - 07:15:43 PDT)
[AMBER] How to use "divergence" command
(Fri Apr 18 2014 - 09:53:08 PDT)
Re: [AMBER] FW: making test not successful in ambertool14
(Fri Apr 18 2014 - 05:59:15 PDT)
[AMBER] making test not successful in ambertool14
(Thu Apr 17 2014 - 05:55:05 PDT)
Mani Bhavaraju
[AMBER] Bad atom type: C0
(Fri Apr 04 2014 - 09:04:54 PDT)
Manikanthan Bhavaraju
Re: [AMBER] Bad atom type: C0
(Fri Apr 04 2014 - 14:55:45 PDT)
[AMBER] Fwd: Bad atom type: C0
(Fri Apr 04 2014 - 08:27:43 PDT)
[AMBER] Fwd: Bad atom type: C0
(Fri Apr 04 2014 - 07:52:23 PDT)
[AMBER] Bad atom type: C0
(Fri Apr 04 2014 - 07:32:21 PDT)
[AMBER] Fwd: Parameters for Ca+2 ion for the decomposition analysis
(Thu Apr 03 2014 - 12:55:46 PDT)
[AMBER] Parameters for Ca+2 ion for the decomposition analysis
(Thu Apr 03 2014 - 12:22:01 PDT)
Marc van der Kamp
Re: [AMBER] diferent results
(Tue Apr 22 2014 - 08:10:49 PDT)
Marcus Arieno
Re: [AMBER] SHAWKTRAJ, a new trajectory analysis tool
(Tue Apr 01 2014 - 08:52:54 PDT)
Marlet Martinez
Re: [AMBER] strip some atoms to compute RMSD
(Thu Apr 24 2014 - 08:41:23 PDT)
Re: [AMBER] strip some atoms to compute RMSD
(Thu Apr 24 2014 - 01:57:15 PDT)
Re: [AMBER] strip some atoms to compute RMSD
(Tue Apr 22 2014 - 08:43:23 PDT)
[AMBER] strip some atoms to compute RMSD
(Tue Apr 22 2014 - 04:56:40 PDT)
Mary Varughese
[AMBER] MMPBSA
(Mon Apr 21 2014 - 22:00:53 PDT)
Milo Westler
Re: [AMBER] REMD with pmemd.cuda
(Tue Apr 08 2014 - 09:49:08 PDT)
Re: [AMBER] REMD with pmemd.cuda
(Tue Apr 08 2014 - 07:46:45 PDT)
Re: [AMBER] REMD with pmemd.cuda
(Tue Apr 08 2014 - 07:36:20 PDT)
[AMBER] REMD with pmemd.cuda
(Mon Apr 07 2014 - 18:04:52 PDT)
mish
Re: [AMBER] How to use Divalent ion parameters in tleap
(Mon Apr 28 2014 - 00:27:27 PDT)
[AMBER] How to use Divalent ion parameters in tleap
(Fri Apr 25 2014 - 07:40:23 PDT)
MOHD HOMAIDUR RAHMAN
[AMBER] Regarding simulation of alanine molecules in water box
(Tue Apr 29 2014 - 03:47:33 PDT)
Re: [AMBER] Regarding Interaction energy calculation
(Wed Apr 16 2014 - 05:16:20 PDT)
[AMBER] Regarding Interaction energy calculation
(Fri Apr 04 2014 - 21:05:35 PDT)
[AMBER] Regarding Interaction energy calculation
(Fri Apr 04 2014 - 01:57:49 PDT)
Re: [AMBER] SHAWKTRAJ, a new trajectory analysis tool
(Tue Apr 01 2014 - 10:04:29 PDT)
Muthukumaran R
[AMBER] Running parallel simulations on different no of cores
(Sat Apr 19 2014 - 10:31:48 PDT)
Neha Gandhi
[AMBER] distance restraints
(Thu Apr 24 2014 - 03:04:32 PDT)
[AMBER] PCA analysis and histogram
(Mon Apr 14 2014 - 04:45:42 PDT)
[AMBER] Karplus J-coupling
(Tue Apr 08 2014 - 02:32:39 PDT)
[AMBER] averaged NMR distance
(Sun Apr 06 2014 - 20:00:01 PDT)
newamber list
[AMBER] temperature increments
(Wed Apr 23 2014 - 19:30:54 PDT)
Re: [AMBER] rdf averaging problem
(Mon Apr 14 2014 - 20:35:22 PDT)
Re: [AMBER] rdf averaging problem
(Mon Apr 14 2014 - 09:58:11 PDT)
Re: [AMBER] rdf averaging problem
(Fri Apr 11 2014 - 16:32:27 PDT)
Re: [AMBER] rdf averaging problem
(Fri Apr 11 2014 - 12:13:29 PDT)
[AMBER] rdf averaging problem
(Thu Apr 10 2014 - 15:08:49 PDT)
Re: [AMBER] comparing RDF plots
(Wed Apr 09 2014 - 13:34:28 PDT)
Re: [AMBER] number of ions (integral) too much in RDF plot
(Wed Apr 09 2014 - 10:52:40 PDT)
Re: [AMBER] number of ions (integral) too much in RDF plot
(Wed Apr 09 2014 - 10:17:36 PDT)
Re: [AMBER] comparing RDF plots
(Wed Apr 09 2014 - 10:15:07 PDT)
Nhai
Re: [AMBER] REMD with pmemd.cuda
(Tue Apr 08 2014 - 00:37:29 PDT)
Nitin Sharma
[AMBER] simulated annelaing of protein ligand complex
(Fri Apr 25 2014 - 11:46:17 PDT)
Re: [AMBER] AMBER minimization problem
(Thu Apr 24 2014 - 08:38:57 PDT)
Re: [AMBER] MMPBSA error
(Thu Apr 24 2014 - 07:52:15 PDT)
[AMBER] MMPBSA error
(Thu Apr 24 2014 - 07:05:47 PDT)
Re: [AMBER] strip some atoms to compute RMSD
(Tue Apr 22 2014 - 08:47:26 PDT)
[AMBER] simulated annelaing condtions and requiremnets
(Sun Apr 20 2014 - 06:47:42 PDT)
Re: [AMBER] truncatiing water molecules
(Wed Apr 02 2014 - 08:38:48 PDT)
Re: [AMBER] truncatiing water molecules
(Wed Apr 02 2014 - 07:57:12 PDT)
Re: [AMBER] truncatiing water molecules
(Wed Apr 02 2014 - 06:03:13 PDT)
[AMBER] truncatiing water molecules
(Wed Apr 02 2014 - 04:36:27 PDT)
Pallavi Mohanty
[AMBER] Query regrading simulation
(Fri Apr 04 2014 - 02:02:20 PDT)
[AMBER] Query regrading simulation
(Fri Apr 04 2014 - 00:00:27 PDT)
[AMBER] query regarding simulation!
(Thu Apr 03 2014 - 23:40:49 PDT)
Pengfei Li
Re: [AMBER] How to use Divalent ion parameters in tleap
(Fri Apr 25 2014 - 08:12:32 PDT)
Re: [AMBER] How to use Divalent ion parameters in tleap
(Fri Apr 25 2014 - 08:08:56 PDT)
Re: [AMBER] RESP procedure
(Thu Apr 24 2014 - 10:36:35 PDT)
Re: [AMBER] SHAWKTRAJ, a new trajectory analysis tool
(Tue Apr 01 2014 - 20:13:53 PDT)
Pierpaolo Cacciotto
[AMBER] pmemd.cuda error amber14
(Mon Apr 28 2014 - 09:05:09 PDT)
Quynh Vo
Re: [AMBER] Question about volume when switching from NPT to NVE ensemble
(Thu Apr 24 2014 - 12:58:15 PDT)
[AMBER] Question about volume when switching from NPT to NVE ensemble
(Thu Apr 24 2014 - 11:08:08 PDT)
Ray Luo, Ph.D.
Re: [AMBER] Inconsistent results of MMPBSA.py with option inp=1 and inp=2
(Fri Apr 04 2014 - 09:29:49 PDT)
Rebeca García Fandiño
[AMBER] SDS parameters in AMBER
(Tue Apr 15 2014 - 05:28:58 PDT)
Robert Molt
Re: [AMBER] Minimization with (0, 0, 0) coordinates
(Tue Apr 29 2014 - 08:24:10 PDT)
Ross Walker
[AMBER] Reminder: AMBER Molecular Dynamics Workshop Barcelona Jun 2-6. Pre-Registration closes Apr 28th.
(Thu Apr 24 2014 - 11:32:55 PDT)
Re: [AMBER] AMBER Workshop Announcement
(Mon Apr 21 2014 - 08:03:07 PDT)
Re: [AMBER] AMBER Workshop Announcement
(Sat Apr 19 2014 - 10:51:41 PDT)
[AMBER] AMBER Workshop Announcement
(Thu Apr 17 2014 - 09:26:43 PDT)
[AMBER-Developers] AMBER Workshop Announcement
(Thu Apr 17 2014 - 08:47:35 PDT)
Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure."
(Wed Apr 16 2014 - 10:27:45 PDT)
Sajeewa Pemasinghe
Re: [AMBER] Distance constraints
(Wed Apr 02 2014 - 07:40:01 PDT)
Re: [AMBER] Distance constraints
(Wed Apr 02 2014 - 06:53:53 PDT)
sammia khatak
Re: [AMBER] new error
(Fri Apr 04 2014 - 06:26:17 PDT)
[AMBER] new error
(Fri Apr 04 2014 - 05:21:33 PDT)
Re: [AMBER] leap error
(Thu Apr 03 2014 - 21:40:39 PDT)
Re: [AMBER] leap error
(Thu Apr 03 2014 - 10:18:17 PDT)
Re: [AMBER] leap error
(Thu Apr 03 2014 - 09:02:29 PDT)
[AMBER] leap error
(Thu Apr 03 2014 - 08:49:09 PDT)
Scott Le Grand
Re: [AMBER] KShake problem with GPU
(Wed Apr 09 2014 - 08:01:54 PDT)
Setyanto Md
Re: [AMBER] AMBER Workshop Announcement
(Mon Apr 28 2014 - 20:02:23 PDT)
Re: [AMBER] PCA analysis and histogram
(Mon Apr 21 2014 - 01:19:51 PDT)
Re: [AMBER] AMBER Workshop Announcement
(Mon Apr 21 2014 - 01:15:54 PDT)
Re: [AMBER] Asking about using Vector Analysis: Thermo
(Fri Apr 11 2014 - 02:13:14 PDT)
Re: [AMBER] Asking about using Vector Analysis: Thermo
(Tue Apr 08 2014 - 07:38:49 PDT)
[AMBER] Asking about using Vector Analysis: Thermo
(Wed Apr 02 2014 - 22:35:44 PDT)
[AMBER] Asking about using Vector Analysis: Thermo
(Wed Apr 02 2014 - 20:10:26 PDT)
Re: [AMBER] How to update cpptraj and setting donor/acceptormask
(Tue Apr 01 2014 - 20:03:00 PDT)
Shulin Zhuang
Re: [AMBER] Error when runing sietraj for AMBER trajectory
(Thu Apr 10 2014 - 22:41:49 PDT)
[AMBER] Error when runing sietraj for AMBER trajectory
(Thu Apr 10 2014 - 22:34:14 PDT)
Soren Wacker
Re: [AMBER] FFTW3 related error when compiling AmberTools13 on Fedora20
(Thu Apr 24 2014 - 10:37:02 PDT)
Re: [AMBER] FFTW3 related error when compiling AmberTools13 on Fedora20
(Wed Apr 23 2014 - 16:24:17 PDT)
[AMBER] FFTW3 related error when compiling AmberTools13 on Fedora20
(Wed Apr 23 2014 - 13:51:31 PDT)
Soumendranath Bhakat
[AMBER] Corresponding PDB and snapshot PDB
(Sun Apr 27 2014 - 05:00:50 PDT)
[AMBER] Fwd: MMPBSA query
(Fri Apr 25 2014 - 00:04:29 PDT)
Re: [AMBER] MMPBSA query
(Thu Apr 24 2014 - 23:53:12 PDT)
Re: [AMBER] Corresponding dry trajectory and PDB
(Thu Apr 24 2014 - 05:22:23 PDT)
[AMBER] Corresponding dry trajectory and PDB
(Thu Apr 24 2014 - 03:45:21 PDT)
Re: [AMBER] error in loading protein
(Tue Apr 08 2014 - 00:20:18 PDT)
Re: [AMBER] Protein-ligand interaction
(Sun Apr 06 2014 - 09:09:50 PDT)
Re: [AMBER] protein-ligand interaction
(Sun Apr 06 2014 - 04:54:33 PDT)
Re: [AMBER] Ligand-residue interaction plot
(Sat Apr 05 2014 - 08:59:45 PDT)
Re: [AMBER] Principal component analysis
(Sat Apr 05 2014 - 03:30:40 PDT)
Re: [AMBER] Ligand-residue interaction plot
(Sat Apr 05 2014 - 03:27:53 PDT)
Sourav Purohit
[AMBER] Accelerated MD
(Sun Apr 27 2014 - 04:01:08 PDT)
[AMBER] Accelerated MD
(Sat Apr 26 2014 - 04:18:19 PDT)
[AMBER] Accelerated MD
(Mon Apr 21 2014 - 02:34:29 PDT)
[AMBER] MMPBSA
(Sun Apr 13 2014 - 23:35:29 PDT)
[AMBER] Fwd: MMPBSA
(Sun Apr 13 2014 - 12:15:32 PDT)
[AMBER] MMPBSA
(Sun Apr 13 2014 - 12:04:53 PDT)
[AMBER] MMPBSA
(Sun Apr 13 2014 - 07:09:44 PDT)
[AMBER] Fwd: MMPBSA
(Sun Apr 13 2014 - 03:20:21 PDT)
[AMBER] MMPBSA
(Sun Apr 13 2014 - 02:39:17 PDT)
Souvik Sur
[AMBER] Error using MMPBSA.py
(Fri Apr 04 2014 - 03:00:04 PDT)
Suchetana Gupta
Re: [AMBER] Quantification of alpha helix
(Tue Apr 29 2014 - 11:06:02 PDT)
[AMBER] Quantification of alpha helix
(Tue Apr 29 2014 - 08:06:56 PDT)
sunita.tifrh.res.in
[AMBER] could not extend the MD simulation
(Thu Apr 24 2014 - 05:18:59 PDT)
Tamara Meirelles
[AMBER] US+QM/MM enzyme + substrate - howto
(Mon Apr 07 2014 - 00:26:05 PDT)
Thomas Evangelidis
Re: [AMBER] Accelerated MD
(Mon Apr 28 2014 - 14:42:16 PDT)
Re: [AMBER] negative dihedral energy with ff14ipq
(Mon Apr 28 2014 - 05:05:08 PDT)
Re: [AMBER] negative dihedral energy with ff14ipq
(Mon Apr 28 2014 - 02:17:12 PDT)
Re: [AMBER] Accelerated MD
(Sun Apr 27 2014 - 16:26:29 PDT)
[AMBER] negative dihedral energy with ff14ipq
(Sun Apr 27 2014 - 12:42:50 PDT)
tong
[AMBER] Inconsistent results of MMPBSA.py with option inp=1 and inp=2
(Fri Apr 04 2014 - 07:57:04 PDT)
Urszula Uciechowska
[AMBER] distance restraint
(Mon Apr 14 2014 - 00:51:42 PDT)
[AMBER] error in input file /nmropt=1
(Wed Apr 09 2014 - 01:22:57 PDT)
Re: [AMBER] error in input file /nmropt=1
(Wed Apr 09 2014 - 00:22:03 PDT)
Re: [AMBER] error in input file /nmropt=1 with dist.RST
(Tue Apr 08 2014 - 06:31:41 PDT)
Re: [AMBER] error in input file /nmropt=1 with dist.RST
(Tue Apr 08 2014 - 06:12:56 PDT)
[AMBER] error in input file /nmropt=1
(Tue Apr 08 2014 - 05:57:58 PDT)
[AMBER] igb=1
(Fri Apr 04 2014 - 03:47:39 PDT)
[AMBER] Distance constraints
(Wed Apr 02 2014 - 06:33:23 PDT)
Valentina D'Atri
[AMBER] how to protonate phosphate groups of nucleotides
(Wed Apr 30 2014 - 10:13:32 PDT)
Valentina Romano
Re: [AMBER] Minimization with restraints
(Wed Apr 30 2014 - 05:45:24 PDT)
[AMBER] Minimization with restraints
(Wed Apr 30 2014 - 02:42:02 PDT)
Re: [AMBER] AMBER minimization problem
(Thu Apr 24 2014 - 07:58:12 PDT)
Re: [AMBER] AMBER minimization problem
(Thu Apr 24 2014 - 06:52:03 PDT)
Re: [AMBER] AMBER minimization problem
(Thu Apr 24 2014 - 01:22:29 PDT)
[AMBER] AMBER minimization problem
(Wed Apr 23 2014 - 09:11:54 PDT)
Ved Prakash
Re: [AMBER] RESP procedure
(Mon Apr 21 2014 - 12:05:31 PDT)
Re: [AMBER] AMBER Workshop Announcement
(Fri Apr 18 2014 - 21:34:50 PDT)
Vijay Manickam Achari
Re: [AMBER] Fw: loading multiple prepin file in xleap - gives warning
(Thu Apr 03 2014 - 21:16:11 PDT)
[AMBER] Fw: loading multiple prepin file in xleap - gives warning
(Wed Apr 02 2014 - 23:20:16 PDT)
[AMBER] loading multiple prepin file in xleap - gives warning
(Wed Apr 02 2014 - 02:57:31 PDT)
Vlad Cojocaru
Re: [AMBER] Accelerated MD
(Mon Apr 28 2014 - 15:06:07 PDT)
Re: [AMBER] Accelerated MD
(Sun Apr 27 2014 - 22:15:35 PDT)
Re: [AMBER] Accelerated MD
(Sun Apr 27 2014 - 14:50:59 PDT)
Re: [AMBER] Accelerated MD
(Sun Apr 27 2014 - 07:26:39 PDT)
Re: [AMBER] positive value of delta G in MMPBSA calculation
(Thu Apr 24 2014 - 04:36:24 PDT)
Vytautas Rakeviius
[AMBER] I make box with solvatebox complex TIP3PBOX 15.0 and unfilled gap remains near wall
(Wed Apr 09 2014 - 05:39:12 PDT)
wmsmith.uci.edu
Re: [AMBER] MM-PBSA for two drug molecules
(Fri Apr 25 2014 - 18:09:38 PDT)
ye renlo
Re: [AMBER] ATOMIC NUMBER section in prmtop file - Sustiva example:potential bug
(Sat Apr 05 2014 - 08:56:32 PDT)
Re: [AMBER] ATOMIC NUMBER section in prmtop file - Sustiva example
(Sat Apr 05 2014 - 07:39:38 PDT)
Yeng-Tseng Wang
[AMBER] About the error "Unable to correctly identify element CU" in QMMM simulation
(Mon Apr 07 2014 - 20:43:54 PDT)
Yin, Guowei
Re: [AMBER] Extract velocity from the restart file
(Wed Apr 30 2014 - 08:14:28 PDT)
[AMBER] Extract velocity from the restart file
(Tue Apr 29 2014 - 14:03:42 PDT)
Yip Yew Mun
Re: [AMBER] How to extract each frame of a trajectory as individual .mdcrd files?
(Wed Apr 30 2014 - 08:45:30 PDT)
[AMBER] How to extract each frame of a trajectory as individual .mdcrd files?
(Wed Apr 30 2014 - 06:28:48 PDT)
[AMBER] Can I do PCA on simply a particular domain of the whole protein?
(Sat Apr 19 2014 - 21:38:11 PDT)
zahra khatti
[AMBER] ptraj in parallel
(Wed Apr 30 2014 - 08:56:49 PDT)
Re: [AMBER] problem with installation amber12 and ambertools13 in ubuntu
(Sat Apr 26 2014 - 12:04:46 PDT)
Re: [AMBER] problem with installation amber12 and ambertools13 in ubuntu
(Fri Apr 25 2014 - 21:18:31 PDT)
[AMBER] problem with installation amber12 and ambertools13 in ubuntu
(Fri Apr 25 2014 - 11:21:42 PDT)
Re: [AMBER] installation error
(Fri Apr 25 2014 - 00:38:17 PDT)
[AMBER] installation error
(Thu Apr 24 2014 - 08:50:04 PDT)
[AMBER] diferent results
(Tue Apr 22 2014 - 07:55:25 PDT)
zottisad
[AMBER] problems with Amber12 installation - cuda and mpi
(Fri Apr 25 2014 - 20:24:52 PDT)
石坪江梨花
[AMBER] 【AMBER12】Including water when using General Amber Force Field leaprc.gaff
(Sat Apr 19 2014 - 03:22:48 PDT)
黄
[AMBER] Nonbond Energy for Single Water Molecule ?
(Mon Apr 14 2014 - 07:59:20 PDT)
[AMBER] Problems with the gas energy of H3O+ and H2O
(Fri Apr 11 2014 - 07:46:09 PDT)
전선희
[AMBER] average problem........
(Thu Apr 24 2014 - 21:11:01 PDT)
Last message date
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Wed Apr 30 2014 - 11:00:02 PDT
Archived on
: Fri Dec 20 2024 - 05:54:58 PST
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