Amber Archive Apr 2010 by author
724 messages
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Starting
Wed Mar 31 2010 - 22:00:04 PDT,
Ending
Fri Apr 30 2010 - 21:00:03 PDT
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030081094
[AMBER] make a new residue FAD-CYS
(Mon Apr 19 2010 - 00:29:26 PDT)
aapeters.ncsu.edu
RE: [AMBER] QM/MM cut problem
(Thu Apr 29 2010 - 04:58:49 PDT)
RE: [AMBER] QM/MM cut problem
(Tue Apr 20 2010 - 11:27:46 PDT)
[AMBER] QM/MM cut problem
(Tue Apr 20 2010 - 09:36:18 PDT)
[AMBER] QM/MM + PIMD
(Fri Apr 16 2010 - 10:36:19 PDT)
RE: [AMBER] Amber10 Cuda compile failure
(Wed Apr 14 2010 - 14:16:28 PDT)
[AMBER] Amber10 Cuda compile failure
(Mon Apr 12 2010 - 14:35:49 PDT)
[AMBER] Amber11, pure QM PBC
(Mon Apr 12 2010 - 09:07:26 PDT)
Ahmad, Rafi
[AMBER] Steered/Targeted MD
(Thu Apr 15 2010 - 09:08:46 PDT)
Alan
[AMBER] xgrid in opempi 1.4.1 still broken
(Fri Apr 30 2010 - 08:04:24 PDT)
Re: [AMBER] a possible typo bug while building pmemd with mpi
(Thu Apr 29 2010 - 11:08:24 PDT)
Re: [AMBER] a possible typo bug while building pmemd with mpi
(Thu Apr 29 2010 - 09:46:22 PDT)
Re: [AMBER] a possible typo bug while building pmemd with mpi
(Thu Apr 29 2010 - 09:13:03 PDT)
[AMBER] Re: a possible typo bug while building pmemd with mpi
(Thu Apr 29 2010 - 08:45:56 PDT)
[AMBER] a possible typo bug while building pmemd with mpi
(Thu Apr 29 2010 - 08:18:29 PDT)
Re: [AMBER] failed to compile Amber11 with mpi on Mac
(Thu Apr 29 2010 - 07:59:22 PDT)
[AMBER] Re: failed to compile Amber11 with mpi on Mac
(Thu Apr 29 2010 - 07:51:56 PDT)
[AMBER] failed to compile Amber11 with mpi on Mac
(Thu Apr 29 2010 - 07:41:20 PDT)
[AMBER] AmberTools.pdf (AT 1.4)
(Thu Apr 29 2010 - 06:48:41 PDT)
[AMBER] Re: to test nab with openmp
(Thu Apr 29 2010 - 03:09:22 PDT)
[AMBER] Re: to test nab with openmp
(Thu Apr 29 2010 - 02:13:18 PDT)
[AMBER] to test nab with openmp
(Thu Apr 29 2010 - 00:42:59 PDT)
[AMBER] sleap from AT 1.4 doesn't seem ok
(Wed Apr 28 2010 - 11:35:12 PDT)
Re: [AMBER] Compiling AmberTools 1.4 on MacOS10.5
(Tue Apr 27 2010 - 10:43:06 PDT)
Re: [AMBER] ambertools 1.4, tests
(Tue Apr 27 2010 - 08:12:49 PDT)
[AMBER] ambertools 1.4, tests
(Tue Apr 27 2010 - 03:49:18 PDT)
[AMBER] new ambertools folder distribution and Makefile_at
(Mon Apr 26 2010 - 09:58:12 PDT)
[AMBER] about parmjoin
(Wed Apr 21 2010 - 01:40:04 PDT)
Re: [AMBER] Chirality of amines in GAFF
(Wed Apr 14 2010 - 06:23:28 PDT)
Re: [AMBER] trying to use antechamber with -nc 0 for a molecule
(Mon Apr 12 2010 - 09:14:35 PDT)
Re: [AMBER] trying to use antechamber with -nc 0 for a molecule
(Mon Apr 12 2010 - 08:29:57 PDT)
[AMBER] trying to use antechamber with -nc 0 for a molecule
(Mon Apr 12 2010 - 07:03:13 PDT)
Alessandro Nascimento
[AMBER] mutate function in NAB
(Tue Apr 20 2010 - 11:11:41 PDT)
Alex Boncheff
[AMBER] MOPAC2009 output results into antechamber
(Wed Apr 21 2010 - 08:14:58 PDT)
Amedeo Capobianco
[AMBER] slightly off topic: suggestions for DNA single strand simulations
(Sun Apr 11 2010 - 14:11:02 PDT)
Amire-Brahimi Benjamin
[AMBER] Constraint minimisation before MD simulation
(Tue Apr 27 2010 - 14:48:31 PDT)
Andrew Olson
Re: [AMBER] makeANG_rst values
(Tue Apr 06 2010 - 14:21:19 PDT)
[AMBER] makeANG_rst values
(Sat Apr 03 2010 - 14:52:42 PDT)
Andrew Voronkov
Re: Re: [AMBER] how is pH treated in Amber - other than constant pH simulations
(Tue Apr 20 2010 - 06:24:15 PDT)
Re: Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups?
(Tue Apr 20 2010 - 05:28:37 PDT)
Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups?
(Tue Apr 20 2010 - 04:27:50 PDT)
[AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups?
(Tue Apr 20 2010 - 03:23:15 PDT)
Re: Re: [AMBER] how is pH treated in Amber - other than constant pH simulations
(Tue Apr 20 2010 - 00:32:35 PDT)
[AMBER] Fwd: Re: RE: question on section 2 of MM-PBSA tutorial
(Fri Apr 16 2010 - 13:57:54 PDT)
Re: Re: [AMBER] how is pH treated in Amber - other than constant pH simulations
(Fri Apr 16 2010 - 11:17:32 PDT)
[AMBER] how is pH treated in Amber - other than constant pH simulations
(Fri Apr 16 2010 - 08:44:36 PDT)
[AMBER] question on section 2 of MM-PBSA tutorial
(Thu Apr 08 2010 - 00:14:17 PDT)
aneesh cna
[AMBER] Regarding RDF calculation in Ptraj
(Fri Apr 02 2010 - 21:49:06 PDT)
Anna Dejardin
Re: [AMBER] AMBER10 installation: make test error 1
(Wed Apr 07 2010 - 02:47:39 PDT)
Anselm Horn
[AMBER] Setup of defined salt concentrations
(Tue Apr 20 2010 - 06:16:33 PDT)
Asfa Ali
Re: [AMBER] regarding sqm
(Thu Apr 22 2010 - 06:17:13 PDT)
[AMBER] regarding sqm
(Wed Apr 21 2010 - 23:51:32 PDT)
Re: [AMBER] Simulation of complex
(Wed Apr 21 2010 - 04:39:34 PDT)
Re: [AMBER] Simulation of complex
(Wed Apr 21 2010 - 03:51:04 PDT)
[AMBER] Simulation of complex
(Wed Apr 21 2010 - 00:19:23 PDT)
[AMBER] Simulation of complex
(Mon Apr 19 2010 - 08:22:17 PDT)
Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations
(Wed Apr 14 2010 - 10:02:25 PDT)
Re: [AMBER] regarding parameter file creation of dna-lig complex
(Tue Apr 13 2010 - 21:40:45 PDT)
Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations
(Tue Apr 13 2010 - 21:21:44 PDT)
[AMBER] regarding parameter file creation of dna-lig complex
(Tue Apr 13 2010 - 12:37:15 PDT)
[AMBER] Regarding parameter files of dna-lig complex
(Mon Apr 12 2010 - 23:08:18 PDT)
[AMBER] regarding antechamber
(Sun Apr 11 2010 - 23:17:11 PDT)
[AMBER] antechamber
(Tue Apr 06 2010 - 00:30:13 PDT)
Re: [AMBER] rna simulation
(Sun Apr 04 2010 - 23:47:38 PDT)
Re: [AMBER] rna simulation
(Sun Apr 04 2010 - 23:12:59 PDT)
[AMBER] rna simulation
(Sun Apr 04 2010 - 22:42:33 PDT)
Atro Tossavainen
Re: [AMBER] amber10 installation on SGI IRIX 6.5
(Mon Apr 05 2010 - 22:58:18 PDT)
Babu Kannappan
[AMBER] problem with XLEAP on X-client run on windows machine...
(Mon Apr 12 2010 - 06:22:37 PDT)
Balazs Jojart
Re: [AMBER] molecular surface area
(Thu Apr 22 2010 - 23:26:58 PDT)
Barbault Florent
Re: [AMBER] non bonded interactions (vanderwaal and electrostatic)
(Wed Apr 07 2010 - 12:14:08 PDT)
Beale, John
[AMBER] Solvent
(Fri Apr 09 2010 - 08:41:51 PDT)
[AMBER] Segmentation Fault
(Thu Apr 01 2010 - 11:52:34 PDT)
[AMBER] SASA
(Thu Apr 01 2010 - 03:39:26 PDT)
Ben Roberts
Re: [AMBER] "go" keyword in ptraj
(Fri Apr 30 2010 - 11:36:14 PDT)
[AMBER] "go" keyword in ptraj
(Fri Apr 30 2010 - 06:34:28 PDT)
Re: [AMBER] a possible typo bug while building pmemd with mpi
(Thu Apr 29 2010 - 10:13:56 PDT)
Re: [AMBER] forcefield parameters for TiO2/peptides?
(Thu Apr 29 2010 - 08:11:40 PDT)
[AMBER] Antechamber, GAFF and methylimidazole typing
(Fri Apr 23 2010 - 14:32:57 PDT)
ben rodriguez
[AMBER] Tesla C2050 atom limit?
(Wed Apr 28 2010 - 17:44:43 PDT)
Bill Miller III
Re: [AMBER] Problem from ala scanning
(Fri Apr 30 2010 - 16:08:57 PDT)
Re: [AMBER] Problem from ala scanning
(Fri Apr 30 2010 - 07:52:37 PDT)
Re: [AMBER] joining out files
(Thu Apr 29 2010 - 04:06:08 PDT)
Re: Re: Re: [AMBER] how do MM_PBSA without water
(Thu Apr 22 2010 - 04:04:48 PDT)
Re: [AMBER] solvent accessible surface
(Wed Apr 21 2010 - 20:41:02 PDT)
Re: [AMBER] Error: Sander output is missing values
(Wed Apr 21 2010 - 09:25:28 PDT)
Re: [AMBER] Error: Sander output is missing values
(Tue Apr 20 2010 - 04:36:52 PDT)
Re: Re: Re: [AMBER] how do MM_PBSA without water
(Mon Apr 19 2010 - 06:25:40 PDT)
Re: Re: [AMBER] how do MM_PBSA without water
(Sun Apr 18 2010 - 08:36:56 PDT)
Re: Re: [AMBER] error when running mmpbsa
(Sun Apr 18 2010 - 06:50:22 PDT)
Re: [AMBER] how do MM_PBSA without water
(Sun Apr 18 2010 - 06:18:53 PDT)
Re: [AMBER] Trajectory Smoothing
(Thu Apr 15 2010 - 04:09:28 PDT)
Re: [AMBER] energy decomposition
(Wed Apr 07 2010 - 14:45:18 PDT)
Re: [AMBER] MMPBSA-ON-CLUSTER
(Sun Apr 04 2010 - 05:37:06 PDT)
Re: [AMBER] MMPBSA-ON-CLUSTER
(Sat Apr 03 2010 - 19:09:15 PDT)
Re: [AMBER] MMPBSA-ON-CLUSTER
(Sat Apr 03 2010 - 05:15:31 PDT)
Bill Ross
Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more
(Fri Apr 30 2010 - 10:07:57 PDT)
Re: [AMBER] question about mass card of frcmod file
(Thu Apr 29 2010 - 16:07:25 PDT)
Re: [AMBER] joining out files
(Thu Apr 29 2010 - 12:49:25 PDT)
Re: [AMBER] how to load topology file
(Tue Apr 27 2010 - 15:27:00 PDT)
Re: [AMBER] Constraint minimisation before MD simulation
(Tue Apr 27 2010 - 15:05:46 PDT)
Re: [AMBER] Addions grid ?
(Tue Apr 27 2010 - 11:32:29 PDT)
Re: [AMBER] Addions grid ?
(Tue Apr 27 2010 - 11:09:49 PDT)
Re: [AMBER] Addions grid ?
(Tue Apr 27 2010 - 10:01:36 PDT)
Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between
(Mon Apr 26 2010 - 10:23:21 PDT)
Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between
(Mon Apr 26 2010 - 10:19:28 PDT)
Re: [AMBER] problem on running saveAmberParm
(Fri Apr 23 2010 - 11:00:29 PDT)
Re: [AMBER] problem on running saveAmberParm
(Fri Apr 23 2010 - 10:27:27 PDT)
Re: [AMBER] H-bond analysis in ptraj
(Fri Apr 23 2010 - 10:03:58 PDT)
Re: [AMBER] Do molecular dynamics in the limited space
(Fri Apr 23 2010 - 10:00:11 PDT)
Re: [AMBER] vdW question.
(Thu Apr 22 2010 - 10:14:15 PDT)
Re: Re: Re: Re: [AMBER] how do MM_PBSA without water
(Thu Apr 22 2010 - 09:55:00 PDT)
Re: [AMBER] vdW question.
(Thu Apr 22 2010 - 09:40:33 PDT)
Re: [AMBER] Do molecular dynamics in the limited space
(Wed Apr 21 2010 - 09:59:39 PDT)
Re: [AMBER] Simulation of complex
(Wed Apr 21 2010 - 09:34:02 PDT)
Re: [AMBER] Setup of defined salt concentrations
(Tue Apr 20 2010 - 10:29:24 PDT)
Re: [AMBER] Setup of defined salt concentrations
(Tue Apr 20 2010 - 10:13:06 PDT)
Re: [AMBER] Error: Sander output is missing values
(Tue Apr 20 2010 - 10:06:22 PDT)
Re: [AMBER] remove water from system
(Tue Apr 20 2010 - 10:02:32 PDT)
Re: [AMBER] Simulation of complex
(Mon Apr 19 2010 - 09:48:56 PDT)
Re: [AMBER] Trajectory Smoothing
(Sun Apr 18 2010 - 12:12:56 PDT)
Re: [AMBER] 1-4 EEL
(Fri Apr 16 2010 - 09:47:04 PDT)
Re: [AMBER] BOND TYPE
(Fri Apr 16 2010 - 09:26:47 PDT)
Re: [AMBER] periodic boundary condition
(Thu Apr 15 2010 - 11:12:03 PDT)
Re: [AMBER] periodic boundary condition
(Thu Apr 15 2010 - 08:01:16 PDT)
Re: [AMBER] 1-4 EEL
(Thu Apr 15 2010 - 07:56:47 PDT)
Re: [AMBER] Trajectory Smoothing
(Thu Apr 15 2010 - 07:47:22 PDT)
Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations
(Wed Apr 14 2010 - 10:25:47 PDT)
Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations
(Wed Apr 14 2010 - 09:43:10 PDT)
Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Wed Apr 14 2010 - 09:38:23 PDT)
Re: [AMBER] regarding parameter file creation of dna-lig complex
(Tue Apr 13 2010 - 13:29:25 PDT)
Re: [AMBER] Regarding parameter files of dna-lig complex
(Tue Apr 13 2010 - 10:01:14 PDT)
Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Tue Apr 13 2010 - 09:57:28 PDT)
Re: [AMBER] vacuum bubbles generated after heating
(Mon Apr 12 2010 - 13:49:47 PDT)
Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Mon Apr 12 2010 - 11:13:25 PDT)
Re: [AMBER] vacuum bubbles generated after heating
(Mon Apr 12 2010 - 10:41:30 PDT)
Re:Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame
(Fri Apr 09 2010 - 08:57:00 PDT)
Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame
(Thu Apr 08 2010 - 09:44:24 PDT)
Re: [AMBER] contiguous trajectory without iwrap=1
(Wed Apr 07 2010 - 17:02:50 PDT)
Re: [AMBER] contiguous trajectory without iwrap=1
(Wed Apr 07 2010 - 16:11:15 PDT)
Re: [AMBER] Problems during AMBER 10 compilation.
(Tue Apr 06 2010 - 10:14:44 PDT)
Re: [AMBER] Problems during AMBER 10 compilation.
(Tue Apr 06 2010 - 10:04:52 PDT)
Re: [AMBER] amber10 installation on SGI IRIX 6.5
(Mon Apr 05 2010 - 13:44:33 PDT)
Re: [AMBER] rna simulation
(Mon Apr 05 2010 - 10:50:27 PDT)
Re: [AMBER] rna simulation
(Mon Apr 05 2010 - 10:32:50 PDT)
Re: [AMBER] problem with frcmod parameter
(Fri Apr 02 2010 - 10:03:37 PDT)
Carlos Simmerling
Re: [AMBER] nmr order parameter and autocorrelation
(Fri Apr 30 2010 - 13:47:00 PDT)
Re: [AMBER] Question: ptraj masks
(Wed Apr 28 2010 - 14:28:37 PDT)
Re: [AMBER] problem rejoining segmented out files in long simulation
(Wed Apr 28 2010 - 08:10:58 PDT)
Re: [AMBER] Question about RMSD in AMBER
(Tue Apr 27 2010 - 18:14:46 PDT)
Re: [AMBER] Constraint minimisation before MD simulation
(Tue Apr 27 2010 - 14:58:32 PDT)
Re: Re: RE: [AMBER] about IGB
(Mon Apr 26 2010 - 04:11:29 PDT)
Re: [AMBER] The system has extended beyond the extent of the virtual box
(Mon Apr 26 2010 - 03:50:00 PDT)
Re: RE: [AMBER] about IGB
(Sun Apr 25 2010 - 03:54:28 PDT)
Re: Re: [AMBER] remove water from system
(Wed Apr 21 2010 - 03:29:56 PDT)
Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups?
(Tue Apr 20 2010 - 06:01:58 PDT)
Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups?
(Tue Apr 20 2010 - 04:36:50 PDT)
Re: [AMBER] regarding running Nudged Elastic Band Approach with amber10
(Tue Apr 20 2010 - 03:20:28 PDT)
Re: [AMBER] remove water from system
(Tue Apr 20 2010 - 03:06:21 PDT)
Re: [AMBER] elevated temperature MD
(Mon Apr 19 2010 - 10:21:57 PDT)
Re: [AMBER] Trajectory Smoothing
(Sun Apr 18 2010 - 12:34:17 PDT)
Re: [AMBER] how is pH treated in Amber - other than constant pH simulations
(Fri Apr 16 2010 - 09:10:42 PDT)
Re: Re: [AMBER] the volume is always getting bigger and bigger until crash
(Wed Apr 14 2010 - 17:50:04 PDT)
Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Wed Apr 14 2010 - 05:37:48 PDT)
Re: [AMBER] the volume is always getting bigger and bigger until crash
(Wed Apr 14 2010 - 03:05:14 PDT)
Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Tue Apr 13 2010 - 19:46:52 PDT)
Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Tue Apr 13 2010 - 04:57:06 PDT)
Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Mon Apr 12 2010 - 07:02:01 PDT)
Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Mon Apr 12 2010 - 05:13:31 PDT)
Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)...
(Mon Apr 12 2010 - 04:35:12 PDT)
Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Mon Apr 12 2010 - 04:09:45 PDT)
Re: [AMBER] contiguous trajectory without iwrap=1
(Wed Apr 07 2010 - 18:13:24 PDT)
Re: [AMBER] error in reading namelist cntrl
(Mon Apr 05 2010 - 05:22:16 PDT)
Re: [AMBER] undo iwrap wrapping
(Mon Apr 05 2010 - 03:30:53 PDT)
Re: [AMBER] Water models ?
(Thu Apr 01 2010 - 06:07:49 PDT)
Re: [AMBER] reg-Generalized Born Approach
(Thu Apr 01 2010 - 05:12:13 PDT)
case
Re: [AMBER] xgrid in opempi 1.4.1 still broken
(Fri Apr 30 2010 - 09:35:02 PDT)
Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more
(Fri Apr 30 2010 - 07:41:11 PDT)
Re: [AMBER] failed to compile Amber11 with mpi on Mac
(Thu Apr 29 2010 - 08:08:31 PDT)
Re: [AMBER] sleap from AT 1.4 doesn't seem ok
(Thu Apr 29 2010 - 06:43:59 PDT)
Re: [AMBER] new ambertools folder distribution and Makefile_at
(Mon Apr 26 2010 - 13:11:10 PDT)
Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between
(Mon Apr 26 2010 - 05:50:39 PDT)
[AMBER] Announcement: release of Amber11 and AmberTools 1.4
(Mon Apr 26 2010 - 05:41:28 PDT)
Re: [AMBER] pmemd.cuda problem
(Sun Apr 25 2010 - 09:23:42 PDT)
Re: [AMBER] problem on running saveAmberParm
(Fri Apr 23 2010 - 10:52:11 PDT)
Re: [AMBER] Do molecular dynamics in the limited space
(Fri Apr 23 2010 - 05:50:32 PDT)
Re: [AMBER] Thole screening in sander
(Wed Apr 14 2010 - 08:09:49 PDT)
Re: [AMBER] Automatic assignment of HID, HIP, HIE??
(Tue Apr 13 2010 - 09:42:51 PDT)
Re: [AMBER] Asking help for some analysis section
(Tue Apr 13 2010 - 07:39:29 PDT)
Re: [AMBER] loadmol2 Segmentation fault
(Tue Apr 13 2010 - 05:18:51 PDT)
Re: [AMBER] loadmol2 Segmentation fault
(Tue Apr 13 2010 - 05:16:28 PDT)
Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Tue Apr 13 2010 - 04:59:04 PDT)
Re: [AMBER] Amber11, pure QM PBC
(Mon Apr 12 2010 - 09:18:05 PDT)
Re: [AMBER] trying to use antechamber with -nc 0 for a molecule
(Mon Apr 12 2010 - 07:23:50 PDT)
Re: [AMBER] regarding antechamber
(Mon Apr 12 2010 - 04:43:24 PDT)
Re: [AMBER] amber 5 manual
(Thu Apr 08 2010 - 13:01:45 PDT)
Re: [AMBER] amber 5 manual
(Thu Apr 08 2010 - 11:36:03 PDT)
Re: [AMBER] regGB
(Thu Apr 08 2010 - 07:59:47 PDT)
Re: [AMBER] angle force constants in GAFF
(Thu Apr 08 2010 - 05:27:43 PDT)
Re: [AMBER] Umbrella Sampling with distances; setting of r1 and r4 in the restraint
(Wed Apr 07 2010 - 11:51:06 PDT)
Re: [AMBER] makeANG_rst values
(Tue Apr 06 2010 - 15:00:14 PDT)
Re: [AMBER] Problems during AMBER 10 compilation.
(Tue Apr 06 2010 - 06:55:01 PDT)
Re: [AMBER] Problems during AMBER 10 compilation.
(Tue Apr 06 2010 - 05:55:40 PDT)
Re: [AMBER] Problems during AMBER 10 compilation.
(Tue Apr 06 2010 - 05:23:01 PDT)
Re: [AMBER] Problems during AMBER 10 compilation.
(Tue Apr 06 2010 - 04:58:02 PDT)
Re: [AMBER] antechamber
(Tue Apr 06 2010 - 04:46:21 PDT)
Re: [AMBER] Re: ligand exchange
(Tue Apr 06 2010 - 04:42:13 PDT)
Re: [AMBER] error in reading namelist cntrl
(Mon Apr 05 2010 - 07:17:28 PDT)
Re: [AMBER] error in reading namelist cntrl
(Mon Apr 05 2010 - 05:53:16 PDT)
Re: [AMBER] antechamber
(Mon Apr 05 2010 - 04:41:14 PDT)
Re: [AMBER] makeANG_rst values
(Sat Apr 03 2010 - 15:18:00 PDT)
Re: [AMBER] problem when doing bond in tleap
(Sat Apr 03 2010 - 07:34:05 PDT)
Re: [AMBER] COOH group:extra undesired bond::NO reply :-(
(Sat Apr 03 2010 - 07:31:59 PDT)
Re: [AMBER] problem with frcmod parameter
(Fri Apr 02 2010 - 08:16:53 PDT)
Re: [AMBER] How to perform backbone and residues restraint at the same time
(Fri Apr 02 2010 - 06:57:34 PDT)
Re: [AMBER] Problems during AMBER 10 compilation.
(Thu Apr 01 2010 - 05:53:05 PDT)
Re: [AMBER] SASA
(Thu Apr 01 2010 - 05:17:36 PDT)
Re: [AMBER] antechamber
(Thu Apr 01 2010 - 05:14:19 PDT)
Re: [AMBER] reg-Generalized Born Approach
(Thu Apr 01 2010 - 05:12:03 PDT)
Cen Gao
Re: [AMBER] amber <-> desmond conversion tools
(Tue Apr 13 2010 - 22:25:43 PDT)
Chih-Ying Lin
[AMBER] SASA
(Sun Apr 04 2010 - 17:39:45 PDT)
Cristina Sisu
[AMBER] explicit water MMPBSA
(Tue Apr 27 2010 - 06:54:56 PDT)
Daniel Roe
Re: [AMBER] Trajectory Smoothing
(Sat Apr 17 2010 - 13:52:13 PDT)
Re: [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test
(Mon Apr 12 2010 - 08:12:29 PDT)
Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)...
(Mon Apr 12 2010 - 05:29:53 PDT)
Re: [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test
(Mon Apr 12 2010 - 05:12:44 PDT)
Re: [AMBER] USING PTRAJ TO PROCESS PMEMD TRAJECTORY COORDINTES DATA
(Tue Apr 06 2010 - 09:25:53 PDT)
Re: [AMBER] Regarding RDF calculation in Ptraj
(Mon Apr 05 2010 - 05:04:31 PDT)
David A. Case
Re: [AMBER] MOPAC2009 output results into antechamber
(Wed Apr 21 2010 - 10:03:26 PDT)
Re: [AMBER] Trajectory Smoothing
(Sun Apr 18 2010 - 11:19:56 PDT)
Re: [AMBER] Trajectory Smoothing
(Sun Apr 18 2010 - 00:37:24 PDT)
Re: [AMBER] NMR refinment issues
(Sat Apr 17 2010 - 01:53:44 PDT)
Re: [AMBER] Unit of analyze modes with ptraj
(Thu Apr 15 2010 - 14:40:51 PDT)
Re: [AMBER] loadmol2 Segmentation fault
(Thu Apr 15 2010 - 08:02:38 PDT)
Re: [AMBER] Chirality of amines in GAFF
(Wed Apr 14 2010 - 15:34:01 PDT)
David Watson
Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more
(Fri Apr 30 2010 - 07:29:35 PDT)
Re: [AMBER] a possible typo bug while building pmemd with mpi
(Thu Apr 29 2010 - 09:22:33 PDT)
Re: [AMBER] failed to compile Amber11 with mpi on Mac
(Thu Apr 29 2010 - 07:54:08 PDT)
Re: [AMBER] ambertools 1.4, tests
(Tue Apr 27 2010 - 06:31:36 PDT)
Dean Cuebas
Re: [AMBER] a possible typo bug while building pmemd with mpi
(Fri Apr 30 2010 - 10:52:10 PDT)
Re: [AMBER] Compiling AmberTools 1.4 on MacOS10.5
(Tue Apr 27 2010 - 12:42:16 PDT)
[AMBER] Compiling AmberTools 1.4 on MacOS10.5
(Tue Apr 27 2010 - 10:26:37 PDT)
Re: [AMBER] Setup of defined salt concentrations
(Tue Apr 20 2010 - 09:14:17 PDT)
Re: [AMBER] how is pH treated in Amber - other than constant pH simulations
(Tue Apr 20 2010 - 08:08:24 PDT)
Re: [AMBER] Simulation of complex
(Mon Apr 19 2010 - 09:52:00 PDT)
Re: [AMBER] how is pH treated in Amber - other than constant pH simulations
(Fri Apr 16 2010 - 13:05:43 PDT)
Re: [AMBER] how is pH treated in Amber - other than constant pH simulations
(Fri Apr 16 2010 - 09:53:34 PDT)
Re: [AMBER] BOND TYPE corrections
(Fri Apr 16 2010 - 09:02:20 PDT)
Re: [AMBER] BOND TYPE
(Thu Apr 15 2010 - 19:08:43 PDT)
Re: [AMBER] How do you know when to include improper dihedrals????
(Thu Apr 15 2010 - 08:33:31 PDT)
Re: [AMBER] How do you know when to include improper dihedrals????
(Thu Apr 15 2010 - 08:23:12 PDT)
Re: [AMBER] Chirality of amines in GAFF
(Wed Apr 14 2010 - 15:12:51 PDT)
[AMBER] Automatic assignment of HID, HIP, HIE??
(Tue Apr 13 2010 - 09:36:09 PDT)
[AMBER] How do you know when to include improper dihedrals????
(Mon Apr 12 2010 - 12:30:07 PDT)
[AMBER] Files for Charged serine in proteins?
(Tue Apr 06 2010 - 09:39:04 PDT)
Dian Jiao
Re: [AMBER] PMEMD compiling errors
(Fri Apr 23 2010 - 13:26:47 PDT)
[AMBER] PMEMD compiling errors
(Fri Apr 23 2010 - 11:25:47 PDT)
Diddo Diddens
[AMBER] Thole screening in sander
(Wed Apr 14 2010 - 07:31:23 PDT)
Diego Javier Alonso de Armiño
Re: Re[4]: [AMBER] developing amber force field
(Fri Apr 09 2010 - 09:52:20 PDT)
Dima A Sabbah
Re: [AMBER] problem in MMPBSA
(Sun Apr 18 2010 - 12:02:11 PDT)
Re: Re: [AMBER] problem in MMPBSA
(Sun Apr 18 2010 - 11:52:55 PDT)
Re: [AMBER] problem in MMPBSA
(Sat Apr 17 2010 - 10:09:05 PDT)
[AMBER] Second Request
(Mon Apr 12 2010 - 06:59:56 PDT)
[AMBER] mmpbsa-problem
(Fri Apr 09 2010 - 09:30:59 PDT)
Dmitri Nilov
Re: [AMBER] antechamber
(Thu Apr 01 2010 - 00:37:13 PDT)
Dmitry Mukha
[AMBER] QMMM Iron
(Thu Apr 01 2010 - 03:07:08 PDT)
[AMBER] QMMM Iron
(Thu Apr 01 2010 - 02:15:23 PDT)
Dmitry Nilov
Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between
(Mon Apr 26 2010 - 03:53:15 PDT)
Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between
(Mon Apr 26 2010 - 02:33:01 PDT)
Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups?
(Tue Apr 20 2010 - 04:46:20 PDT)
Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups?
(Tue Apr 20 2010 - 04:41:26 PDT)
Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups?
(Tue Apr 20 2010 - 03:43:52 PDT)
Re: [AMBER] how to add a gradually reduced restraint
(Mon Apr 19 2010 - 07:45:22 PDT)
Re: [AMBER] How do you know when to include improper dihedrals????
(Thu Apr 15 2010 - 05:42:21 PDT)
Re: [AMBER] How do you know when to include improper dihedrals????
(Thu Apr 15 2010 - 03:05:13 PDT)
[AMBER] Chirality of amines in GAFF
(Wed Apr 14 2010 - 00:43:47 PDT)
Re: [AMBER] antechamber
(Thu Apr 01 2010 - 03:05:48 PDT)
Emmanuel Baribefe Naziga
[AMBER] Vlimit error in ABMD
(Mon Apr 12 2010 - 09:06:44 PDT)
Re: [AMBER] contiguous trajectory without iwrap=1
(Wed Apr 07 2010 - 16:56:42 PDT)
[AMBER] contiguous trajectory without iwrap=1
(Wed Apr 07 2010 - 16:03:34 PDT)
Eruysal, Ferdi
[AMBER] amber10 installation on SGI IRIX 6.5
(Mon Apr 05 2010 - 13:37:49 PDT)
fancy2012
Re:Re: [AMBER] How to prepare the two tolopogy files when doing TI calculation?
(Tue Apr 13 2010 - 05:58:53 PDT)
[AMBER] How to prepare the two tolopogy files when doing TI calculation?
(Tue Apr 13 2010 - 05:29:17 PDT)
Fernando Martín García
[AMBER] Nucleic acid aperture
(Fri Apr 16 2010 - 01:52:34 PDT)
FyD
Re: [AMBER] forcefield parameters for TiO2/peptides?
(Thu Apr 29 2010 - 15:56:39 PDT)
Re: [AMBER] Fortran runtime error: Bad value during integer read
(Thu Apr 29 2010 - 12:55:05 PDT)
Re: [AMBER] loadmol2 Segmentation fault
(Thu Apr 15 2010 - 10:23:09 PDT)
Re: [AMBER] loadmol2 Segmentation fault
(Thu Apr 15 2010 - 01:23:24 PDT)
Re: [AMBER] loadmol2 Segmentation fault
(Thu Apr 15 2010 - 00:44:45 PDT)
Re: [AMBER] loadmol2 Segmentation fault
(Wed Apr 14 2010 - 12:56:26 PDT)
Re: [AMBER] Chirality of amines in GAFF
(Wed Apr 14 2010 - 12:51:52 PDT)
Re: [AMBER] loadmol2 Segmentation fault
(Tue Apr 13 2010 - 11:25:51 PDT)
Re: [AMBER] loadmol2 Segmentation fault
(Tue Apr 13 2010 - 03:51:11 PDT)
Re: [AMBER] loadmol2 Segmentation fault
(Tue Apr 13 2010 - 03:30:40 PDT)
g t
Re: [AMBER] problem rejoining segmented out files in long simulation
(Wed Apr 28 2010 - 09:10:20 PDT)
[AMBER] problem rejoining segmented out files in long simulation
(Wed Apr 28 2010 - 08:04:59 PDT)
Ganesh Kamath
[AMBER] radius of gyration
(Thu Apr 15 2010 - 12:42:29 PDT)
Re: [AMBER] Solvent
(Fri Apr 09 2010 - 08:53:36 PDT)
[AMBER] energy decomposition
(Wed Apr 07 2010 - 14:29:08 PDT)
[AMBER] non bonded interactions (vanderwaal and electrostatic)
(Wed Apr 07 2010 - 11:44:04 PDT)
[AMBER] question about EVB
(Tue Apr 06 2010 - 11:45:28 PDT)
[AMBER] radius of gyration
(Tue Apr 06 2010 - 11:43:22 PDT)
Ganesh Krishnan
Re: [AMBER] Trajectory Smoothing
(Sun Apr 18 2010 - 13:22:43 PDT)
Re: [AMBER] Trajectory Smoothing
(Sun Apr 18 2010 - 12:53:12 PDT)
Re: [AMBER] Trajectory Smoothing
(Sun Apr 18 2010 - 12:02:34 PDT)
Re: [AMBER] Trajectory Smoothing
(Sun Apr 18 2010 - 10:25:47 PDT)
Re: [AMBER] Trajectory Smoothing
(Sat Apr 17 2010 - 23:50:58 PDT)
Re: [AMBER] Trajectory Smoothing
(Sat Apr 17 2010 - 09:43:41 PDT)
[AMBER] Trajectory Smoothing
(Wed Apr 14 2010 - 19:23:15 PDT)
George Tzotzos
[AMBER] Request for MD protocol
(Tue Apr 20 2010 - 07:07:11 PDT)
German Erlenkamp
Re: [AMBER] Installation on sles11 on ibm-power6-cpus
(Fri Apr 23 2010 - 00:35:04 PDT)
[AMBER] Installation on sles11 on ibm-power6-cpus
(Mon Apr 12 2010 - 00:50:15 PDT)
geyan
Re: Re: RE: [AMBER] about IGB
(Sun Apr 25 2010 - 22:42:32 PDT)
Re: RE: [AMBER] about IGB
(Sun Apr 25 2010 - 01:50:17 PDT)
[AMBER] about IGB
(Fri Apr 23 2010 - 18:08:51 PDT)
Re: [AMBER] H-bond analysis in ptraj
(Thu Apr 22 2010 - 22:54:22 PDT)
[AMBER] molecular surface area
(Thu Apr 22 2010 - 22:49:01 PDT)
Re: Re: Re: [AMBER] how do MM_PBSA without water
(Thu Apr 22 2010 - 01:21:05 PDT)
Re: Re: Re: [AMBER] how do MM_PBSA without water
(Wed Apr 21 2010 - 01:44:53 PDT)
Re: Re: Re: [AMBER] how do MM_PBSA without water
(Mon Apr 19 2010 - 00:33:23 PDT)
Re: Re: [AMBER] how do MM_PBSA without water
(Sun Apr 18 2010 - 08:20:57 PDT)
[AMBER] how do MM_PBSA without water
(Sun Apr 18 2010 - 00:48:06 PDT)
gokul algates
[AMBER] RAMD
(Sun Apr 11 2010 - 22:51:39 PDT)
Gustavo Seabra
Re: [AMBER] QM/MM + PIMD
(Fri Apr 16 2010 - 12:20:12 PDT)
Re: [AMBER] QMMM Iron
(Thu Apr 01 2010 - 11:20:37 PDT)
Hasan Alniss
[AMBER] A bugfix for thiazole-imidazole rings
(Wed Apr 28 2010 - 04:55:08 PDT)
Homa Azizian
Re: [AMBER] joining out files
(Thu Apr 29 2010 - 14:29:47 PDT)
Re: [AMBER] joining out files
(Thu Apr 29 2010 - 04:03:55 PDT)
[AMBER] joining out files
(Wed Apr 28 2010 - 20:37:39 PDT)
[AMBER] BOND TYPE
(Thu Apr 15 2010 - 18:46:49 PDT)
[AMBER] distrbuting an excess charge
(Sun Apr 11 2010 - 22:50:30 PDT)
Hopkins, Robert
RE: [AMBER] Stability Calculation Using MMPBSA.py?
(Thu Apr 29 2010 - 13:24:31 PDT)
[AMBER] Stability Calculation Using MMPBSA.py?
(Thu Apr 29 2010 - 12:36:45 PDT)
Hyma vathi
Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between
(Mon Apr 26 2010 - 09:58:35 PDT)
Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between
(Mon Apr 26 2010 - 02:55:59 PDT)
[AMBER] WARNING: There is a bond of 8.894214 angstroms between
(Mon Apr 26 2010 - 02:19:30 PDT)
Re: [AMBER] Error: Sander output is missing values
(Wed Apr 21 2010 - 08:50:33 PDT)
Re: [AMBER] Error: Sander output is missing values
(Tue Apr 20 2010 - 08:08:31 PDT)
[AMBER] Error: Sander output is missing values
(Tue Apr 20 2010 - 03:31:32 PDT)
Re: [AMBER] error in reading namelist cntrl
(Mon Apr 05 2010 - 07:03:09 PDT)
[AMBER] error in reading namelist cntrl
(Mon Apr 05 2010 - 05:17:26 PDT)
[AMBER] thermodynamic integration
(Fri Apr 02 2010 - 23:00:12 PDT)
Ibrahim Moustafa
Re: [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test
(Mon Apr 12 2010 - 06:39:07 PDT)
Re: [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test
(Fri Apr 09 2010 - 16:14:25 PDT)
[AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test
(Fri Apr 09 2010 - 15:40:47 PDT)
Ilyas Yildirim
Re: [AMBER] AMBER VS QM energy calculations for dihedrals
(Wed Apr 28 2010 - 07:32:42 PDT)
Re: [AMBER] Comparing dihedral energy curves
(Mon Apr 26 2010 - 10:15:53 PDT)
[AMBER] Chirality Restraint
(Wed Apr 07 2010 - 10:46:25 PDT)
imtiaz shafiq
[AMBER] correct syntax for assinging scmask to two atoms of different molecules
(Thu Apr 01 2010 - 07:00:47 PDT)
[AMBER] SANDER BOMB in subroutine sc_check_and_adjust Atom coordinate disagreement
(Thu Apr 01 2010 - 06:15:20 PDT)
InSuk Joung
Re: [AMBER] Setup of defined salt concentrations
(Tue Apr 20 2010 - 07:44:24 PDT)
Re: [AMBER] developing amber force field
(Thu Apr 08 2010 - 18:44:14 PDT)
Jacky Zhao
Re: [AMBER] contiguous trajectory without iwrap=1
(Wed Apr 07 2010 - 18:01:09 PDT)
Jagdeesh C
[AMBER] Ptraj Problem
(Wed Apr 07 2010 - 21:35:57 PDT)
jani vinod
Re: [AMBER] regarding running Nudged Elastic Band Approach with amber10
(Tue Apr 20 2010 - 20:12:28 PDT)
Re: [AMBER] regarding running Nudged Elastic Band Approach with amber10
(Mon Apr 19 2010 - 21:11:52 PDT)
[AMBER] regarding running Nudged Elastic Band Approach with amber10
(Mon Apr 19 2010 - 02:18:29 PDT)
Re: [AMBER] vacuum bubbles generated after heating
(Tue Apr 13 2010 - 02:26:34 PDT)
Jason Swails
Re: [AMBER] TER dfinition at the middile of pdb file
(Fri Apr 30 2010 - 20:29:23 PDT)
Re: [AMBER] a possible typo bug while building pmemd with mpi
(Fri Apr 30 2010 - 20:12:30 PDT)
Re: [AMBER] how to write one ptraj file into several smaller files
(Fri Apr 30 2010 - 05:08:37 PDT)
Re: [AMBER] joining out files
(Thu Apr 29 2010 - 14:40:21 PDT)
Re: [AMBER] Stability Calculation Using MMPBSA.py?
(Thu Apr 29 2010 - 12:49:12 PDT)
Re: [AMBER] a possible typo bug while building pmemd with mpi
(Thu Apr 29 2010 - 09:57:46 PDT)
Re: [AMBER] a possible typo bug while building pmemd with mpi
(Thu Apr 29 2010 - 08:50:28 PDT)
Re: [AMBER] failed to compile Amber11 with mpi on Mac
(Thu Apr 29 2010 - 07:51:26 PDT)
Re: [AMBER] Fortran runtime error: Bad value during integer read
(Thu Apr 29 2010 - 06:30:45 PDT)
Re: [AMBER] Fortran runtime error: Bad value during integer read
(Thu Apr 29 2010 - 05:10:25 PDT)
Re: [AMBER] problem rejoining segmented out files in long simulation
(Wed Apr 28 2010 - 08:31:03 PDT)
Re: [AMBER]Fortran runtime error: Bad value during integer read
(Tue Apr 27 2010 - 21:38:13 PDT)
Re: [AMBER]Fortran runtime error: Bad value during integer read
(Tue Apr 27 2010 - 21:15:45 PDT)
Re: [AMBER] Compiling AmberTools 1.4 on MacOS10.5
(Tue Apr 27 2010 - 10:34:33 PDT)
Re: [AMBER] ambertools 1.4, tests
(Tue Apr 27 2010 - 09:05:33 PDT)
Re: [AMBER]Fortran runtime error: Bad value during integer read
(Tue Apr 27 2010 - 05:15:37 PDT)
Re: Re: [AMBER] H-bond analysis in ptraj
(Sat Apr 24 2010 - 05:19:26 PDT)
Re: [AMBER] bond command
(Thu Apr 22 2010 - 17:52:11 PDT)
Re: [AMBER] regarding sqm
(Thu Apr 22 2010 - 05:15:26 PDT)
Re: [AMBER] vdW question.
(Wed Apr 21 2010 - 19:29:39 PDT)
Re: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ?
(Wed Apr 21 2010 - 13:02:10 PDT)
Re: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ?
(Wed Apr 21 2010 - 06:35:38 PDT)
Re: [AMBER] regarding running Nudged Elastic Band Approach with amber10
(Wed Apr 21 2010 - 05:10:58 PDT)
Re: [AMBER] mm-pbsa *_com.all.out files
(Wed Apr 21 2010 - 05:00:19 PDT)
Re: Re: Re: [AMBER] how do MM_PBSA without water
(Wed Apr 21 2010 - 04:55:36 PDT)
Re: Re: [AMBER] remove water from system
(Wed Apr 21 2010 - 04:37:47 PDT)
Re: [AMBER] Error: Sander output is missing values
(Tue Apr 20 2010 - 08:41:03 PDT)
Re: [AMBER] remove water from system
(Tue Apr 20 2010 - 05:16:42 PDT)
Re: [AMBER] problem in MMPBSA
(Mon Apr 19 2010 - 04:28:06 PDT)
Re: [AMBER] Trajectory Smoothing
(Sat Apr 17 2010 - 14:45:22 PDT)
Re: [AMBER] problem in MMPBSA
(Sat Apr 17 2010 - 13:53:06 PDT)
Re: [AMBER] error when running mmpbsa
(Sat Apr 17 2010 - 07:58:41 PDT)
Re: [AMBER] chirality restraints for non-standard residue
(Fri Apr 16 2010 - 11:37:43 PDT)
Re: [AMBER] how is pH treated in Amber - other than constant pH simulations
(Fri Apr 16 2010 - 11:25:49 PDT)
Re: [AMBER] periodic boundary condition
(Thu Apr 15 2010 - 09:39:25 PDT)
Re: [AMBER] periodic boundary condition
(Thu Apr 15 2010 - 04:02:39 PDT)
Re: [AMBER] Entropy-problem
(Wed Apr 14 2010 - 15:31:37 PDT)
Re: [AMBER] Chirality of amines in GAFF
(Wed Apr 14 2010 - 05:44:39 PDT)
Re: [AMBER] Regarding parameter files of dna-lig complex
(Tue Apr 13 2010 - 06:46:49 PDT)
Re: [AMBER] how to pick certain water molecular from a .mdcrd
(Tue Apr 13 2010 - 05:13:36 PDT)
Re: [AMBER] distrbuting an excess charge
(Mon Apr 12 2010 - 03:16:30 PDT)
Re: [AMBER] vacuum bubbles generated after heating
(Mon Apr 12 2010 - 03:11:45 PDT)
Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)...
(Mon Apr 12 2010 - 03:03:35 PDT)
Re: [AMBER] vlimit exceeded for step
(Fri Apr 09 2010 - 16:59:01 PDT)
Re: [AMBER] Install AMBER problem.
(Fri Apr 09 2010 - 16:38:54 PDT)
Re: [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test
(Fri Apr 09 2010 - 16:02:25 PDT)
Re: [AMBER] vlimit exceeded for step
(Fri Apr 09 2010 - 05:36:33 PDT)
Re: Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame
(Thu Apr 08 2010 - 18:52:24 PDT)
Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame
(Thu Apr 08 2010 - 05:51:34 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Thu Apr 08 2010 - 05:45:43 PDT)
Re: [AMBER] Ptraj Problem
(Wed Apr 07 2010 - 21:47:59 PDT)
Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame
(Wed Apr 07 2010 - 21:03:31 PDT)
Re: [AMBER] Traceback: not available, complile with -ftrace = frame
(Wed Apr 07 2010 - 07:00:05 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Wed Apr 07 2010 - 06:36:13 PDT)
Re: [AMBER] rna simulation
(Mon Apr 05 2010 - 02:34:48 PDT)
Re: [AMBER] MMPBSA-ON-CLUSTER
(Sat Apr 03 2010 - 21:18:23 PDT)
Re: [AMBER] MMPBSA-ON-CLUSTER
(Sat Apr 03 2010 - 06:43:38 PDT)
Re: [AMBER] Problem with an output file
(Thu Apr 01 2010 - 21:21:52 PDT)
Jianing
[AMBER] question about cluster analysis
(Tue Apr 27 2010 - 20:01:11 PDT)
Re:Re: [AMBER] how to add a gradually reduced restraint
(Tue Apr 20 2010 - 00:49:14 PDT)
[AMBER] how to add a gradually reduced restraint
(Mon Apr 19 2010 - 02:07:00 PDT)
Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Wed Apr 14 2010 - 18:33:07 PDT)
Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Wed Apr 14 2010 - 06:13:22 PDT)
Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Wed Apr 14 2010 - 05:25:28 PDT)
Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Tue Apr 13 2010 - 19:44:33 PDT)
Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Tue Apr 13 2010 - 06:25:29 PDT)
Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Tue Apr 13 2010 - 06:15:14 PDT)
Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Mon Apr 12 2010 - 22:17:46 PDT)
Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Mon Apr 12 2010 - 21:57:38 PDT)
Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Mon Apr 12 2010 - 05:37:30 PDT)
Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Mon Apr 12 2010 - 05:12:08 PDT)
Jim Miller
[AMBER] question about mass card of frcmod file
(Thu Apr 29 2010 - 14:50:52 PDT)
Jio M
Re: [AMBER] chirality restraints for non-standard residue
(Sun Apr 18 2010 - 01:57:05 PDT)
Re: [AMBER] chirality restraints for non-standard residue
(Fri Apr 16 2010 - 12:18:42 PDT)
Re: [AMBER] chirality restraints for non-standard residue
(Fri Apr 16 2010 - 11:54:12 PDT)
[AMBER] chirality restraints for non-standard residue
(Fri Apr 16 2010 - 04:15:08 PDT)
Re: [AMBER] 1-4 EEL
(Thu Apr 15 2010 - 23:32:36 PDT)
[AMBER] 1-4 EEL
(Thu Apr 15 2010 - 00:47:40 PDT)
[AMBER] 1-4 EEL
(Wed Apr 14 2010 - 04:44:08 PDT)
[AMBER] COOH group:extra undesired bond
(Tue Apr 06 2010 - 21:09:31 PDT)
Re: [AMBER] COOH group:extra undesired bond::NO reply :-(
(Sun Apr 04 2010 - 00:25:12 PDT)
[AMBER] COOH group:extra undesired bond::NO reply :-(
(Fri Apr 02 2010 - 23:34:45 PDT)
John S
[AMBER] Re: ligand exchange
(Tue Apr 06 2010 - 01:35:39 PDT)
[AMBER] ligand exchange
(Mon Apr 05 2010 - 15:05:34 PDT)
Josh Berryman
[AMBER] PMEMD missing type? - bugfix
(Fri Apr 16 2010 - 06:25:01 PDT)
João Henriques
Re: [AMBER] Fortran runtime error: Bad value during integer read
(Fri Apr 30 2010 - 05:28:51 PDT)
Re: [AMBER] Fortran runtime error: Bad value during integer read
(Thu Apr 29 2010 - 11:39:39 PDT)
Re: [AMBER] Fortran runtime error: Bad value during integer read
(Thu Apr 29 2010 - 06:19:13 PDT)
Re: [AMBER] Fortran runtime error: Bad value during integer read
(Thu Apr 29 2010 - 05:32:58 PDT)
Re: [AMBER] Fortran runtime error: Bad value during integer read
(Thu Apr 29 2010 - 04:20:00 PDT)
[AMBER] Fortran runtime error: Bad value during integer read
(Wed Apr 28 2010 - 09:09:35 PDT)
João Sardinha
Re: [AMBER] angle force constants in GAFF
(Thu Apr 08 2010 - 05:59:35 PDT)
[AMBER] angle force constants in GAFF
(Thu Apr 08 2010 - 04:11:00 PDT)
Juan Carlos
RE: [AMBER] PROBLEM WITH PMEMD PERFORMANCE
(Thu Apr 15 2010 - 02:03:46 PDT)
[AMBER] PROBLEM WITH PMEMD PERFORMANCE
(Mon Apr 12 2010 - 03:24:12 PDT)
Re: [AMBER] USING PTRAJ TO PROCESS PMEMD TRAJECTORY COORDINTES DATA
(Thu Apr 08 2010 - 03:49:08 PDT)
[AMBER] USING PTRAJ TO PROCESS PMEMD TRAJECTORY COORDINTES DATA
(Tue Apr 06 2010 - 00:35:40 PDT)
juan zeng
Re: [AMBER] periodic boundary condition
(Fri Apr 16 2010 - 00:34:53 PDT)
[AMBER] periodic boundary condition
(Wed Apr 14 2010 - 22:11:52 PDT)
[AMBER] periodic boundary condition
(Wed Apr 14 2010 - 02:34:40 PDT)
kamlesh sahu
Re: [AMBER] The system has extended beyond the extent of the virtual box
(Mon Apr 26 2010 - 17:23:17 PDT)
[AMBER] The system has extended beyond the extent of the virtual box
(Mon Apr 26 2010 - 01:31:23 PDT)
Karl N. Kirschner
Re: [AMBER] How do you know when to include improper dihedrals????
(Thu Apr 15 2010 - 06:18:02 PDT)
Re: Re[2]: [AMBER] developing amber force field
(Fri Apr 09 2010 - 03:12:14 PDT)
kecy_w.sina.com
[AMBER] how to achieve the 2D periodic boundary
(Fri Apr 02 2010 - 06:59:53 PDT)
Kevin Hauser
Re: [AMBER] vdW question.
(Wed Apr 21 2010 - 20:26:50 PDT)
Kshatresh Dutta Dubey
Re: [AMBER] Unit of atomic fluctuation unit
(Mon Apr 05 2010 - 23:22:51 PDT)
Lachele Foley (Lists)
[AMBER] OT: GLYLIB C libraries for molecular data
(Wed Apr 28 2010 - 16:02:42 PDT)
Re: [AMBER] how to load topology file
(Tue Apr 27 2010 - 15:32:44 PDT)
Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)...
(Mon Apr 12 2010 - 05:51:07 PDT)
Re: [AMBER] problem with XLEAP on X-client run on windows machine...
(Sun Apr 11 2010 - 18:23:09 PDT)
lee lior
[AMBER] Problem with an output file
(Thu Apr 01 2010 - 21:00:49 PDT)
Lekpa Duukori
Re: [AMBER] Comparing dihedral energy curves
(Mon Apr 26 2010 - 11:56:50 PDT)
[AMBER] Comparing dihedral energy curves
(Mon Apr 26 2010 - 09:34:24 PDT)
Levi Pierce
Re: [AMBER] pmemd.cuda problem
(Mon Apr 26 2010 - 09:19:46 PDT)
Re: [AMBER] pmemd.cuda problem
(Sat Apr 24 2010 - 19:04:47 PDT)
[AMBER] pmemd.cuda problem
(Sat Apr 24 2010 - 16:18:57 PDT)
[AMBER] PMEMD.CUDA on GTX275
(Wed Apr 14 2010 - 21:36:40 PDT)
Lijiang Yang
[AMBER] A possible pmemd bug
(Thu Apr 22 2010 - 04:59:42 PDT)
liu junjun
Re: [AMBER] about skinnb
(Wed Apr 28 2010 - 14:25:58 PDT)
Re: [AMBER] about skinnb
(Wed Apr 28 2010 - 13:27:35 PDT)
Re: [AMBER] about skinnb
(Wed Apr 28 2010 - 13:02:42 PDT)
Re: [AMBER] about skinnb
(Wed Apr 28 2010 - 12:05:21 PDT)
[AMBER] about skinnb
(Tue Apr 27 2010 - 10:08:48 PDT)
luzhenw1.msu.edu
Re: [AMBER] nmr order parameter and autocorrelation
(Fri Apr 30 2010 - 14:39:01 PDT)
[AMBER] nmr order parameter and autocorrelation
(Fri Apr 30 2010 - 13:43:00 PDT)
M. L. Dodson
Re: [AMBER] QM/MM cut problem
(Tue Apr 20 2010 - 10:04:35 PDT)
manikanthan bhavaraju
[AMBER] Fwd: .rst file corrupted
(Fri Apr 09 2010 - 08:48:52 PDT)
Marek Maly
Re: [AMBER] Addions grid ?
(Tue Apr 27 2010 - 14:05:10 PDT)
Re: [AMBER] Addions grid ?
(Tue Apr 27 2010 - 11:22:41 PDT)
Re: [AMBER] Addions grid ?
(Tue Apr 27 2010 - 10:58:04 PDT)
[AMBER] Addions grid ?
(Tue Apr 27 2010 - 07:59:16 PDT)
Re: Fw: Fwd: Fw: Fw: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ?
(Tue Apr 27 2010 - 07:32:04 PDT)
Re: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ?
(Wed Apr 21 2010 - 16:07:39 PDT)
Re: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ?
(Wed Apr 21 2010 - 10:29:39 PDT)
[AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ?
(Tue Apr 20 2010 - 12:54:04 PDT)
Matthias Wildauer
Re: [AMBER] About restart-job
(Wed Apr 14 2010 - 05:53:50 PDT)
Re: [AMBER] Umbrella Sampling with distances; setting of r1 and r4 in the restraint
(Wed Apr 07 2010 - 11:53:53 PDT)
[AMBER] Umbrella Sampling with distances; setting of r1 and r4 in the restraint
(Wed Apr 07 2010 - 11:04:45 PDT)
maya maya
Re: [AMBER] regGB
(Thu Apr 08 2010 - 23:37:53 PDT)
[AMBER] regGB
(Thu Apr 08 2010 - 03:51:23 PDT)
Re: [AMBER] reg-Generalized Born Approach
(Wed Mar 31 2010 - 21:49:20 PDT)
Mengjuei Hsieh
Re: [AMBER] Fortran runtime error: Bad value during integer read
(Wed Apr 28 2010 - 18:33:42 PDT)
Re: [AMBER] ambertools 1.4, tests
(Tue Apr 27 2010 - 11:37:29 PDT)
mish
Re: [AMBER] mmpbsa-job-killed
(Thu Apr 08 2010 - 04:17:11 PDT)
moitrayee.mbu.iisc.ernet.in
[AMBER] problem with paiwise energy decomposition using mm-pbsa
(Fri Apr 23 2010 - 11:50:14 PDT)
[AMBER] mm-pbsa *_com.all.out files
(Tue Apr 20 2010 - 23:07:55 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Wed Apr 07 2010 - 21:45:44 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Wed Apr 07 2010 - 05:42:24 PDT)
monica.imtech.res.in
[AMBER] distance mapping
(Fri Apr 30 2010 - 07:51:48 PDT)
Re: [AMBER] how to write one ptraj file into several smaller files
(Fri Apr 30 2010 - 06:19:45 PDT)
[AMBER] antechamber
(Sun Apr 04 2010 - 22:52:36 PDT)
Re: [AMBER] antechamber
(Sun Apr 04 2010 - 21:41:48 PDT)
Re: [AMBER] antechamber
(Thu Apr 01 2010 - 02:53:44 PDT)
Re: [AMBER] Problem with solvationbox command
(Thu Apr 01 2010 - 02:08:32 PDT)
[AMBER] antechamber
(Wed Mar 31 2010 - 23:57:43 PDT)
N.R. Jena
Re: [AMBER] Simulation of complex
(Wed Apr 21 2010 - 04:10:20 PDT)
Re: [AMBER] Simulation of complex
(Wed Apr 21 2010 - 04:05:31 PDT)
Nancy
[AMBER] Does the frequency of output affect MD simulation in AMBER10?
(Mon Apr 12 2010 - 04:06:05 PDT)
Necmettin Pirinccioglu
Re[4]: [AMBER] developing amber force field
(Fri Apr 09 2010 - 03:57:14 PDT)
Re[2]: [AMBER] developing amber force field
(Fri Apr 09 2010 - 02:03:51 PDT)
[AMBER] developing amber force field
(Thu Apr 08 2010 - 12:46:10 PDT)
Nicee
Re: [AMBER] vacuum bubbles generated after heating
(Tue Apr 13 2010 - 05:53:40 PDT)
[AMBER] vacuum bubbles generated after heating
(Mon Apr 12 2010 - 02:59:32 PDT)
Nicholas Musolino
Re: [AMBER] mm-pbsa: self assembly
(Tue Apr 20 2010 - 04:59:17 PDT)
Re: [AMBER] elevated temperature MD
(Mon Apr 19 2010 - 10:31:05 PDT)
Re: [AMBER] Force constant
(Sun Apr 18 2010 - 11:38:33 PDT)
Re: [AMBER] Force constant
(Sun Apr 18 2010 - 09:08:14 PDT)
nicholus bhattacharjee
[AMBER] Asking help for some analysis section
(Tue Apr 13 2010 - 07:04:03 PDT)
[AMBER] Unit of atomic fluctuation unit
(Mon Apr 05 2010 - 22:39:26 PDT)
Palermo Giulia
[AMBER] AMBER VS QM energy calculations for dihedrals
(Wed Apr 28 2010 - 07:09:50 PDT)
Parish, Carol
[AMBER] amber <-> desmond conversion tools
(Tue Apr 13 2010 - 11:13:22 PDT)
Paul Brandt
[AMBER] undo iwrap wrapping
(Mon Apr 05 2010 - 00:21:22 PDT)
Paul S. Nerenberg
Re: [AMBER] nmr order parameter and autocorrelation
(Fri Apr 30 2010 - 15:19:51 PDT)
Re: [AMBER] Compiling pmemd (Amber 10) with OpenMPI, pathscale, etc.
(Thu Apr 22 2010 - 16:50:57 PDT)
[AMBER] Compiling pmemd (Amber 10) with OpenMPI, pathscale, etc.
(Thu Apr 22 2010 - 15:58:07 PDT)
pellegrini
Re: [AMBER] Strange atom charge in topology file
(Tue Apr 20 2010 - 08:12:01 PDT)
[AMBER] Strange atom charge in topology file
(Tue Apr 20 2010 - 06:20:33 PDT)
Peter Schmidtke
RE: [AMBER] PMEMD.CUDA on GTX275
(Wed Apr 14 2010 - 23:14:38 PDT)
Piotr Cieplak
[AMBER] MM parameters for TiO2
(Fri Apr 30 2010 - 14:57:28 PDT)
Re: [AMBER] Fortran runtime error: Bad value during integer read
(Thu Apr 29 2010 - 13:56:54 PDT)
Re: [AMBER] Fortran runtime error: Bad value during integer read
(Thu Apr 29 2010 - 13:50:51 PDT)
Re: [AMBER] Fortran runtime error: Bad value during integer read
(Thu Apr 29 2010 - 10:56:59 PDT)
pxq
Re: Re: Re: [AMBER] error when running mmpbsa
(Sun Apr 18 2010 - 19:49:37 PDT)
Re: Re: [AMBER] error when running mmpbsa
(Sun Apr 18 2010 - 04:34:44 PDT)
[AMBER] error when running mmpbsa
(Sat Apr 17 2010 - 07:25:35 PDT)
[AMBER] how to pick certain water molecular from a .mdcrd
(Mon Apr 12 2010 - 23:35:08 PDT)
[AMBER] how to pick certain water molecular from a .mdcrd
(Mon Apr 12 2010 - 07:08:38 PDT)
[AMBER] not sure of the atomtype in .prep
(Mon Apr 05 2010 - 06:02:35 PDT)
Re: Re: [AMBER] problem when doing bond in tleap
(Sun Apr 04 2010 - 08:09:38 PDT)
[AMBER] problem when doing bond in tleap
(Sat Apr 03 2010 - 00:32:59 PDT)
Re: Re: [AMBER] problem with frcmod parameter
(Fri Apr 02 2010 - 19:10:02 PDT)
[AMBER] problem with frcmod parameter
(Fri Apr 02 2010 - 07:50:59 PDT)
Ramu Anandakrishnan
Fw: Fwd: Fw: Fw: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ?
(Tue Apr 27 2010 - 05:43:17 PDT)
Re: [AMBER] How to prepare the two tolopogy files when doing TIcalculation?
(Tue Apr 13 2010 - 05:40:46 PDT)
Rilei Yu
[AMBER] Problem from ala scanning
(Fri Apr 30 2010 - 07:31:25 PDT)
Re: [AMBER] Entropy-problem
(Wed Apr 14 2010 - 18:47:02 PDT)
[AMBER] Entropy-problem
(Wed Apr 14 2010 - 15:11:36 PDT)
[AMBER] About restart-job
(Tue Apr 13 2010 - 15:48:14 PDT)
Re: [AMBER] vlimit exceeded for step
(Sat Apr 10 2010 - 00:47:33 PDT)
RE: [AMBER] mmpbsa-job-killed
(Fri Apr 09 2010 - 16:57:49 PDT)
Re: [AMBER] vlimit exceeded for step
(Fri Apr 09 2010 - 16:50:56 PDT)
[AMBER] vlimit exceeded for step
(Thu Apr 08 2010 - 23:52:31 PDT)
[AMBER] mmpbsa-job-killed
(Thu Apr 08 2010 - 04:07:25 PDT)
Re: [AMBER] MMPBSA-ON-CLUSTER
(Sun Apr 04 2010 - 03:13:12 PDT)
Re: [AMBER] MMPBSA-ON-CLUSTER
(Sat Apr 03 2010 - 20:42:57 PDT)
Re: [AMBER] MMPBSA-ON-CLUSTER
(Sat Apr 03 2010 - 18:56:49 PDT)
[AMBER] Sorry for my multiple-email (making mistake!)
(Sat Apr 03 2010 - 05:12:51 PDT)
[AMBER] MMPBSA-ON-CLUSTER
(Sat Apr 03 2010 - 03:17:47 PDT)
[AMBER] 转发: MMPBSA-on-cluster
(Sat Apr 03 2010 - 03:15:25 PDT)
[AMBER] MMPBSA-on-cluster
(Sat Apr 03 2010 - 02:47:31 PDT)
Re: [AMBER] How to perform backbone and residues restraint at the same time
(Sat Apr 03 2010 - 02:40:27 PDT)
[AMBER] How to perform backbone and residues restraint at the same time
(Thu Apr 01 2010 - 19:20:55 PDT)
Robert Duke
Re: [AMBER] about skinnb
(Wed Apr 28 2010 - 14:04:36 PDT)
Re: [AMBER] about skinnb
(Wed Apr 28 2010 - 12:16:53 PDT)
Re: [AMBER] about skinnb
(Tue Apr 27 2010 - 10:32:34 PDT)
Re: [AMBER] A possible pmemd bug
(Thu Apr 22 2010 - 07:01:24 PDT)
Re: [AMBER] effect of pre-processor flags on pmemd?
(Wed Apr 21 2010 - 13:31:20 PDT)
Re: [AMBER] PMEMD missing type? - bugfix
(Fri Apr 16 2010 - 08:54:36 PDT)
Re: [AMBER] PMEMD missing type? - bugfix
(Fri Apr 16 2010 - 07:02:05 PDT)
Re: [AMBER] Amber10 Cuda compile failure
(Mon Apr 12 2010 - 14:53:07 PDT)
Re: [AMBER] USING PTRAJ TO PROCESS PMEMD TRAJECTORY COORDINTES DATA
(Tue Apr 06 2010 - 06:20:50 PDT)
rolandmarques.aol.com
Re: [AMBER] NMR refinment issues
(Thu Apr 15 2010 - 12:54:32 PDT)
[AMBER] NMR refinment issues
(Wed Apr 14 2010 - 09:17:44 PDT)
ros
Re: [AMBER] vdW question.
(Thu Apr 22 2010 - 08:43:25 PDT)
[AMBER] vdW question.
(Wed Apr 21 2010 - 18:41:38 PDT)
Ross Walker
RE: [AMBER] "go" keyword in ptraj
(Fri Apr 30 2010 - 06:43:10 PDT)
RE: [AMBER] QM/MM cut problem
(Thu Apr 29 2010 - 05:59:52 PDT)
RE: [AMBER] QM/MM cut problem
(Thu Apr 29 2010 - 02:09:11 PDT)
RE: [AMBER] Tesla C2050 atom limit?
(Thu Apr 29 2010 - 01:12:22 PDT)
RE: [AMBER] pmemd.cuda problem
(Mon Apr 26 2010 - 00:36:16 PDT)
RE: [AMBER] pmemd.cuda problem
(Sat Apr 24 2010 - 18:43:24 PDT)
RE: [AMBER] about IGB
(Fri Apr 23 2010 - 22:55:43 PDT)
RE: [AMBER] PMEMD compiling errors
(Fri Apr 23 2010 - 12:09:19 PDT)
RE: [AMBER] question about Amber Tutorial-A1
(Fri Apr 23 2010 - 08:04:24 PDT)
RE: [AMBER] A possible pmemd bug
(Thu Apr 22 2010 - 16:47:49 PDT)
RE: [AMBER] Compiling pmemd (Amber 10) with OpenMPI, pathscale, etc.
(Thu Apr 22 2010 - 16:23:37 PDT)
RE: [AMBER] QM/MM cut problem
(Tue Apr 20 2010 - 15:43:51 PDT)
RE: [AMBER] QM/MM cut problem
(Tue Apr 20 2010 - 10:20:07 PDT)
RE: [AMBER] regarding running Nudged Elastic Band Approach with amber10
(Mon Apr 19 2010 - 13:30:56 PDT)
[AMBER] RE: RE: question on section 2 of MM-PBSA tutorial
(Fri Apr 16 2010 - 18:29:31 PDT)
RE: [AMBER] PMEMD missing type? - bugfix
(Fri Apr 16 2010 - 09:11:50 PDT)
RE: [AMBER] PMEMD missing type? - bugfix
(Fri Apr 16 2010 - 08:48:03 PDT)
RE: [AMBER] PROBLEM WITH PMEMD PERFORMANCE
(Thu Apr 15 2010 - 23:38:11 PDT)
RE: [AMBER] PMEMD.CUDA on GTX275
(Wed Apr 14 2010 - 23:31:54 PDT)
RE: [AMBER] PMEMD.CUDA on GTX275
(Wed Apr 14 2010 - 22:56:56 PDT)
RE: [AMBER] Amber10 Cuda compile failure
(Wed Apr 14 2010 - 20:04:09 PDT)
RE: [AMBER] Is the variation of C-Cl bond length normal?
(Tue Apr 13 2010 - 12:57:03 PDT)
RE: [AMBER] PROBLEM WITH PMEMD PERFORMANCE
(Tue Apr 13 2010 - 09:00:13 PDT)
RE: [AMBER] Amber11, pure QM PBC
(Tue Apr 13 2010 - 08:57:12 PDT)
RE: [AMBER] Amber10 Cuda compile failure
(Tue Apr 13 2010 - 08:54:59 PDT)
RE: [AMBER] Amber10 Cuda compile failure
(Mon Apr 12 2010 - 14:57:36 PDT)
RE: [AMBER] vlimit exceeded for step
(Fri Apr 09 2010 - 11:59:53 PDT)
RE: [AMBER] multiconformational RESP fitting with antechamber
(Thu Apr 08 2010 - 22:54:41 PDT)
RE: [AMBER] I do need your help, please
(Thu Apr 08 2010 - 22:52:19 PDT)
RE: [AMBER] mmpbsa-job-killed
(Thu Apr 08 2010 - 22:30:43 PDT)
RE: [AMBER] Segmentation Fault
(Thu Apr 01 2010 - 12:14:42 PDT)
RE: [AMBER] QMMM Iron
(Thu Apr 01 2010 - 11:09:45 PDT)
RE: [AMBER] QMMM Iron
(Thu Apr 01 2010 - 09:00:32 PDT)
Rui Li
RE: [AMBER] question about Amber Tutorial-A1
(Fri Apr 23 2010 - 21:57:54 PDT)
[AMBER] question about Amber Tutorial-A1
(Fri Apr 23 2010 - 03:55:26 PDT)
Re: [AMBER] loadmol2 Segmentation fault
(Wed Apr 14 2010 - 23:39:52 PDT)
Re: [AMBER] loadmol2 Segmentation fault
(Tue Apr 13 2010 - 23:30:20 PDT)
[AMBER] loadmol2 Segmentation fault
(Tue Apr 13 2010 - 02:55:34 PDT)
Samuel Genheden
[AMBER] Unit of analyze modes with ptraj
(Thu Apr 15 2010 - 11:22:21 PDT)
[AMBER] Unit of analyze modes with ptraj
(Tue Apr 06 2010 - 02:54:28 PDT)
Scott Brozell
Re: [AMBER] A possible pmemd bug
(Thu Apr 22 2010 - 14:19:58 PDT)
Re: [AMBER] loadmol2 Segmentation fault
(Wed Apr 14 2010 - 13:02:41 PDT)
Re: [AMBER] loadmol2 Segmentation fault
(Wed Apr 14 2010 - 12:07:02 PDT)
Scott Le Grand
RE: [AMBER] Tesla C2050 atom limit?
(Thu Apr 29 2010 - 00:02:17 PDT)
Seetin, Matthew
RE: [AMBER] Umbrella Sampling with distances; setting of r1 and r4 in the restraint
(Wed Apr 07 2010 - 11:50:33 PDT)
RE: [AMBER] Chirality Restraint
(Wed Apr 07 2010 - 10:58:47 PDT)
Senthil Natesan
[AMBER] freezing selected residues
(Fri Apr 30 2010 - 10:11:20 PDT)
[AMBER] Amber99FFSB parameter files for Gaussian
(Wed Apr 07 2010 - 07:43:15 PDT)
shamoon siddiqui
Re: [AMBER] rna simulation
(Sun Apr 04 2010 - 23:59:47 PDT)
Re: [AMBER] rna simulation
(Sun Apr 04 2010 - 23:23:34 PDT)
Re: [AMBER] rna simulation
(Sun Apr 04 2010 - 22:50:47 PDT)
Shozeb Haider
Re: [AMBER] Simulation of complex
(Mon Apr 19 2010 - 08:26:21 PDT)
Shulin Zhuang
Re: [AMBER] H-bond analysis in ptraj
(Thu Apr 22 2010 - 23:57:31 PDT)
[AMBER] Re: Is the variation of C-Cl bond length normal?
(Tue Apr 13 2010 - 11:25:58 PDT)
[AMBER] Is the variation of C-Cl bond length normal?
(Mon Apr 12 2010 - 15:26:12 PDT)
Siddharth Rastogi
[AMBER] how to load topology file
(Tue Apr 27 2010 - 15:21:33 PDT)
[AMBER] bond command
(Thu Apr 22 2010 - 17:31:02 PDT)
Silvia Carlotto
Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)...
(Mon Apr 12 2010 - 04:30:36 PDT)
[AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)...
(Mon Apr 12 2010 - 02:08:50 PDT)
Srivatsan
[AMBER] Hydrogen Bond Analysis - explanation needed
(Fri Apr 23 2010 - 02:42:33 PDT)
steinbrt.rci.rutgers.edu
Re: [AMBER] vdW question.
(Thu Apr 22 2010 - 00:22:14 PDT)
Re: [AMBER] Simulation of complex
(Wed Apr 21 2010 - 04:03:40 PDT)
Re: [AMBER] Simulation of complex
(Wed Apr 21 2010 - 02:24:12 PDT)
[AMBER] Printing the reaction field in pbsa
(Tue Apr 20 2010 - 08:30:36 PDT)
Re: [AMBER] Request for MD protocol
(Tue Apr 20 2010 - 07:14:31 PDT)
Re: [AMBER] Simulation of complex
(Mon Apr 19 2010 - 08:42:43 PDT)
Re: [AMBER] How to prepare the two tolopogy files when doing TI calculation?
(Tue Apr 13 2010 - 05:35:46 PDT)
Re: [AMBER] thermodynamic integration
(Sat Apr 03 2010 - 08:02:45 PDT)
Re: [AMBER] correct syntax for assinging scmask to two atoms of different molecules
(Thu Apr 01 2010 - 07:14:04 PDT)
Steve Seibold
[AMBER] elevated Temperature MD
(Tue Apr 20 2010 - 09:30:40 PDT)
[AMBER] elevated temperature MD
(Mon Apr 19 2010 - 10:10:08 PDT)
Taufik Al-Sarraj
Re: [AMBER] radius of gyration
(Fri Apr 16 2010 - 07:28:36 PDT)
[AMBER] angle between DNA (vector) and a plane
(Thu Apr 15 2010 - 10:04:14 PDT)
Thomas Cheatham
Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations
(Tue Apr 13 2010 - 20:13:55 PDT)
Re: [AMBER] how to pick certain water molecular from a .mdcrd
(Tue Apr 13 2010 - 20:00:27 PDT)
Thomas Cheatham III
RE: [AMBER] "go" keyword in ptraj
(Fri Apr 30 2010 - 08:39:21 PDT)
Re: [AMBER] vlimit exceeded for step
(Fri Apr 09 2010 - 08:02:34 PDT)
Thomas Zeiser
[AMBER] effect of pre-processor flags on pmemd?
(Wed Apr 21 2010 - 13:12:17 PDT)
tianyuan meng
[AMBER] problem on running saveAmberParm
(Thu Apr 22 2010 - 18:54:39 PDT)
Titus, Jamie (bairdje)
[AMBER] ff99SB-ILDN
(Tue Apr 27 2010 - 11:38:32 PDT)
Tom Joseph
Re: [AMBER] PROBLEM WITH PMEMD PERFORMANCE
(Mon Apr 12 2010 - 08:16:03 PDT)
Tom Williams
Re: [AMBER] forcefield parameters for TiO2/peptides?
(Thu Apr 29 2010 - 14:03:48 PDT)
[AMBER] forcefield parameters for TiO2/peptides?
(Wed Apr 28 2010 - 13:31:01 PDT)
Trevor Gokey
Re: [AMBER] Fortran runtime error :bad value duiring floating point read
(Thu Apr 08 2010 - 03:36:24 PDT)
Trojan 007
RE: [AMBER] Install AMBER problem.
(Sat Apr 10 2010 - 17:55:43 PDT)
[AMBER] Install AMBER problem.
(Fri Apr 09 2010 - 16:07:53 PDT)
vijayaraj.clri.res.in
[AMBER] mm-pbsa: self assembly
(Tue Apr 20 2010 - 04:45:42 PDT)
Vlad Cojocaru
Re: [AMBER] RAMD random number generator
(Thu Apr 15 2010 - 01:20:09 PDT)
Re: [AMBER] RAMD
(Mon Apr 12 2010 - 01:48:36 PDT)
Waad RHAIEM
[AMBER] RAMD random number generator
(Wed Apr 14 2010 - 07:20:59 PDT)
[AMBER] (no subject)
(Wed Apr 14 2010 - 07:12:15 PDT)
William Flak
[AMBER] RESP Iodine
(Sun Apr 25 2010 - 04:52:21 PDT)
Re: [AMBER] Force constant
(Sun Apr 18 2010 - 09:56:53 PDT)
[AMBER] Force constant
(Sun Apr 18 2010 - 08:54:55 PDT)
Re: [AMBER] amber 5 manual
(Thu Apr 08 2010 - 12:48:33 PDT)
[AMBER] I do need your help, please
(Thu Apr 08 2010 - 12:04:50 PDT)
[AMBER] dummy atom
(Wed Apr 07 2010 - 08:21:31 PDT)
[AMBER] amber 5 manual
(Wed Apr 07 2010 - 08:10:26 PDT)
xuemeiwang1103
[AMBER] Water models ?
(Thu Apr 01 2010 - 06:01:05 PDT)
Yi Shang
Re: [AMBER] Question about RMSD in AMBER
(Wed Apr 28 2010 - 08:44:51 PDT)
Re: [AMBER] Strange atom charge in topology file
(Tue Apr 20 2010 - 07:21:07 PDT)
Re: [AMBER] Strange atom charge in topology file
(Tue Apr 20 2010 - 07:02:23 PDT)
[AMBER] multiconformational RESP fitting with antechamber
(Thu Apr 08 2010 - 12:28:12 PDT)
Ying Yang
Re: [AMBER]Fortran runtime error: Bad value during integer read
(Tue Apr 27 2010 - 19:53:44 PDT)
[AMBER]Fortran runtime error: Bad value during integer read
(Mon Apr 26 2010 - 23:59:54 PDT)
Yingjie Lin
[AMBER] Question: ptraj masks
(Wed Apr 28 2010 - 14:22:19 PDT)
Re: [AMBER] Question about RMSD in AMBER
(Wed Apr 28 2010 - 07:57:04 PDT)
[AMBER] Question about RMSD in AMBER
(Tue Apr 27 2010 - 17:42:55 PDT)
Yu Chen
Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more
(Fri Apr 30 2010 - 11:20:30 PDT)
Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more
(Fri Apr 30 2010 - 08:46:55 PDT)
Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more
(Fri Apr 30 2010 - 08:25:35 PDT)
[AMBER] Undefined symbols: "___builtin___strcpy_chk" and more
(Fri Apr 30 2010 - 07:10:44 PDT)
[AMBER] AmberTool 1.4 with Intel 10.1.014 on snow leopard
(Thu Apr 29 2010 - 11:54:16 PDT)
Yunfen Wang
Re:Re: [AMBER] H-bond analysis in ptraj
(Fri Apr 23 2010 - 17:56:38 PDT)
Re:Re: [AMBER] remove water from system
(Wed Apr 21 2010 - 02:42:38 PDT)
Re:Re: [AMBER] remove water from system
(Tue Apr 20 2010 - 17:53:36 PDT)
Re:Re: [AMBER] the volume is always getting bigger and bigger until crash
(Wed Apr 14 2010 - 17:47:38 PDT)
[AMBER] the volume is always getting bigger and bigger until crash
(Wed Apr 14 2010 - 00:56:11 PDT)
Re:Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame
(Thu Apr 08 2010 - 18:35:20 PDT)
Re:Re: [AMBER] Fortran runtime error :bad value duiring floating point read
(Thu Apr 08 2010 - 05:02:43 PDT)
Re:Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame
(Wed Apr 07 2010 - 23:33:58 PDT)
Re:Re: [AMBER] Traceback: not available, complile with -ftrace = frame
(Wed Apr 07 2010 - 20:51:39 PDT)
Yunfen Wang
[AMBER] how to write one ptraj file into several smaller files
(Fri Apr 30 2010 - 05:00:02 PDT)
[AMBER] H-bond analysis in ptraj
(Thu Apr 22 2010 - 20:30:27 PDT)
[AMBER] solvent accessible surface
(Wed Apr 21 2010 - 20:27:11 PDT)
[AMBER] remove water from system
(Tue Apr 20 2010 - 01:09:01 PDT)
[AMBER] analysis for solvation effect for protein
(Sat Apr 17 2010 - 01:21:14 PDT)
[AMBER] Fortran runtime error :bad value duiring floating point read
(Thu Apr 08 2010 - 03:05:50 PDT)
[AMBER] Traceback: not available, complile with -ftrace = frame
(Wed Apr 07 2010 - 06:56:33 PDT)
Yunjie Zhao
Re: [AMBER] Do molecular dynamics in the limited space
(Thu Apr 22 2010 - 19:35:10 PDT)
[AMBER] Do molecular dynamics in the limited space
(Wed Apr 21 2010 - 06:40:31 PDT)
zgong.hust
Re: Re: [AMBER] problem in MMPBSA
(Sat Apr 17 2010 - 18:49:01 PDT)
[AMBER] problem in MMPBSA
(Sat Apr 17 2010 - 08:06:47 PDT)
[AMBER] problem in MMPBSA
(Fri Apr 16 2010 - 06:23:57 PDT)
zoran matovic
Re: [AMBER] trying to use antechamber with -nc 0 for a molecule
(Mon Apr 12 2010 - 08:50:03 PDT)
Zuzanna K. Scigacz
[AMBER] Problems during AMBER 10 compilation.
(Thu Apr 01 2010 - 05:10:16 PDT)
Zuzanna K. Ścigacz
Re: [AMBER] Problems during AMBER 10 compilation.
(Tue Apr 06 2010 - 10:37:36 PDT)
Re: [AMBER] Problems during AMBER 10 compilation.
(Tue Apr 06 2010 - 06:13:54 PDT)
Re: [AMBER] Problems during AMBER 10 compilation.
(Tue Apr 06 2010 - 05:40:49 PDT)
Re: [AMBER] Problems during AMBER 10 compilation.
(Tue Apr 06 2010 - 05:09:28 PDT)
Re: [AMBER] Problems during AMBER 10 compilation.
(Tue Apr 06 2010 - 02:17:18 PDT)
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Fri Apr 30 2010 - 21:00:03 PDT
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