Amber Archive Mar 2010 by author
756 messages
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Starting
Mon Mar 01 2010 - 04:00:03 PST,
Ending
Wed Mar 31 2010 - 14:00:02 PDT
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Adrian Roitberg
Re: [AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency
(Wed Mar 31 2010 - 11:50:23 PDT)
Re: [AMBER] membranes
(Wed Mar 31 2010 - 08:24:37 PDT)
[AMBER] membranes
(Wed Mar 31 2010 - 07:29:17 PDT)
Re: [AMBER] problem with steered MD
(Tue Mar 23 2010 - 15:50:19 PDT)
Re: [AMBER] problem with steered MD
(Tue Mar 23 2010 - 07:16:35 PDT)
Re: [AMBER] How to obtain an ideal helix structure of Alanine 5 peptide (ACE-Ala5-NME) ?
(Thu Mar 18 2010 - 14:36:06 PDT)
Re: [AMBER] Extract potential energy from ptraj?
(Tue Mar 09 2010 - 20:18:04 PST)
Aiko Matsumoto
[AMBER] RESP, AM1BCC & geometries
(Tue Mar 16 2010 - 06:34:55 PDT)
Alan
Re: [AMBER] transforming Antechamber GAFF parameters into another force field
(Sun Mar 28 2010 - 04:51:11 PDT)
Re: [AMBER] about amber force field
(Mon Mar 22 2010 - 08:20:11 PDT)
Re: [AMBER] about amber force field
(Mon Mar 22 2010 - 07:47:26 PDT)
Re: [AMBER] about amber force field
(Mon Mar 22 2010 - 07:43:47 PDT)
Re: [AMBER] about amber force field
(Mon Mar 22 2010 - 06:59:35 PDT)
Re: [AMBER] ATP charge convergence
(Fri Mar 19 2010 - 09:34:22 PDT)
[AMBER] antechamber changing atom name case, is it right?
(Thu Mar 18 2010 - 10:03:36 PDT)
Re: [AMBER] IMPROPER TERM CONTRIBUTION
(Thu Mar 18 2010 - 08:47:57 PDT)
Re: [AMBER] IMPROPER TERM CONTRIBUTION
(Thu Mar 18 2010 - 08:04:15 PDT)
Re: [AMBER] IMPROPER TERM CONTRIBUTION
(Wed Mar 17 2010 - 05:17:16 PDT)
albert albert
Re: [AMBER] Installation error of amber10 after compile Ambertools1.3
(Mon Mar 01 2010 - 03:43:31 PST)
Alessandro Nascimento
[AMBER] Using 6-12 / 10-12 potential in AMBER
(Tue Mar 23 2010 - 08:44:01 PDT)
[AMBER] 10Gb Interconnect profile
(Tue Mar 09 2010 - 06:42:17 PST)
Alexander Metz
AW: Re: [AMBER] can't get the final "snapshot_statistics.out" file
(Mon Mar 15 2010 - 04:52:50 PDT)
Amedeo Capobianco
Re: [AMBER] DEBIAN: cannot get rid of xleap SOLVED
(Wed Mar 31 2010 - 12:01:35 PDT)
[AMBER] DEBIAN: cannot get rid of xleap
(Wed Mar 31 2010 - 10:31:54 PDT)
Amire-Brahimi Benjamin
Re: [AMBER] combining coordinate and velocity files into one
(Tue Mar 09 2010 - 15:02:06 PST)
[AMBER] combining coordinate and velocity files into one
(Sun Mar 07 2010 - 13:42:57 PST)
Ananya Paul
Re: [AMBER] problem to generate parameters files from NMR solved DNA structure
(Thu Mar 11 2010 - 05:40:54 PST)
[AMBER] problem to generate parameters files from NMR solved DNA structure
(Wed Mar 10 2010 - 23:30:08 PST)
Re: [AMBER] problem to generate parameters files of DNA
(Wed Mar 10 2010 - 06:37:40 PST)
[AMBER] problem to generate parameters files of DNA
(Wed Mar 10 2010 - 02:18:28 PST)
Andrew Olson
Re: [AMBER] sander bomb and maxpr question
(Wed Mar 24 2010 - 07:08:15 PDT)
Re: [AMBER] sander bomb and maxpr question
(Wed Mar 17 2010 - 15:30:05 PDT)
[AMBER] sander bomb and maxpr question
(Wed Mar 17 2010 - 11:51:36 PDT)
Andrew Voronkov
Re: Re: [AMBER] ligand-protein complex parametrization problems
(Fri Mar 12 2010 - 04:17:16 PST)
[AMBER] ligand-protein complex parametrization problems
(Thu Mar 11 2010 - 07:39:52 PST)
aneesh cna
[AMBER] Regarding problem with self guided molecular dynamics
(Mon Mar 22 2010 - 23:02:18 PDT)
[AMBER] Regarding SGLD
(Tue Mar 16 2010 - 06:40:02 PDT)
Re: [AMBER] ATP force field
(Tue Mar 09 2010 - 01:11:36 PST)
[AMBER] Regarding energy in mdout file in SANDER
(Wed Mar 03 2010 - 02:19:33 PST)
Anna Dejardin
Re: [AMBER] AMBER10 installation: make test error 1
(Wed Mar 31 2010 - 08:09:00 PDT)
[AMBER] AMBER10 installation: make test error 1
(Fri Mar 05 2010 - 06:30:37 PST)
Re: [AMBER] AmberTools1.3 installation error
(Thu Mar 04 2010 - 02:43:54 PST)
Re: [AMBER] AmberTools1.3 installation error
(Wed Mar 03 2010 - 06:20:09 PST)
Re: [AMBER] AmberTools1.3 installation error
(Wed Mar 03 2010 - 03:47:28 PST)
Antonios Samiotakis
Re: [AMBER] Lennard Jones potential
(Thu Mar 18 2010 - 16:50:51 PDT)
Arash Farahmand
[AMBER] G03: ONIOM
(Fri Mar 12 2010 - 06:59:33 PST)
Asfa Ali
Re: [AMBER] regarding ambertools
(Sat Mar 20 2010 - 09:53:42 PDT)
[AMBER] regarding ambertools
(Fri Mar 19 2010 - 10:52:40 PDT)
Re: [AMBER] regarding NMR structures
(Tue Mar 16 2010 - 23:51:41 PDT)
[AMBER] regarding NMR structures
(Tue Mar 16 2010 - 06:08:20 PDT)
Re: [AMBER] Difference of ff99 and ff03 in building DNA duplex
(Thu Mar 11 2010 - 20:40:37 PST)
Re: [AMBER] Fortran run time error
(Tue Mar 09 2010 - 20:25:29 PST)
[AMBER] Fortran run time error
(Tue Mar 09 2010 - 06:30:54 PST)
[AMBER] Distortions
(Tue Mar 09 2010 - 05:03:08 PST)
[AMBER] Distortions
(Mon Mar 08 2010 - 01:22:26 PST)
Re: [AMBER] AMBER
(Thu Mar 04 2010 - 21:24:15 PST)
[AMBER] AMBER
(Thu Mar 04 2010 - 01:16:31 PST)
[AMBER] Segmentation fault
(Wed Mar 03 2010 - 07:20:28 PST)
Aurum Bai
[AMBER] MMPBSA err!
(Mon Mar 08 2010 - 06:30:06 PST)
Balazs Jojart
Re: [AMBER] membranes
(Wed Mar 31 2010 - 09:00:26 PDT)
Re: [AMBER] membranes
(Wed Mar 31 2010 - 07:56:24 PDT)
Re: [AMBER] how to get the hydrophobic area for a particlar region
(Sat Mar 27 2010 - 05:28:13 PDT)
Re: [AMBER] how to get the hydrophobic area for a particlar region
(Thu Mar 25 2010 - 11:14:33 PDT)
Re: [OFFLIST] Re: [AMBER] Protein + Bilayer Simulations: Role of salt
(Tue Mar 02 2010 - 23:32:50 PST)
Barbault Florent
Re: [AMBER] atom-type cz ???
(Wed Mar 03 2010 - 07:59:58 PST)
[AMBER] atom-type cz ???
(Wed Mar 03 2010 - 05:30:59 PST)
bbalta.itu.edu.tr
Re: [AMBER] serial compilation of pmemd
(Mon Mar 22 2010 - 06:51:02 PDT)
Beale, John
[AMBER] radgyr
(Tue Mar 23 2010 - 03:44:05 PDT)
[AMBER] Large FIle
(Wed Mar 17 2010 - 08:54:14 PDT)
Ben Roberts
Re: [AMBER] is iwrap=1 a key parameter?
(Mon Mar 29 2010 - 06:40:06 PDT)
[AMBER] Specification of solventCap causing atoms to collapse into each other
(Tue Mar 23 2010 - 11:42:44 PDT)
bharat lakhani
[AMBER] Query on Minimization
(Fri Mar 05 2010 - 00:41:36 PST)
[AMBER] Please help me out
(Thu Mar 04 2010 - 03:23:35 PST)
[AMBER] Enquiry regarding MD run
(Tue Mar 02 2010 - 21:42:10 PST)
Bill Ross
Re: [AMBER] reg-Generalized Born Approach
(Wed Mar 31 2010 - 10:13:29 PDT)
Re: [AMBER] tleap savepdb command and organic lignads in proteins
(Tue Mar 30 2010 - 14:48:16 PDT)
RE: [AMBER] issues with pmemd
(Tue Mar 30 2010 - 14:10:16 PDT)
Re: [AMBER] how to deal with the system with negative charge ?
(Tue Mar 30 2010 - 10:19:37 PDT)
RE: [AMBER] transforming Antechamber GAFF parameters into another force field
(Fri Mar 26 2010 - 16:41:12 PDT)
Re: [AMBER] Average structure
(Fri Mar 26 2010 - 09:58:02 PDT)
Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine
(Fri Mar 26 2010 - 09:42:06 PDT)
Re: [AMBER] Antechamber problems.
(Thu Mar 25 2010 - 11:05:36 PDT)
Re: [AMBER] crdgrow AMBER 8
(Wed Mar 24 2010 - 13:01:45 PDT)
Re: [AMBER] Regarding amber molecular dynamics
(Tue Mar 23 2010 - 21:38:20 PDT)
Re: [AMBER] Regarding amber molecular dynamics
(Tue Mar 23 2010 - 11:31:22 PDT)
Re: [AMBER] error in save prmtop
(Tue Mar 23 2010 - 10:37:37 PDT)
Re: [AMBER] Amber: heme atom identification
(Mon Mar 22 2010 - 15:19:14 PDT)
Re: [AMBER] NOT IN RESIDUE TEMPLATES
(Mon Mar 22 2010 - 10:16:47 PDT)
Re: [AMBER] Distance between two atoms vs time
(Mon Mar 22 2010 - 10:03:15 PDT)
Re: [AMBER] Large FIle
(Wed Mar 17 2010 - 10:09:24 PDT)
Re: [AMBER] problem in minimisation
(Wed Mar 17 2010 - 09:58:37 PDT)
Re: [AMBER] IMPROPER TERM CONTRIBUTION
(Wed Mar 17 2010 - 09:45:48 PDT)
Re: [AMBER] How to apply extra dihedrals
(Tue Mar 16 2010 - 20:57:03 PDT)
Re: [AMBER] Minimization Failure
(Tue Mar 16 2010 - 11:36:17 PDT)
Re: [AMBER] Minimization Failure
(Tue Mar 16 2010 - 11:18:29 PDT)
Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?
(Mon Mar 15 2010 - 18:45:12 PDT)
Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?
(Mon Mar 15 2010 - 18:37:43 PDT)
Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?
(Mon Mar 15 2010 - 17:13:35 PDT)
Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?
(Mon Mar 15 2010 - 17:05:50 PDT)
Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?
(Mon Mar 15 2010 - 14:11:34 PDT)
Re: [AMBER] Enquiry regarding MD run
(Mon Mar 15 2010 - 11:45:51 PDT)
Re: [AMBER] Enquiry regarding MD run
(Mon Mar 15 2010 - 10:51:49 PDT)
Re: [AMBER] addions or solvate-which one first
(Sat Mar 13 2010 - 12:25:58 PST)
Re: [AMBER] addions or solvate-which one first
(Sat Mar 13 2010 - 12:18:46 PST)
RE: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type.
(Fri Mar 12 2010 - 12:57:40 PST)
Re: [AMBER] Ptraj problems
(Thu Mar 11 2010 - 10:27:56 PST)
Re: [AMBER] mdinfor error
(Thu Mar 11 2010 - 10:04:20 PST)
Re: [AMBER] mdinfor error
(Thu Mar 11 2010 - 10:03:22 PST)
Re: [AMBER] combining coordinate and velocity files into one
(Tue Mar 09 2010 - 15:39:37 PST)
Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine)
(Tue Mar 09 2010 - 10:07:41 PST)
Re:Re: [AMBER] sander bomb: volume of ucell too big
(Mon Mar 08 2010 - 09:26:02 PST)
Re: [AMBER] AMBER10 installation: make test error 1
(Fri Mar 05 2010 - 16:17:11 PST)
Re: [AMBER] _getcor.f Fortran runtime error: End of file
(Fri Mar 05 2010 - 09:30:18 PST)
Re: [AMBER] Query on Minimization
(Fri Mar 05 2010 - 09:26:28 PST)
Re: [AMBER] Protein Crystal Buried Waters and Amber Simulation ?
(Thu Mar 04 2010 - 16:14:07 PST)
Re: [AMBER] The error information
(Wed Mar 03 2010 - 17:47:04 PST)
Re: [AMBER] Generating cpin file for constant pH in Amber9
(Wed Mar 03 2010 - 11:47:12 PST)
Re: [AMBER] Vdw radii params in antechamber
(Wed Mar 03 2010 - 11:32:20 PST)
Re: [AMBER] Segmentation fault
(Wed Mar 03 2010 - 10:11:02 PST)
Re: [AMBER] AmberTools1.3 installation error
(Wed Mar 03 2010 - 10:02:21 PST)
Re: [AMBER] Enquiry regarding MD run
(Wed Mar 03 2010 - 09:47:21 PST)
Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine)
(Wed Mar 03 2010 - 09:41:36 PST)
Re: [AMBER] Cyclic compounds
(Tue Mar 02 2010 - 10:46:32 PST)
Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine)
(Tue Mar 02 2010 - 10:20:12 PST)
Re: [AMBER] swiss cheese water shell
(Mon Mar 01 2010 - 09:26:30 PST)
Billy Miller III
Re: [AMBER] MM-PBSA not generating snapshot_lig.all.out and snapshot_statistics.out files
(Sat Mar 27 2010 - 12:05:19 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Sat Mar 27 2010 - 07:00:03 PDT)
Re: Re: [AMBER] how to get the hydrophobic area for a particlar region
(Fri Mar 26 2010 - 19:44:40 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Fri Mar 26 2010 - 06:32:22 PDT)
Re: [AMBER] Average structure
(Fri Mar 26 2010 - 05:44:29 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Thu Mar 25 2010 - 19:31:34 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Thu Mar 25 2010 - 06:51:13 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Tue Mar 23 2010 - 06:40:07 PDT)
Re: [AMBER] mmpbsa doesn't work
(Tue Mar 23 2010 - 06:22:55 PDT)
Re: [AMBER] Distance between two atoms vs time
(Mon Mar 22 2010 - 05:57:13 PDT)
Re: [AMBER] Error during MMPBSA calc.
(Fri Mar 19 2010 - 07:15:39 PDT)
Re: [AMBER] MMPBSA calculation
(Thu Mar 18 2010 - 07:45:45 PDT)
Re: [AMBER] MMPBSA.py problem
(Mon Mar 15 2010 - 05:53:57 PDT)
Re: Re: [AMBER] can't get the final "snapshot_statistics.out" file
(Mon Mar 15 2010 - 05:42:11 PDT)
Re: [AMBER] Binding Energy Calculation by QM/MM method
(Sun Mar 14 2010 - 07:40:19 PDT)
Re: [AMBER] can't get the final "snapshot_statistics.out" file
(Sun Mar 14 2010 - 07:21:40 PDT)
Re: [AMBER] MMPBSA.py problem
(Sun Mar 14 2010 - 07:18:20 PDT)
Re: [AMBER] ligand-protein complex parametrization problems
(Thu Mar 11 2010 - 07:50:26 PST)
Re: [AMBER] MMPBSA problems with Fe and Zn
(Mon Mar 01 2010 - 09:18:32 PST)
Re: [AMBER] MMPBSA problems with Fe and Zn
(Mon Mar 01 2010 - 09:11:01 PST)
Re: [AMBER] MMPBSA problems with Fe and Zn
(Mon Mar 01 2010 - 08:21:30 PST)
Carlos Simmerling
Re: [AMBER] reg-Generalized Born Approach
(Wed Mar 31 2010 - 11:21:35 PDT)
Re: [AMBER] disulfide bonds?
(Wed Mar 31 2010 - 06:44:01 PDT)
Re: [AMBER] vlimit error during equilibration step
(Wed Mar 31 2010 - 04:12:38 PDT)
Re: [AMBER] vlimit error during equilibration step
(Tue Mar 30 2010 - 04:29:12 PDT)
Re: Re: [AMBER] minimization really make protein better?
(Tue Mar 30 2010 - 04:22:48 PDT)
Re: [AMBER] AMBER ff99sb
(Tue Mar 30 2010 - 04:19:40 PDT)
Re: [AMBER] simulation under pressure
(Mon Mar 29 2010 - 12:58:40 PDT)
Re: [AMBER] reg REMD
(Mon Mar 29 2010 - 05:02:16 PDT)
Re: [AMBER] minimization really make protein better?
(Mon Mar 29 2010 - 04:35:28 PDT)
Re: [AMBER] AMBER ff99sb
(Mon Mar 29 2010 - 04:32:27 PDT)
Re: [AMBER] MD simulation in gas phase-AMBER 10
(Fri Mar 26 2010 - 08:40:01 PDT)
Re: [AMBER] neb/amber 10
(Fri Mar 26 2010 - 08:13:14 PDT)
Re: [AMBER] MD simulation in gas phase-AMBER 10
(Thu Mar 25 2010 - 10:34:55 PDT)
Re: [AMBER] Lone Pair
(Thu Mar 25 2010 - 10:29:21 PDT)
Re: [AMBER] help for restraint minimization
(Wed Mar 24 2010 - 06:18:52 PDT)
Re: Re: [AMBER] error in save prmtop
(Tue Mar 23 2010 - 07:32:51 PDT)
Re: [AMBER] error in save prmtop
(Tue Mar 23 2010 - 07:08:10 PDT)
Re: [AMBER] radgyr
(Tue Mar 23 2010 - 06:56:01 PDT)
Re: [AMBER] NOT IN RESIDUE TEMPLATES
(Mon Mar 22 2010 - 09:15:41 PDT)
Re: [AMBER] about amber force field
(Mon Mar 22 2010 - 08:37:47 PDT)
Re: [AMBER] about amber force field
(Mon Mar 22 2010 - 08:34:29 PDT)
Re: [AMBER] about amber force field
(Mon Mar 22 2010 - 07:24:39 PDT)
Re: [AMBER] mbonbi and mbondi2
(Sun Mar 21 2010 - 14:01:54 PDT)
Re: [AMBER] general query:RMSD
(Sat Mar 20 2010 - 09:41:57 PDT)
Re: [AMBER] How to obtain an ideal helix structure of Alanine 5 peptide (ACE-Ala5-NME) ?
(Fri Mar 19 2010 - 10:24:14 PDT)
Re: [AMBER] vlimit exceeded for step
(Thu Mar 18 2010 - 07:42:08 PDT)
Re: [AMBER] vlimit exceeded for step
(Thu Mar 18 2010 - 07:29:49 PDT)
Re: [AMBER] ACS Division of Computers in Chemistry: award applications due March 30
(Wed Mar 17 2010 - 17:20:57 PDT)
[AMBER] ACS Division of Computers in Chemistry: award applications due March 30
(Wed Mar 17 2010 - 16:16:20 PDT)
Re: [AMBER] problem in minimisation
(Wed Mar 17 2010 - 08:22:16 PDT)
Re: Re: [AMBER] force field with neutral terminal
(Wed Mar 17 2010 - 08:20:56 PDT)
Re: [AMBER] IMPROPER TERM CONTRIBUTION
(Wed Mar 17 2010 - 05:26:43 PDT)
Re: [AMBER] Calculating Amber Force fields from Wikipedia
(Tue Mar 16 2010 - 18:12:07 PDT)
Re: [AMBER] Calculating Amber Force fields from Wikipedia
(Tue Mar 16 2010 - 16:09:24 PDT)
Re: [AMBER] regarding NMR structures
(Tue Mar 16 2010 - 06:25:30 PDT)
Re: [AMBER] force field with neutral terminal
(Tue Mar 16 2010 - 03:36:36 PDT)
Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?
(Mon Mar 15 2010 - 18:04:59 PDT)
Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?
(Mon Mar 15 2010 - 17:21:38 PDT)
Re: [AMBER] Calculating Amber Force fields from Wikipedia
(Mon Mar 15 2010 - 08:38:05 PDT)
Re: [AMBER] Calculating Amber Force fields from Wikipedia
(Mon Mar 15 2010 - 07:47:36 PDT)
Re: [AMBER] Particle insertion and deletion
(Sun Mar 14 2010 - 14:06:51 PDT)
Re: [AMBER] neb/amber 10
(Sat Mar 13 2010 - 05:21:55 PST)
Re: [AMBER] Enquiry regarding Minimisation
(Sat Mar 13 2010 - 03:48:10 PST)
Re: [AMBER] Ptraj problems
(Thu Mar 11 2010 - 10:56:31 PST)
Re: [AMBER] mdinfor error
(Thu Mar 11 2010 - 03:37:35 PST)
Re: [AMBER] how to do analysis of the local structure
(Thu Mar 11 2010 - 03:31:38 PST)
Re: [AMBER] mdinfor error
(Thu Mar 11 2010 - 03:27:51 PST)
Re: [AMBER] Extract coordinate residues form mdcrd
(Wed Mar 10 2010 - 06:40:17 PST)
Re: [AMBER] Enquiry regarding MD run
(Wed Mar 10 2010 - 06:06:30 PST)
Re: [AMBER] Simulating a protein with nmr structure
(Wed Mar 10 2010 - 03:37:25 PST)
Re: [AMBER] Enquiry regarding MD run
(Wed Mar 10 2010 - 03:36:07 PST)
Re: [AMBER] Distortions
(Tue Mar 09 2010 - 06:01:14 PST)
Re: [AMBER] CIS proline
(Tue Mar 09 2010 - 04:46:35 PST)
Re: [AMBER] question about AMBER 9
(Tue Mar 09 2010 - 03:30:06 PST)
Re: [AMBER] Enquiry regarding MD run
(Tue Mar 09 2010 - 03:31:00 PST)
Re: [AMBER] residual dipolar couplings (RDC)
(Fri Mar 05 2010 - 15:21:18 PST)
Re: [AMBER] Errors while running Amber
(Thu Mar 04 2010 - 05:24:59 PST)
Re: [AMBER] Errors while running Amber
(Thu Mar 04 2010 - 05:00:50 PST)
Re: [AMBER] Amber, CASP again
(Thu Mar 04 2010 - 04:25:19 PST)
Re: [AMBER] Errors while running Amber
(Thu Mar 04 2010 - 04:22:59 PST)
Re: [AMBER] Amber, CASP
(Wed Mar 03 2010 - 18:52:31 PST)
Re: [AMBER] neb/amber 10
(Wed Mar 03 2010 - 12:57:13 PST)
Re: [AMBER] Parameters for trimethylated Lysine?
(Wed Mar 03 2010 - 03:35:23 PST)
Re: [AMBER] Regarding energy in mdout file in SANDER
(Wed Mar 03 2010 - 03:34:54 PST)
case
Re: [AMBER] reg-Generalized Born Approach
(Wed Mar 31 2010 - 11:42:39 PDT)
Re: [AMBER] DEBIAN: cannot get rid of xleap
(Wed Mar 31 2010 - 11:09:00 PDT)
Re: [AMBER] AMBER10 installation: make test error 1
(Wed Mar 31 2010 - 10:56:33 PDT)
Re: [AMBER] disulfide bonds?
(Wed Mar 31 2010 - 06:46:07 PDT)
[AMBER] Running without flex
(Tue Mar 30 2010 - 11:32:17 PDT)
Re: [AMBER] issues with pmemd
(Tue Mar 30 2010 - 11:23:19 PDT)
Re: [AMBER] FW:
(Tue Mar 30 2010 - 05:36:09 PDT)
Re: [AMBER] how to deal with the system with negative charge ?
(Tue Mar 30 2010 - 05:33:20 PDT)
Re: [AMBER] how to convert to standard Amber PDB input
(Tue Mar 30 2010 - 05:24:14 PDT)
Re: [AMBER] is iwrap=1 a key parameter?
(Mon Mar 29 2010 - 07:19:26 PDT)
Re: [AMBER] Run.dip: Program Error during test run after Amber 10 installation
(Sun Mar 28 2010 - 06:48:03 PDT)
Re: [AMBER] Which shake option to be used
(Sun Mar 28 2010 - 06:35:24 PDT)
Re: [AMBER] Amber:antechamber & heme(metal?) problems
(Sat Mar 27 2010 - 11:49:47 PDT)
Re: [AMBER] simulation under pressure
(Fri Mar 26 2010 - 07:54:10 PDT)
Re: [AMBER] sander bomb and maxpr question
(Fri Mar 26 2010 - 07:53:56 PDT)
Re: [AMBER] Antechamber problems.
(Thu Mar 25 2010 - 10:52:31 PDT)
Re: [AMBER] MD simulation in gas phase-AMBER 10
(Thu Mar 25 2010 - 10:50:10 PDT)
Re: [AMBER] crdgrow
(Thu Mar 25 2010 - 10:48:08 PDT)
Re: [AMBER] MD simulation in gas phase-AMBER 10
(Thu Mar 25 2010 - 10:41:14 PDT)
Re: [AMBER] Script for creating topology files , running minimization and MD simulation using amoeba force field
(Thu Mar 25 2010 - 10:39:36 PDT)
Re: [AMBER] difference in output from bnda and fd_helix functions
(Thu Mar 25 2010 - 10:26:18 PDT)
Re: [AMBER] about amber force field
(Mon Mar 22 2010 - 07:41:43 PDT)
Re: [AMBER] Regd:vlimit
(Sun Mar 21 2010 - 23:10:13 PDT)
Re: [AMBER] vlimit exceeded for step
(Thu Mar 18 2010 - 12:27:40 PDT)
Re: [AMBER] IMPROPER TERM CONTRIBUTION
(Thu Mar 18 2010 - 08:12:07 PDT)
Re: [AMBER] sander bomb and maxpr question
(Wed Mar 17 2010 - 17:36:14 PDT)
Re: [AMBER] sander bomb and maxpr question
(Wed Mar 17 2010 - 12:56:21 PDT)
Re: [AMBER] Confirm compiling Amber10/Tools1.3 breaks with intel v 11.1?
(Wed Mar 17 2010 - 09:01:13 PDT)
Re: [AMBER] IMPROPER TERM CONTRIBUTION
(Wed Mar 17 2010 - 04:49:19 PDT)
Re: [AMBER] Minimization Failure
(Tue Mar 16 2010 - 11:24:44 PDT)
Re: [AMBER] regarding NMR structures
(Tue Mar 16 2010 - 10:05:50 PDT)
Re: [AMBER] regarding NMR structures
(Tue Mar 16 2010 - 09:41:28 PDT)
Re: [AMBER] Fwd: understanding AMBER FORCES parm files?
(Sat Mar 13 2010 - 10:59:50 PST)
Re: [AMBER] Spline order too small when using AMOEBA force field
(Sat Mar 13 2010 - 09:34:34 PST)
Re: Re: [AMBER] ligand-protein complex parametrization problems
(Fri Mar 12 2010 - 05:08:57 PST)
Re: [AMBER] Various Errors in Tests
(Fri Mar 12 2010 - 04:56:39 PST)
Re: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type.
(Fri Mar 12 2010 - 04:47:28 PST)
Re: [AMBER] Difference of ff99 and ff03 in building DNA duplex
(Thu Mar 11 2010 - 19:21:12 PST)
Re: [AMBER] Error decoding variable
(Thu Mar 11 2010 - 07:56:53 PST)
Re: [AMBER] problem to generate parameters files from NMR solved DNA structure
(Thu Mar 11 2010 - 06:04:44 PST)
Re: [AMBER] problem to generate parameters files from NMR solved DNA structure
(Thu Mar 11 2010 - 04:46:58 PST)
Re: [AMBER] ERROR: PGFIO-F-239/namelist read/unit=5/entity name is not member of group.
(Wed Mar 10 2010 - 07:35:01 PST)
Re: [AMBER] problem to generate parameters files of DNA
(Wed Mar 10 2010 - 07:12:27 PST)
Re: [AMBER] problem to generate parameters files of DNA
(Wed Mar 10 2010 - 05:09:47 PST)
Re: [AMBER] Various Errors in Tests
(Tue Mar 09 2010 - 05:42:28 PST)
Re: [AMBER] Removed proton in proteins
(Mon Mar 08 2010 - 07:25:20 PST)
Re: [AMBER] problem with bugfix.all for amber10
(Mon Mar 08 2010 - 07:11:49 PST)
Re: [AMBER] savePdb in leap
(Sat Mar 06 2010 - 07:15:41 PST)
Re: [AMBER] sander bomb: volume of ucell too big
(Sat Mar 06 2010 - 06:50:56 PST)
Re: [AMBER] residual dipolar couplings (RDC)
(Sat Mar 06 2010 - 06:41:09 PST)
Re: [AMBER] AMBER
(Fri Mar 05 2010 - 04:50:47 PST)
Re: [AMBER] Amber, CASP
(Wed Mar 03 2010 - 19:23:26 PST)
Re: [AMBER] atom-type cz ???
(Wed Mar 03 2010 - 18:56:47 PST)
Re: [AMBER] atom-type cz ???
(Wed Mar 03 2010 - 07:26:18 PST)
Re: [AMBER] AmberTools1.3 installation error
(Wed Mar 03 2010 - 06:57:08 PST)
Re: [AMBER] AmberTools1.3 installation error
(Wed Mar 03 2010 - 05:21:05 PST)
Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine)
(Tue Mar 02 2010 - 05:11:16 PST)
Chinh Su Tran To
Re: [AMBER] mdinfor error
(Thu Mar 11 2010 - 03:43:08 PST)
Re: [AMBER] mdinfor error
(Thu Mar 11 2010 - 03:31:23 PST)
[AMBER] mdinfor error
(Thu Mar 11 2010 - 02:34:23 PST)
[AMBER] question about AMBER 9
(Tue Mar 09 2010 - 02:06:18 PST)
Christine Baranski
[AMBER] Energy and Density Unites
(Fri Mar 19 2010 - 06:17:57 PDT)
[AMBER] Protein Crystal Buried Waters and Amber Simulation ?
(Thu Mar 04 2010 - 16:04:16 PST)
Chun-Wei Pao
Re: [AMBER] problem with antechamber for C60
(Tue Mar 23 2010 - 07:44:19 PDT)
[AMBER] problem with antechamber for C60
(Mon Mar 22 2010 - 23:10:59 PDT)
[AMBER] problem with antechamber for C60
(Mon Mar 22 2010 - 20:47:00 PDT)
Cristina Sisu
Re: [AMBER] MMPBSA problems with Fe and Zn
(Mon Mar 01 2010 - 09:20:28 PST)
Re: [AMBER] MMPBSA problems with Fe and Zn
(Mon Mar 01 2010 - 09:05:23 PST)
Re: [AMBER] MMPBSA problems with Fe and Zn
(Mon Mar 01 2010 - 08:04:05 PST)
[AMBER] MMPBSA problems with Fe and Zn
(Mon Mar 01 2010 - 03:53:11 PST)
D.J. Cole
[AMBER] Quantifying Errors in PBSA
(Fri Mar 05 2010 - 11:47:45 PST)
d96543015.ntu.edu.tw
[AMBER] tleap and xleap problem in loading mol2 files
(Thu Mar 11 2010 - 20:51:41 PST)
Daniel Roe
Re: [AMBER] simulation under pressure
(Mon Mar 29 2010 - 19:23:07 PDT)
Re: [AMBER] Post-processing with AMBER 10
(Fri Mar 26 2010 - 14:31:51 PDT)
Re: [AMBER] ptraj hydrogen bond analysis error
(Wed Mar 17 2010 - 15:42:13 PDT)
Danny Xu
[AMBER] residual dipolar couplings (RDC)
(Fri Mar 05 2010 - 14:51:00 PST)
David Watson
Re: [AMBER] Error during MMPBSA calc.
(Fri Mar 19 2010 - 09:16:42 PDT)
Dean Cuebas
Re: [AMBER] Neutral aminogroup of N-terminal residue: N3 atom type choice
(Wed Mar 31 2010 - 13:57:42 PDT)
Re: [AMBER] ligand parameterization
(Wed Mar 24 2010 - 11:33:45 PDT)
Re: [AMBER] ligand parameterization
(Wed Mar 24 2010 - 10:46:41 PDT)
Re: [AMBER] problem with antechamber for C60
(Tue Mar 23 2010 - 13:13:37 PDT)
Re: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type.
(Fri Mar 12 2010 - 14:44:17 PST)
Re: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type.
(Fri Mar 12 2010 - 10:07:21 PST)
Re: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type.
(Fri Mar 12 2010 - 09:39:54 PST)
Deepangi Pandit
Re: [AMBER] Simulating a protein with nmr structure
(Wed Mar 10 2010 - 10:45:12 PST)
deepti nayar
[AMBER] ATP force field
(Mon Mar 08 2010 - 23:14:53 PST)
Denny Bromley
RE: [AMBER] transforming Antechamber GAFF parameters into another force field
(Mon Mar 29 2010 - 09:40:31 PDT)
RE: [AMBER] transforming Antechamber GAFF parameters into another force field
(Fri Mar 26 2010 - 16:26:06 PDT)
[AMBER] transforming Antechamber GAFF parameters into another force field
(Fri Mar 26 2010 - 15:00:26 PDT)
RE: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type.
(Fri Mar 12 2010 - 12:40:12 PST)
RE: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type.
(Fri Mar 12 2010 - 09:50:27 PST)
[AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type.
(Thu Mar 11 2010 - 20:33:05 PST)
RE: [AMBER] Vdw radii params in antechamber
(Wed Mar 03 2010 - 12:58:00 PST)
RE: [AMBER] Vdw radii params in antechamber
(Wed Mar 03 2010 - 10:00:55 PST)
[AMBER] Vdw radii params in antechamber
(Tue Mar 02 2010 - 21:08:11 PST)
Dian Jiao
Re: [AMBER] Post-processing with AMBER 10
(Fri Mar 26 2010 - 15:02:21 PDT)
[AMBER] Post-processing with AMBER 10
(Fri Mar 26 2010 - 14:05:14 PDT)
Re: [AMBER] MD simulation in gas phase-AMBER 10
(Thu Mar 25 2010 - 11:02:15 PDT)
Re: [AMBER] MD simulation in gas phase-AMBER 10
(Thu Mar 25 2010 - 10:45:59 PDT)
[AMBER] MD simulation in gas phase-AMBER 10
(Thu Mar 25 2010 - 10:30:45 PDT)
[AMBER] Particle insertion and deletion
(Sun Mar 14 2010 - 13:14:20 PDT)
Re: [AMBER] Vdw radii params in antechamber
(Wed Mar 03 2010 - 10:17:42 PST)
Dmitri Nilov
Re: [AMBER] Neutral aminogroup of N-terminal residue: N3 atom type choice
(Wed Mar 31 2010 - 07:12:14 PDT)
[AMBER] Neutral aminogroup of N-terminal residue: N3 atom type choice
(Wed Mar 31 2010 - 03:31:44 PDT)
Re: [AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency
(Wed Mar 31 2010 - 01:10:21 PDT)
[AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency
(Tue Mar 30 2010 - 07:41:00 PDT)
Re: Re: [AMBER] minimization really make protein better?
(Tue Mar 30 2010 - 00:03:10 PDT)
Re: [AMBER] problem with steered MD
(Mon Mar 29 2010 - 23:37:51 PDT)
[AMBER] SMD of QM part in QMMM MD simulation
(Sat Mar 27 2010 - 05:39:47 PDT)
Dmitry Mukha
Re: [AMBER] how to deal with the system with negative charge ?
(Tue Mar 30 2010 - 01:47:57 PDT)
Dongshan Wei
Re: [AMBER] How to obtain an ideal helix structure of Alanine 5 peptide (ACE-Ala5-NME) ?
(Fri Mar 19 2010 - 09:39:33 PDT)
[AMBER] How to obtain an ideal helix structure of Alanine 5 peptide (ACE-Ala5-NME) ?
(Thu Mar 18 2010 - 14:28:54 PDT)
Dr. Lars Packschies
[AMBER] Amber 10 and bugfix.all
(Mon Mar 08 2010 - 04:52:50 PST)
Dwight McGee
Re: [AMBER] MMPBSA error
(Fri Mar 26 2010 - 06:45:57 PDT)
Re: [AMBER] MMPBSA error
(Thu Mar 25 2010 - 07:08:13 PDT)
Re: [AMBER] MMPBSA error
(Tue Mar 23 2010 - 07:32:47 PDT)
Re: [AMBER] energy calculation
(Fri Mar 12 2010 - 13:33:04 PST)
Re: [AMBER] how to do analysis of the local structure
(Wed Mar 10 2010 - 22:45:37 PST)
Re: [AMBER] MMPBSA err!
(Mon Mar 08 2010 - 10:29:19 PST)
Re: [AMBER] MMPBSA problems with Fe and Zn
(Mon Mar 01 2010 - 08:14:43 PST)
Ed Pate
[AMBER] amber job hangs
(Fri Mar 26 2010 - 17:29:33 PDT)
Emmanuel Baribefe Naziga
Re: [AMBER] Charge protocol for OLP, HYP
(Mon Mar 15 2010 - 08:53:20 PDT)
Eric Pettersen
Re: [AMBER] ATP charge convergence
(Fri Mar 19 2010 - 09:50:20 PDT)
Re: [AMBER] ATP charge convergence
(Thu Mar 18 2010 - 17:17:58 PDT)
Re: [AMBER] ATP charge convergence
(Thu Mar 18 2010 - 17:11:18 PDT)
[AMBER] ATP charge convergence
(Thu Mar 18 2010 - 17:07:10 PDT)
Fernando Martín García
[AMBER] Error decoding variable
(Mon Mar 08 2010 - 03:34:55 PST)
Francesca Cantini
[AMBER] CIS proline
(Tue Mar 09 2010 - 04:31:08 PST)
[AMBER] Removed proton in proteins
(Mon Mar 08 2010 - 06:32:04 PST)
FyD
Re: [AMBER] OMe fragment
(Wed Mar 03 2010 - 12:51:02 PST)
Re: [AMBER] OMe fragment
(Tue Mar 02 2010 - 21:58:23 PST)
Re: [AMBER] OMe fragment
(Tue Mar 02 2010 - 20:44:00 PST)
Re: [AMBER] OMe fragment
(Tue Mar 02 2010 - 02:29:06 PST)
Ganesh Kamath
Re: [AMBER] issues with pmemd
(Tue Mar 30 2010 - 12:14:54 PDT)
[AMBER] issues with pmemd
(Tue Mar 30 2010 - 10:57:48 PDT)
[AMBER] box of spc water
(Fri Mar 12 2010 - 09:19:08 PST)
[AMBER] electric fields
(Thu Mar 04 2010 - 14:44:04 PST)
[AMBER] force field parameters for isopropanol
(Wed Mar 03 2010 - 07:27:13 PST)
Ganesh Krishnan
Re: [AMBER] Ptraj problems
(Thu Mar 11 2010 - 10:55:07 PST)
[AMBER] Ptraj problems
(Thu Mar 11 2010 - 09:43:05 PST)
[AMBER] PBC interactions
(Mon Mar 01 2010 - 13:51:14 PST)
Gannett, Peter
RE: [AMBER] Large FIle
(Wed Mar 17 2010 - 09:27:40 PDT)
geyan
[AMBER] how to convert to standard Amber PDB input
(Mon Mar 29 2010 - 20:26:17 PDT)
Re: Re: [AMBER] minimization really make protein better?
(Mon Mar 29 2010 - 20:15:55 PDT)
[AMBER] minimization really make protein better?
(Sun Mar 28 2010 - 21:48:21 PDT)
Re: Re: Re: [AMBER] error in save prmtop
(Tue Mar 23 2010 - 07:44:12 PDT)
Re: Re: [AMBER] error in save prmtop
(Tue Mar 23 2010 - 07:30:07 PDT)
[AMBER] error in save prmtop
(Tue Mar 23 2010 - 07:04:34 PDT)
Re: Re: [AMBER] about amber force field
(Mon Mar 22 2010 - 19:36:44 PDT)
[AMBER] about amber force field
(Mon Mar 22 2010 - 01:12:44 PDT)
[AMBER] start from scratch
(Tue Mar 16 2010 - 00:30:49 PDT)
Re: Re: [AMBER] can't get the final "snapshot_statistics.out" file
(Mon Mar 15 2010 - 01:35:50 PDT)
[AMBER] wrong?
(Mon Mar 15 2010 - 01:27:58 PDT)
[AMBER] can't get the final "snapshot_statistics.out" file
(Sat Mar 13 2010 - 19:25:52 PST)
gloglo_at_work
Re: [AMBER] AMBER ff99sb
(Mon Mar 29 2010 - 03:03:33 PDT)
Gould, Ian R
Re: [AMBER] membranes
(Wed Mar 31 2010 - 08:32:49 PDT)
Guillermina Estiu
[AMBER] neb/amber 10
(Wed Mar 03 2010 - 11:12:05 PST)
gurunath katagi
[AMBER] ligand parameterization
(Tue Mar 23 2010 - 23:05:24 PDT)
Gustavo Seabra
Re: [AMBER] transforming Antechamber GAFF parameters into another force field
(Sat Mar 27 2010 - 21:30:54 PDT)
Hannes Loeffler
Re: [AMBER] membranes
(Wed Mar 31 2010 - 09:00:11 PDT)
Re: [AMBER] wrong?
(Mon Mar 15 2010 - 01:34:45 PDT)
[AMBER] chamber error message
(Tue Mar 09 2010 - 05:46:00 PST)
Hyma vathi
[AMBER] free energy contribution of water
(Wed Mar 31 2010 - 04:30:57 PDT)
Re: [AMBER] vlimit exceeded for step
(Thu Mar 18 2010 - 07:35:10 PDT)
[AMBER] vlimit exceeded for step
(Thu Mar 18 2010 - 07:28:29 PDT)
[AMBER] problem in minimisation
(Wed Mar 17 2010 - 08:04:12 PDT)
Igor Sizov
Re: [AMBER] difference in output from bnda and fd_helix functions
(Thu Mar 25 2010 - 12:07:07 PDT)
[AMBER] difference in output from bnda and fd_helix functions
(Wed Mar 24 2010 - 11:19:08 PDT)
Ilyas Yildirim
Re: [AMBER] Difference of ff99 and ff03 in building DNA duplex
(Thu Mar 11 2010 - 21:03:32 PST)
imtiaz shafiq
[AMBER] pKa Calculations Using Thermodynamic Integration
(Wed Mar 31 2010 - 08:02:49 PDT)
Re: [AMBER] tleap savepdb command and organic lignads in proteins
(Wed Mar 31 2010 - 06:43:46 PDT)
Re: [AMBER] tleap savepdb command and organic lignads in proteins
(Tue Mar 30 2010 - 14:45:00 PDT)
Re: [AMBER] tleap savepdb command and organic lignads in proteins
(Tue Mar 30 2010 - 10:50:11 PDT)
[AMBER] tleap savepdb command and organic lignads in proteins
(Tue Mar 30 2010 - 10:43:50 PDT)
[AMBER] Distance between two atoms vs time
(Mon Mar 22 2010 - 05:24:26 PDT)
[AMBER] Protein, Water and Amber
(Sun Mar 07 2010 - 15:15:40 PST)
Re: [AMBER] error - during minimization in AMBER10
(Fri Mar 05 2010 - 20:06:13 PST)
[AMBER] CPU Load for Amber Running In Parallel
(Fri Mar 05 2010 - 19:37:27 PST)
Re: [AMBER] Amber, CASP again
(Thu Mar 04 2010 - 04:36:29 PST)
Re: [AMBER] AMBER
(Thu Mar 04 2010 - 02:09:56 PST)
InSuk Joung
Re: [AMBER] How to apply extra dihedrals
(Tue Mar 16 2010 - 18:03:06 PDT)
Re: [AMBER] addions or solvate-which one first
(Sat Mar 13 2010 - 08:46:03 PST)
[AMBER] sleap help
(Thu Mar 04 2010 - 13:55:15 PST)
Ivan Gladich
[AMBER] Polarization Scaling Down
(Thu Mar 18 2010 - 07:02:52 PDT)
Re: [AMBER] Problem with translate restrt file
(Mon Mar 01 2010 - 11:47:18 PST)
Re: [AMBER] Problem with translate restrt file
(Mon Mar 01 2010 - 10:00:06 PST)
jacky zhao
[AMBER] help for restraint minimization
(Wed Mar 24 2010 - 02:23:38 PDT)
Jagan Mohan
Re: [AMBER] Error during MMPBSA calc.
(Sat Mar 20 2010 - 01:59:12 PDT)
Re: [AMBER] Error during MMPBSA calc.
(Fri Mar 19 2010 - 08:55:27 PDT)
[AMBER] Error during MMPBSA calc.
(Fri Mar 19 2010 - 07:02:13 PDT)
Re: [AMBER] RMSD between two different proteins
(Fri Mar 19 2010 - 02:16:36 PDT)
Re: [AMBER] RMSD between two different proteins
(Fri Mar 19 2010 - 00:26:37 PDT)
Jagdeesh C
[AMBER] RMSD of Specific Atoms
(Sat Mar 27 2010 - 00:29:45 PDT)
[AMBER] Nucgen
(Tue Mar 16 2010 - 22:11:05 PDT)
Jamie Romnes
[AMBER] ptraj hydrogen bond analysis error
(Wed Mar 17 2010 - 14:47:53 PDT)
Re: [AMBER] Generating cpin file for constant pH in Amber9
(Wed Mar 03 2010 - 12:39:05 PST)
Re: [AMBER] Generating cpin file for constant pH in Amber9
(Wed Mar 03 2010 - 11:41:09 PST)
[AMBER] Generating cpin file for constant pH in Amber9
(Wed Mar 03 2010 - 11:11:41 PST)
jani vinod
Re: [AMBER] vlimit error during equilibration step
(Wed Mar 31 2010 - 00:00:12 PDT)
[AMBER] regarding compiling amber10
(Tue Mar 09 2010 - 03:54:50 PST)
Jason Swails
Re: [AMBER] pKa Calculations Using Thermodynamic Integration
(Wed Mar 31 2010 - 08:08:06 PDT)
Re: [AMBER] FW:
(Tue Mar 30 2010 - 10:58:22 PDT)
Re: [AMBER] tleap savepdb command and organic lignads in proteins
(Tue Mar 30 2010 - 10:51:11 PDT)
Re: [AMBER] tleap savepdb command and organic lignads in proteins
(Tue Mar 30 2010 - 10:45:32 PDT)
Re: [AMBER] simulation under pressure
(Mon Mar 29 2010 - 20:30:26 PDT)
Re: [AMBER] Installing AmberTools
(Sun Mar 28 2010 - 08:43:01 PDT)
Re: [AMBER] RMSD of Specific Atoms
(Sat Mar 27 2010 - 07:44:04 PDT)
Re: Re: [AMBER] how to get the hydrophobic area for a particlar region
(Fri Mar 26 2010 - 19:42:04 PDT)
Re: [AMBER] NOT IN RESIDUE TEMPLATES
(Thu Mar 25 2010 - 23:56:14 PDT)
Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine
(Thu Mar 25 2010 - 23:32:03 PDT)
Re: [AMBER] Script for creating topology files , running minimization and MD simulation in amber
(Thu Mar 25 2010 - 23:22:33 PDT)
Re: [AMBER] error in parallel md run
(Thu Mar 25 2010 - 22:54:26 PDT)
Re: [AMBER] Running several jobs under one script
(Thu Mar 25 2010 - 09:27:45 PDT)
Re: [AMBER] MMPBSA error
(Wed Mar 24 2010 - 22:41:06 PDT)
Re: [AMBER] MMPBSA error
(Wed Mar 24 2010 - 21:47:48 PDT)
Re: [AMBER] MMPBSA error
(Tue Mar 23 2010 - 23:21:40 PDT)
Re: [AMBER] Regarding problem with self guided molecular dynamics
(Tue Mar 23 2010 - 10:21:11 PDT)
Re: [AMBER] Using 6-12 / 10-12 potential in AMBER
(Tue Mar 23 2010 - 10:12:09 PDT)
Re: [AMBER] Amber: heme atom identification
(Mon Mar 22 2010 - 15:16:01 PDT)
Re: [AMBER] error when doing MMPBSA
(Sun Mar 21 2010 - 07:43:45 PDT)
Re: [AMBER] Adenine in water
(Sat Mar 20 2010 - 23:41:35 PDT)
Re: [AMBER] regarding ambertools
(Sat Mar 20 2010 - 07:51:54 PDT)
Re: [AMBER] vlimit exceeded for step
(Thu Mar 18 2010 - 09:07:34 PDT)
Re: [AMBER] Large FIle
(Wed Mar 17 2010 - 12:49:53 PDT)
Re: [AMBER] Large FIle
(Wed Mar 17 2010 - 09:12:38 PDT)
Re: [AMBER] Large FIle
(Wed Mar 17 2010 - 09:08:19 PDT)
Re: Re: [AMBER] force field with neutral terminal
(Wed Mar 17 2010 - 08:16:40 PDT)
Re: [AMBER] How to apply extra dihedrals
(Tue Mar 16 2010 - 21:22:06 PDT)
Re: [AMBER] How to apply extra dihedrals
(Tue Mar 16 2010 - 20:29:20 PDT)
Re: [AMBER] Can you give me some suggestion on how to use NetCDF to obtain a binary formate trajectory with AMBER
(Tue Mar 16 2010 - 19:05:21 PDT)
Re: [AMBER] MMPBSA.py problem
(Sun Mar 14 2010 - 09:47:40 PDT)
Re: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type.
(Fri Mar 12 2010 - 13:16:56 PST)
Re: [AMBER] energy calculation
(Fri Mar 12 2010 - 09:25:21 PST)
Re: [AMBER] G03: ONIOM
(Fri Mar 12 2010 - 07:33:22 PST)
Re: [AMBER] tleap and xleap problem in loading mol2 files
(Thu Mar 11 2010 - 21:10:02 PST)
Re: [AMBER] Difference of ff99 and ff03 in building DNA duplex
(Thu Mar 11 2010 - 20:49:16 PST)
[AMBER] Re: Fw:Re:Re: Fw:SOS for mmpbsa
(Thu Mar 11 2010 - 08:25:18 PST)
Re: [AMBER] combining coordinate and velocity files into one
(Tue Mar 09 2010 - 15:15:31 PST)
Re: [AMBER] energy calculation
(Tue Mar 09 2010 - 11:01:55 PST)
Re: [AMBER] regarding compiling amber10
(Tue Mar 09 2010 - 07:07:15 PST)
Re: [AMBER] Fortran run time error
(Tue Mar 09 2010 - 06:50:01 PST)
Re: [AMBER] combining coordinate and velocity files into one
(Sun Mar 07 2010 - 14:48:23 PST)
Re: [AMBER] error - during minimization in AMBER10
(Fri Mar 05 2010 - 20:45:12 PST)
Re: [AMBER] error - during minimization in AMBER10
(Fri Mar 05 2010 - 20:39:21 PST)
Re: [AMBER] _getcor.f Fortran runtime error: End of file
(Fri Mar 05 2010 - 16:19:26 PST)
Re: [AMBER] AMBER10 installation: make test error 1
(Fri Mar 05 2010 - 16:11:40 PST)
Re: [AMBER] savePdb in leap
(Fri Mar 05 2010 - 15:58:50 PST)
Re: [AMBER] Vdw radii params in antechamber
(Wed Mar 03 2010 - 11:53:26 PST)
Re: [AMBER] Generating cpin file for constant pH in Amber9
(Wed Mar 03 2010 - 11:52:18 PST)
Re: [AMBER] Generating cpin file for constant pH in Amber9
(Wed Mar 03 2010 - 11:30:36 PST)
Re: [AMBER] Enquiry regarding MD run
(Tue Mar 02 2010 - 22:04:23 PST)
Re: [AMBER] Vdw radii params in antechamber
(Tue Mar 02 2010 - 21:40:17 PST)
Re: [AMBER] Cyclic compounds
(Tue Mar 02 2010 - 10:50:53 PST)
Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine)
(Tue Mar 02 2010 - 09:37:19 PST)
Re: [AMBER] Cyclic compounds
(Mon Mar 01 2010 - 21:24:08 PST)
Re: [AMBER] OMe fragment
(Mon Mar 01 2010 - 19:07:10 PST)
Re: [AMBER] OMe fragment
(Mon Mar 01 2010 - 18:02:44 PST)
Re: [AMBER] OMe fragment
(Mon Mar 01 2010 - 17:55:45 PST)
Re: [AMBER] PBC interactions
(Mon Mar 01 2010 - 17:37:15 PST)
Re: [AMBER] Problem with translate restrt file
(Mon Mar 01 2010 - 10:24:28 PST)
Re: [AMBER] MMPBSA problems with Fe and Zn
(Mon Mar 01 2010 - 06:07:53 PST)
Jeffrey
Re:Re: [AMBER] PBSOL not equal to PBSUR + PBCAL?
(Thu Mar 18 2010 - 18:41:51 PDT)
[AMBER] MMPBSA calculation
(Thu Mar 18 2010 - 05:23:36 PDT)
[AMBER] PBSOL not equal to PBSUR + PBCAL?
(Thu Mar 18 2010 - 01:01:34 PDT)
Jio M
[AMBER] COOH group:extra undesired bond
(Wed Mar 31 2010 - 09:41:06 PDT)
Re: [AMBER] general query:RMSD
(Sat Mar 27 2010 - 03:38:03 PDT)
Re: [AMBER] general query:RMSD
(Sun Mar 21 2010 - 02:01:04 PDT)
[AMBER] general query:RMSD
(Fri Mar 19 2010 - 13:21:57 PDT)
John Chuang莊曜遠
Re: [AMBER] problem with steered MD
(Mon Mar 29 2010 - 20:25:21 PDT)
John S
[AMBER] Regd:vlimit
(Sun Mar 21 2010 - 21:03:18 PDT)
[AMBER] Check overlap
(Thu Mar 18 2010 - 18:41:09 PDT)
[AMBER] Re: Re :checkoverlap
(Thu Mar 18 2010 - 12:55:55 PDT)
[AMBER] Re :checkoverlap
(Wed Mar 17 2010 - 20:45:37 PDT)
Re: [AMBER] Mask selection
(Fri Mar 12 2010 - 14:44:10 PST)
[AMBER] Mask selection
(Fri Mar 12 2010 - 14:21:12 PST)
Re: [AMBER] Cyclic compounds
(Tue Mar 02 2010 - 10:39:50 PST)
[AMBER] Cyclic compounds
(Mon Mar 01 2010 - 20:50:35 PST)
Karl Kirschner
Re: [AMBER] force field parameters for isopropanol
(Thu Mar 04 2010 - 00:36:16 PST)
kecy_w.sina.com
[AMBER] how to achieve the 2D periodic boundary
(Tue Mar 23 2010 - 18:45:24 PDT)
Kevin Hauser
Re: [AMBER] mbonbi and mbondi2
(Sun Mar 21 2010 - 13:29:44 PDT)
Re: [AMBER] Calculating Amber Force fields from Wikipedia
(Tue Mar 16 2010 - 17:41:08 PDT)
Re: [AMBER] Difference of ff99 and ff03 in building DNA duplex
(Thu Mar 11 2010 - 21:05:42 PST)
Kshatresh Dutta Dubey
Re: [AMBER] Binding Energy Calculation by QM/MM method
(Sun Mar 14 2010 - 11:52:49 PDT)
[AMBER] Binding Energy Calculation by QM/MM method
(Sat Mar 13 2010 - 21:45:17 PST)
[AMBER] Binding Energy Calculation by QM/MM method
(Fri Mar 12 2010 - 21:31:27 PST)
kureeckal ramesh
[AMBER] error - during minimization in AMBER10
(Fri Mar 05 2010 - 19:54:13 PST)
Lachele Foley (Lists)
Re: [AMBER] Charge protocol for OLP, HYP
(Mon Mar 15 2010 - 08:39:31 PDT)
Re: [AMBER] OMe fragment
(Mon Mar 01 2010 - 18:27:53 PST)
Lalit Dubey
Re: [OFFLIST] Re: [AMBER] Protein + Bilayer Simulations: Role of salt
(Mon Mar 01 2010 - 12:28:57 PST)
Re: [AMBER] Protein + Bilayer Simulations: Role of salt
(Mon Mar 01 2010 - 06:43:48 PST)
Lars Packschies
Re: [AMBER] Amber 10 and bugfix.all
(Mon Mar 08 2010 - 08:04:11 PST)
lee lior
[AMBER] DUMPAVE
(Wed Mar 24 2010 - 13:58:32 PDT)
[AMBER] ERROR: PGFIO-F-239/namelist read/unit=5/entity name is not member of group.
(Tue Mar 09 2010 - 13:41:51 PST)
Lekpa Duukori
Re: [AMBER] AMBER plus GLYCAM
(Wed Mar 24 2010 - 16:28:35 PDT)
[AMBER] AMBER plus GLYCAM
(Wed Mar 24 2010 - 15:43:32 PDT)
Re: [AMBER] How to apply extra dihedrals
(Tue Mar 16 2010 - 21:19:52 PDT)
[AMBER] How to apply extra dihedrals
(Tue Mar 16 2010 - 08:19:18 PDT)
Re: [AMBER] OMe fragment
(Wed Mar 03 2010 - 13:48:09 PST)
Re: [AMBER] OMe fragment
(Wed Mar 03 2010 - 10:26:09 PST)
Re: [AMBER] OMe fragment
(Tue Mar 02 2010 - 21:02:47 PST)
Re: [AMBER] OMe fragment
(Tue Mar 02 2010 - 18:40:01 PST)
Re: [AMBER] OMe fragment
(Tue Mar 02 2010 - 07:03:43 PST)
Re: [AMBER] OMe fragment
(Mon Mar 01 2010 - 18:08:55 PST)
[AMBER] OMe fragment
(Mon Mar 01 2010 - 14:37:55 PST)
lidansa.mail.ustc.edu.cn
Re: [AMBER] Missing values for MM BGAS:error in mm-pbsa
(Wed Mar 24 2010 - 18:07:29 PDT)
Lili Peng
[AMBER] Extract potential energy from ptraj?
(Tue Mar 09 2010 - 20:05:56 PST)
M. L. Dodson
Re: [AMBER] Neutral aminogroup of N-terminal residue: N3 atom type choice
(Wed Mar 31 2010 - 06:41:30 PDT)
Re: [AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency
(Wed Mar 31 2010 - 06:36:05 PDT)
Re: [AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency
(Tue Mar 30 2010 - 08:09:27 PDT)
Re: [AMBER] SMD of QM part in QMMM MD simulation
(Sat Mar 27 2010 - 06:27:16 PDT)
Re: [AMBER] How to obtain an ideal helix structure of Alanine 5 peptide (ACE-Ala5-NME) ?
(Thu Mar 18 2010 - 17:49:14 PDT)
Re: [AMBER] Calculating Amber Force fields from Wikipedia
(Tue Mar 16 2010 - 14:58:00 PDT)
Re: [AMBER] Calculating Amber Force fields from Wikipedia
(Mon Mar 15 2010 - 20:45:26 PDT)
Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?
(Mon Mar 15 2010 - 20:20:31 PDT)
Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?
(Mon Mar 15 2010 - 18:31:31 PDT)
Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?
(Mon Mar 15 2010 - 14:24:38 PDT)
Madhurima Jana
[AMBER] angular velocity trajectory
(Mon Mar 29 2010 - 21:48:37 PDT)
Mannan
Re: [AMBER] AMBER ff99sb
(Tue Mar 30 2010 - 03:26:44 PDT)
[AMBER] AMBER ff99sb
(Mon Mar 29 2010 - 02:04:59 PDT)
[AMBER] Parameters for trimethylated Lysine?
(Wed Mar 03 2010 - 02:14:03 PST)
manoj singh
Re: [AMBER] Script for creating topology files , running minimization and MD simulation in amber
(Thu Mar 25 2010 - 22:24:47 PDT)
Marek Maly
Re: [AMBER] simulation under pressure
(Tue Mar 30 2010 - 02:53:25 PDT)
[AMBER] MMPBSA in case of highly water accessible molecules ?
(Tue Mar 09 2010 - 13:43:11 PST)
Mark Williamson
Re: [AMBER] chamber error message
(Tue Mar 09 2010 - 13:10:09 PST)
Markus Kaukonen
Re: [AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency
(Wed Mar 31 2010 - 11:34:32 PDT)
Re: [AMBER] PBC interactions
(Mon Mar 01 2010 - 23:35:19 PST)
Matthew Tessier
RE: [AMBER] membranes
(Wed Mar 31 2010 - 08:22:58 PDT)
mattia
Re: [AMBER] about amber force field
(Mon Mar 22 2010 - 08:04:01 PDT)
Re: [AMBER] about amber force field
(Mon Mar 22 2010 - 06:08:48 PDT)
Re: [AMBER] MMPBSA problems with Fe and Zn
(Mon Mar 01 2010 - 04:00:56 PST)
maya maya
Re: [AMBER] reg-Generalized Born Approach
(Wed Mar 31 2010 - 11:19:01 PDT)
[AMBER] reg-Generalized Born Approach
(Wed Mar 31 2010 - 08:51:33 PDT)
[AMBER] reg REMD
(Mon Mar 29 2010 - 04:49:08 PDT)
meandme meandme
[AMBER] schlegel diagram
(Tue Mar 30 2010 - 03:22:45 PDT)
MENZIES G. (569332)
[AMBER] FW:
(Tue Mar 30 2010 - 03:45:34 PDT)
mish
[AMBER] MM-PBSA not generating snapshot_lig.all.out and snapshot_statistics.out files
(Sat Mar 27 2010 - 11:25:49 PDT)
moitrayee.mbu.iisc.ernet.in
Re: [AMBER] Energy units in mm-pbsa calculations
(Tue Mar 30 2010 - 03:34:05 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Sat Mar 27 2010 - 10:21:39 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Fri Mar 26 2010 - 23:59:40 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Fri Mar 26 2010 - 07:41:37 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Fri Mar 26 2010 - 05:34:41 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Thu Mar 25 2010 - 09:42:10 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Thu Mar 25 2010 - 03:44:59 PDT)
Re: [AMBER] Missing values for MM BGAS:error in mm-pbsa
(Thu Mar 25 2010 - 00:05:34 PDT)
[AMBER] Missing values for MM BGAS:error in mm-pbsa
(Wed Mar 24 2010 - 11:53:26 PDT)
[AMBER] Energy units in mm-pbsa calculations
(Tue Mar 23 2010 - 05:57:30 PDT)
N.R. Jena
Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine
(Fri Mar 26 2010 - 05:59:06 PDT)
Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine
(Thu Mar 25 2010 - 22:58:00 PDT)
Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine
(Thu Mar 25 2010 - 22:43:38 PDT)
Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine)
(Mon Mar 08 2010 - 23:04:22 PST)
Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine)
(Thu Mar 04 2010 - 02:40:13 PST)
Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine)
(Tue Mar 02 2010 - 20:20:21 PST)
Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine)
(Tue Mar 02 2010 - 08:59:38 PST)
[AMBER] parameter file for modified nucleosides (O6-methyl guanine)
(Tue Mar 02 2010 - 04:53:39 PST)
[AMBER] parameter file for modified nucleosides (O6-methyl guanine)
(Tue Mar 02 2010 - 04:24:59 PST)
Nancy
Re:Re: [AMBER] is iwrap=1 a key parameter?
(Mon Mar 29 2010 - 22:11:17 PDT)
[AMBER] is iwrap=1 a key parameter?
(Mon Mar 29 2010 - 05:49:24 PDT)
[AMBER] AMBER prmtop and mdcrd files to CHARMM psf and dcd files
(Wed Mar 17 2010 - 19:42:52 PDT)
[AMBER] Can you give me some suggestion on how to use NetCDF to obtain a binary formate trajectory with AMBER
(Tue Mar 16 2010 - 18:51:25 PDT)
[AMBER] how to do analysis of the local structure
(Wed Mar 10 2010 - 23:13:30 PST)
[AMBER] how to do analysis of the local structure
(Wed Mar 10 2010 - 21:17:29 PST)
Re:Re: [AMBER] sander bomb: volume of ucell too big
(Sat Mar 06 2010 - 23:13:43 PST)
[AMBER] sander bomb: volume of ucell too big
(Fri Mar 05 2010 - 23:25:35 PST)
Nicee
Re: [AMBER] vlimit error during equilibration step
(Wed Mar 31 2010 - 00:26:02 PDT)
Re: [AMBER] vlimit error during equilibration step
(Tue Mar 30 2010 - 21:04:21 PDT)
Re: [AMBER] vlimit error during equilibration step
(Tue Mar 30 2010 - 04:48:17 PDT)
[AMBER] vlimit error during equilibration step
(Mon Mar 29 2010 - 21:37:28 PDT)
[AMBER] (no subject)
(Mon Mar 29 2010 - 21:31:51 PDT)
Re: [AMBER] error in parallel md run
(Fri Mar 26 2010 - 01:17:13 PDT)
[AMBER] error in parallel md run
(Thu Mar 25 2010 - 22:43:22 PDT)
Re: [AMBER] addions or solvate-which one first
(Sun Mar 14 2010 - 21:00:22 PDT)
[AMBER] addions or solvate-which one first
(Sat Mar 13 2010 - 02:51:06 PST)
Nicholas Musolino
Re: [AMBER] transforming Antechamber GAFF parameters into another force field
(Fri Mar 26 2010 - 15:16:04 PDT)
nicholus bhattacharjee
[AMBER] Which shake option to be used
(Sun Mar 28 2010 - 03:21:51 PDT)
Re: [AMBER] problem with steered MD
(Wed Mar 24 2010 - 21:37:37 PDT)
Re: [AMBER] problem with steered MD
(Tue Mar 23 2010 - 08:34:52 PDT)
[AMBER] problem with steered MD
(Tue Mar 23 2010 - 05:41:26 PDT)
Re: [AMBER] RMSD between two different proteins
(Fri Mar 19 2010 - 01:17:42 PDT)
[AMBER] RMSD between two different proteins
(Fri Mar 19 2010 - 00:10:04 PDT)
Re: [AMBER] Simulating a protein with nmr structure
(Thu Mar 11 2010 - 03:10:42 PST)
[AMBER] Simulating a protein with nmr structure
(Wed Mar 10 2010 - 01:50:23 PST)
Nkwe Monama
[AMBER] Running several jobs under one script
(Thu Mar 25 2010 - 02:47:57 PDT)
Re: [AMBER] Errors while running Amber
(Fri Mar 05 2010 - 06:46:59 PST)
Re: [AMBER] Errors while running Amber
(Fri Mar 05 2010 - 01:17:03 PST)
Re: [AMBER] Errors while running Amber
(Thu Mar 04 2010 - 05:17:50 PST)
Re: [AMBER] Errors while running Amber
(Thu Mar 04 2010 - 04:56:52 PST)
[AMBER] Errors while running Amber
(Thu Mar 04 2010 - 03:05:10 PST)
Palanimuthu M
Re: [AMBER] Script for creating topology files , running minimization and MD simulation in amber
(Thu Mar 25 2010 - 22:55:53 PDT)
[AMBER] Script for creating topology files , running minimization and MD simulation in amber
(Thu Mar 25 2010 - 22:23:07 PDT)
Re: [AMBER] Regarding amber molecular dynamics
(Tue Mar 23 2010 - 21:01:55 PDT)
[AMBER] Regarding amber molecular dynamics
(Tue Mar 23 2010 - 10:34:53 PDT)
[AMBER] Regarding amber molecular dynamics
(Tue Mar 23 2010 - 10:41:49 PDT)
Pallavi Mohanty
Re: [AMBER] Enquiry regarding MD run
(Mon Mar 15 2010 - 10:59:17 PDT)
Re: [AMBER] Enquiry regarding MD run
(Mon Mar 15 2010 - 01:07:16 PDT)
[AMBER] Enquiry regarding MD run
(Mon Mar 15 2010 - 00:29:58 PDT)
[AMBER] Enquiry regarding Minimisation
(Sat Mar 13 2010 - 02:50:22 PST)
Re: [AMBER] Enquiry regarding MD run
(Wed Mar 10 2010 - 06:02:21 PST)
Re: [AMBER] Enquiry regarding MD run
(Wed Mar 10 2010 - 02:11:51 PST)
[AMBER] Enquiry regarding MD run
(Mon Mar 08 2010 - 20:42:32 PST)
pandb09.lzu.cn
[AMBER] Error in MMPBSA
(Sun Mar 28 2010 - 17:14:44 PDT)
[AMBER] Bad atom type Br
(Thu Mar 25 2010 - 02:05:04 PDT)
pellegrini
Re: [AMBER] Problem with solvationbox command
(Wed Mar 24 2010 - 03:26:43 PDT)
[AMBER] Problem with solvationbox command
(Tue Mar 23 2010 - 06:11:17 PDT)
[AMBER] Solvatebox on Amber8
(Tue Mar 23 2010 - 03:29:32 PDT)
Peter Charles Kahuna
[AMBER] IMPROPER TERM CONTRIBUTION
(Wed Mar 17 2010 - 02:43:30 PDT)
[AMBER] PARMSCAN
(Thu Mar 04 2010 - 05:39:13 PST)
Peter Schmidtke
[AMBER] savePdb in leap
(Fri Mar 05 2010 - 05:47:34 PST)
Philipp Marquetand
Re: [AMBER] Various Errors in Tests
(Fri Mar 12 2010 - 03:19:08 PST)
Re: [AMBER] Various Errors in Tests
(Tue Mar 09 2010 - 02:52:24 PST)
[AMBER] Various Errors in Tests
(Tue Mar 09 2010 - 02:45:28 PST)
Re: [AMBER] Amber 10 and bugfix.all
(Mon Mar 08 2010 - 05:23:36 PST)
[AMBER] problem with bugfix.all for amber10
(Mon Mar 08 2010 - 04:43:47 PST)
pxq
Re: Re: Re: [AMBER] error when doing MMPBSA
(Tue Mar 23 2010 - 17:43:18 PDT)
Re: Re: [AMBER] error when doing MMPBSA
(Mon Mar 22 2010 - 17:32:42 PDT)
Re: Re: [AMBER] error when doing MMPBSA
(Mon Mar 22 2010 - 01:51:44 PDT)
Re: Re: [AMBER] error when doing MMPBSA
(Sun Mar 21 2010 - 07:52:29 PDT)
[AMBER] error when doing MMPBSA
(Sun Mar 21 2010 - 00:27:59 PDT)
qiaoyan
Re: Re: [AMBER] how to get the hydrophobic area for a particlar region
(Fri Mar 26 2010 - 19:26:02 PDT)
[AMBER] how to get the hydrophobic area for a particlar region
(Wed Mar 24 2010 - 19:59:14 PDT)
[AMBER] mmpbsa doesn't work
(Mon Mar 22 2010 - 20:38:48 PDT)
Qinqin Ji
[AMBER] Difference of ff99 and ff03 in building DNA duplex
(Thu Mar 11 2010 - 19:08:14 PST)
Rama krishnan
Re: Re: [AMBER] can't get the final "snapshot_statistics.out" file
(Mon Mar 15 2010 - 05:23:54 PDT)
Ramya Narasimhan
Re: Re: Re: Re: [AMBER] force field with neutral terminal
(Thu Mar 18 2010 - 23:24:34 PDT)
Re: Re: Re: [AMBER] force field with neutral terminal
(Thu Mar 18 2010 - 22:07:34 PDT)
Re: Re: [AMBER] force field with neutral terminal
(Tue Mar 16 2010 - 23:59:04 PDT)
[AMBER] force field with neutral terminal
(Tue Mar 16 2010 - 00:56:21 PDT)
Ray Luo
Re: [AMBER] how to get the hydrophobic area for a particlar region
(Thu Mar 25 2010 - 11:36:39 PDT)
Re: [AMBER] how to get the hydrophobic area for a particlar region
(Thu Mar 25 2010 - 09:49:27 PDT)
Re: [AMBER] PBSOL not equal to PBSUR + PBCAL?
(Wed Mar 24 2010 - 14:00:44 PDT)
Re: [AMBER] Energy units in mm-pbsa calculations
(Wed Mar 24 2010 - 10:48:28 PDT)
Re: [AMBER] error when doing MMPBSA
(Mon Mar 22 2010 - 09:54:40 PDT)
Re: [AMBER] error when doing MMPBSA
(Sun Mar 21 2010 - 12:06:29 PDT)
Re: [AMBER] MMPBSA calculation
(Thu Mar 18 2010 - 10:09:06 PDT)
Re: [AMBER] PBSOL not equal to PBSUR + PBCAL?
(Thu Mar 18 2010 - 09:59:40 PDT)
[AMBER] Re: Fw:SOS for mmpbsa
(Wed Mar 10 2010 - 10:17:07 PST)
Ray Luo, Ph.D.
Re: Re: [AMBER] error when doing MMPBSA
(Mon Mar 22 2010 - 21:43:10 PDT)
Rilei Yu
[AMBER] NAMD-parameter set up
(Fri Mar 26 2010 - 04:22:37 PDT)
[AMBER] minimization residues around the ligand
(Mon Mar 08 2010 - 17:56:21 PST)
[AMBER] CITATION PROBLEM ABOUT i-APBS
(Tue Mar 02 2010 - 04:12:55 PST)
Robert Duke
Re: [AMBER] issues with pmemd
(Tue Mar 30 2010 - 11:18:43 PDT)
Re: [AMBER] amber job hangs
(Fri Mar 26 2010 - 17:53:43 PDT)
Re: [AMBER] Errors while running Amber
(Fri Mar 05 2010 - 05:37:00 PST)
Robert Konecny
Re: [AMBER] CITATION PROBLEM ABOUT i-APBS
(Tue Mar 02 2010 - 11:08:29 PST)
Robert Wohlhueter
[AMBER] sleap not built
(Mon Mar 15 2010 - 15:51:24 PDT)
Roman Osman
Re: [AMBER] Particle insertion and deletion
(Sun Mar 14 2010 - 14:12:25 PDT)
ros
[AMBER] Adenine in water
(Fri Mar 19 2010 - 06:42:23 PDT)
Ross Walker
RE: [AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency
(Tue Mar 30 2010 - 14:10:45 PDT)
RE: [AMBER] issues with pmemd
(Tue Mar 30 2010 - 14:05:04 PDT)
RE: [AMBER] AMBER plus GLYCAM
(Wed Mar 24 2010 - 16:00:55 PDT)
RE: [AMBER] Problems on Tutorial A8
(Wed Mar 24 2010 - 11:22:10 PDT)
RE: [AMBER] Problem with solvationbox command
(Tue Mar 23 2010 - 15:22:46 PDT)
RE: [AMBER] ACS Division of Computers in Chemistry: award applications due March 30
(Wed Mar 17 2010 - 17:09:46 PDT)
RE: [AMBER] ACS Division of Computers in Chemistry: award applications due March 30
(Wed Mar 17 2010 - 17:03:29 PDT)
RE: [AMBER] Nucgen
(Tue Mar 16 2010 - 22:52:11 PDT)
RE: [AMBER] Confirm compiling Amber10/Tools1.3 breaks with intel v 11.1?
(Tue Mar 16 2010 - 22:48:30 PDT)
RE: [AMBER] Calculating Amber Force fields from Wikipedia
(Mon Mar 15 2010 - 19:16:29 PDT)
RE: [AMBER] Binding Energy Calculation by QM/MM method
(Sun Mar 14 2010 - 11:13:40 PDT)
[AMBER] RE: About amber10 installation
(Sat Mar 13 2010 - 10:22:44 PST)
RE: [AMBER] Difference of ff99 and ff03 in building DNA duplex
(Thu Mar 11 2010 - 20:49:40 PST)
RE: [AMBER] 10Gb Interconnect profile
(Wed Mar 10 2010 - 07:07:27 PST)
RE: [AMBER] CPU Load for Amber Running In Parallel
(Fri Mar 05 2010 - 20:47:27 PST)
RE: [AMBER] Errors while running Amber
(Fri Mar 05 2010 - 08:51:32 PST)
rui
[AMBER] energy calculation
(Tue Mar 09 2010 - 10:37:22 PST)
s. Bill
[AMBER] Lone Pair
(Thu Mar 25 2010 - 06:29:39 PDT)
[AMBER] mbonbi and mbondi2
(Sun Mar 21 2010 - 12:55:58 PDT)
[AMBER] PDB Database
(Sun Mar 21 2010 - 03:08:07 PDT)
Re: [AMBER] MMPBSA.py problem
(Mon Mar 15 2010 - 02:00:23 PDT)
[AMBER] MMPBSA.py problem
(Sun Mar 14 2010 - 03:56:25 PDT)
Re: [AMBER] ptraj rms
(Sat Mar 13 2010 - 08:08:41 PST)
[AMBER] ptraj rms
(Sat Mar 13 2010 - 07:36:51 PST)
Sarra Geranil
[AMBER] RMSF calculation is correct ?
(Tue Mar 02 2010 - 09:35:07 PST)
Sasha Buzko
[AMBER] How to find conserved coordinated waters?
(Mon Mar 29 2010 - 14:51:30 PDT)
sculiujl
[AMBER] how to deal with the system with negative charge ?
(Tue Mar 30 2010 - 04:10:13 PDT)
[AMBER] how to deal with the system with negative charge ?
(Tue Mar 30 2010 - 01:20:18 PDT)
Senthil Natesan
[AMBER] Run.dip: Program Error during test run after Amber 10 installation
(Fri Mar 26 2010 - 13:44:43 PDT)
Shaandar Nyamtulga
[AMBER] CASP
(Sun Mar 28 2010 - 23:47:50 PDT)
[AMBER] Amber, CASP again
(Thu Mar 04 2010 - 00:52:20 PST)
[AMBER] Amber, CASP
(Wed Mar 03 2010 - 18:48:55 PST)
Shaikh Abdul R S Ramaju
RE: [AMBER] Amber:antechamber & heme(metal?) problems
(Sun Mar 28 2010 - 23:00:11 PDT)
Shulin Zhuang
Re: [AMBER] MMPBSA error
(Fri Mar 26 2010 - 14:32:08 PDT)
Re: [AMBER] MMPBSA error
(Thu Mar 25 2010 - 23:22:02 PDT)
Re: [AMBER] MMPBSA error
(Wed Mar 24 2010 - 21:57:32 PDT)
sikander azam
Re: [AMBER] NOT IN RESIDUE TEMPLATES
(Thu Mar 25 2010 - 23:34:40 PDT)
[AMBER] NOT IN RESIDUE TEMPLATES
(Mon Mar 22 2010 - 09:11:17 PDT)
[AMBER] _getcor.f Fortran runtime error: End of file
(Fri Mar 05 2010 - 00:25:58 PST)
[AMBER] _getcor.f Fortran runtime error: End of file
(Thu Mar 04 2010 - 02:26:49 PST)
Silvia Carlotto
[AMBER] Extract coordinate residues form mdcrd
(Wed Mar 10 2010 - 06:38:47 PST)
SimonKao
[AMBER] Amber:antechamber & heme(metal?) problems
(Fri Mar 26 2010 - 13:40:36 PDT)
[AMBER] Amber: heme atom identification
(Mon Mar 22 2010 - 09:05:40 PDT)
Soumya Lipsa Rath
Re: [AMBER] MMPBSA error
(Fri Mar 26 2010 - 01:50:35 PDT)
Re: [AMBER] MMPBSA error
(Fri Mar 26 2010 - 01:48:35 PDT)
Re: [AMBER] MMPBSA error
(Thu Mar 25 2010 - 20:43:08 PDT)
Re: [AMBER] MMPBSA error
(Wed Mar 24 2010 - 19:52:46 PDT)
Re: [AMBER] MMPBSA error
(Tue Mar 23 2010 - 21:51:30 PDT)
[AMBER] MMPBSA error
(Tue Mar 23 2010 - 01:21:41 PDT)
steinbrt.rci.rutgers.edu
Re: [AMBER] wrong?
(Mon Mar 15 2010 - 01:49:54 PDT)
Re: [AMBER] Protein, Water and Amber
(Mon Mar 08 2010 - 00:54:59 PST)
Steve Seibold
[AMBER] antechamber problems
(Thu Mar 25 2010 - 11:15:34 PDT)
[AMBER] Antechamber problems.
(Thu Mar 25 2010 - 10:44:18 PDT)
[AMBER] crdgrow AMBER 8
(Wed Mar 24 2010 - 12:45:57 PDT)
[AMBER] crdgrow
(Wed Mar 24 2010 - 09:15:58 PDT)
Sushil Mishra
[AMBER] Binding cooprativety and binding order of ligands
(Thu Mar 25 2010 - 10:53:41 PDT)
Re: [AMBER] PDB Database
(Sun Mar 21 2010 - 03:29:02 PDT)
Re: [AMBER] Enquiry regarding MD run
(Mon Mar 15 2010 - 02:00:19 PDT)
Re: [AMBER] Enquiry regarding MD run
(Mon Mar 15 2010 - 00:44:22 PDT)
[AMBER] Fwd: Xleap : Improper torsions applied
(Mon Mar 08 2010 - 08:32:44 PST)
[AMBER] Xleap : Improper torsions applied
(Mon Mar 08 2010 - 06:55:26 PST)
Syed Tarique Moin
Re: [AMBER] _getcor.f Fortran runtime error: End of file
(Fri Mar 05 2010 - 02:44:42 PST)
Taufik Al-Sarraj
Re: [AMBER] Minimization Failure
(Wed Mar 24 2010 - 12:39:21 PDT)
Re: [AMBER] Minimization Failure
(Tue Mar 16 2010 - 11:37:28 PDT)
Re: [AMBER] Minimization Failure
(Tue Mar 16 2010 - 11:26:42 PDT)
[AMBER] Minimization Failure
(Tue Mar 16 2010 - 11:04:53 PDT)
[AMBER] trajectory momentum for a substructure
(Mon Mar 08 2010 - 10:20:01 PST)
Thomas Cheatham
Re: [AMBER] Difference of ff99 and ff03 in building DNA duplex
(Thu Mar 11 2010 - 19:21:51 PST)
Re: [AMBER] Vdw radii params in antechamber
(Wed Mar 03 2010 - 11:55:39 PST)
Thomas Cheatham III
Re: [AMBER] How to find conserved coordinated waters?
(Mon Mar 29 2010 - 14:57:48 PDT)
Re: [AMBER] Mask selection
(Fri Mar 12 2010 - 14:23:30 PST)
Thomas Stockner
Re: [AMBER] Installing AmberTools
(Sun Mar 28 2010 - 11:00:57 PDT)
[AMBER] Installing AmberTools
(Sun Mar 28 2010 - 06:39:38 PDT)
tianyuan meng
[AMBER] Problems on Tutorial A8
(Wed Mar 24 2010 - 00:15:58 PDT)
Tom Joseph
Re: [AMBER] Fortran run time error
(Tue Mar 09 2010 - 06:49:22 PST)
Trevor Gokey
RE: [AMBER] Confirm compiling Amber10/Tools1.3 breaks with intel v 11.1?
(Tue Mar 16 2010 - 23:04:58 PDT)
[AMBER] Confirm compiling Amber10/Tools1.3 breaks with intel v 11.1?
(Tue Mar 16 2010 - 21:34:26 PDT)
Vlad Cojocaru
Re: [AMBER] membranes
(Wed Mar 31 2010 - 08:44:26 PDT)
waleed zalloum
[AMBER] Average structure
(Fri Mar 26 2010 - 04:55:17 PDT)
Wei Zhang
Re: [AMBER] sleap not built
(Mon Mar 15 2010 - 16:27:49 PDT)
whimsica.aol.com
Re: [AMBER] Calculating Amber Force fields from Wikipedia
(Tue Mar 16 2010 - 17:43:41 PDT)
Re: [AMBER] Calculating Amber Force fields from Wikipedia
(Tue Mar 16 2010 - 17:32:02 PDT)
Re: [AMBER] Calculating Amber Force fields from Wikipedia
(Tue Mar 16 2010 - 14:30:34 PDT)
Re: [AMBER] Calculating Amber Force fields from Wikipedia
(Mon Mar 15 2010 - 19:42:50 PDT)
Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?
(Mon Mar 15 2010 - 18:52:39 PDT)
Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?
(Mon Mar 15 2010 - 17:32:03 PDT)
Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?
(Mon Mar 15 2010 - 17:10:26 PDT)
Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?
(Mon Mar 15 2010 - 17:00:34 PDT)
[AMBER] Can anyone tell me what the parm99.dat values correspond to?
(Mon Mar 15 2010 - 13:58:28 PDT)
Re: [AMBER] Calculating Amber Force fields from Wikipedia
(Mon Mar 15 2010 - 08:32:57 PDT)
[AMBER] Calculating Amber Force fields from Wikipedia
(Mon Mar 15 2010 - 06:46:22 PDT)
[AMBER] unsubscribe
(Mon Mar 15 2010 - 00:40:54 PDT)
[AMBER] Fwd: understanding AMBER FORCES parm files?
(Sat Mar 13 2010 - 10:18:37 PST)
Workalemhu Berhanu
[AMBER] Script for creating topology files , running minimization and MD simulation using amoeba force field
(Thu Mar 25 2010 - 07:31:22 PDT)
[AMBER] Spline order too small when using AMOEBA force field
(Sat Mar 13 2010 - 04:42:55 PST)
xuemeiwang1103
[AMBER] disulfide bonds?
(Wed Mar 31 2010 - 06:32:02 PDT)
Yang Li
RE: [AMBER] simulation under pressure
(Mon Mar 29 2010 - 18:40:41 PDT)
RE: [AMBER] simulation under pressure
(Mon Mar 29 2010 - 12:53:01 PDT)
[AMBER] simulation under pressure
(Mon Mar 22 2010 - 20:05:45 PDT)
zhihong ke
[AMBER] The error information
(Wed Mar 03 2010 - 17:38:08 PST)
Last message date
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Wed Mar 31 2010 - 14:00:02 PDT
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: Fri Apr 26 2024 - 05:54:03 PDT
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