Amber Archive Apr 2009 by author
589 messages
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Starting
Wed Apr 01 2009 - 01:18:07 PDT,
Ending
Wed May 20 2009 - 13:55:33 PDT
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Alan
[AMBER] antechamber and wrong net charge with gasteiger method
(Tue Apr 14 2009 - 10:41:30 PDT)
Re: [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm
(Sun Apr 12 2009 - 08:58:18 PDT)
[AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm
(Sun Apr 12 2009 - 02:30:15 PDT)
[AMBER] zwitterionic form of ARG and antechamber
(Mon Apr 06 2009 - 05:33:31 PDT)
[AMBER] testing RRR with antechamber
(Mon Apr 06 2009 - 05:10:27 PDT)
[AMBER] NALA-ALA-CALA peptide with antechamber
(Fri Apr 03 2009 - 09:33:17 PDT)
Alessandro Nascimento
[AMBER] antechamber & multiple low-energy conformations
(Fri Apr 03 2009 - 05:01:39 PDT)
Re: [AMBER] Failure to compile amber9 serial ifort gcc
(Wed Apr 01 2009 - 04:09:42 PDT)
Alessandro S. Nascimento
Re: [AMBER] hbond-error in amber9
(Thu Apr 30 2009 - 03:46:02 PDT)
Andrew Voronkov
[AMBER] Papers on Amber package usage
(Sat Apr 25 2009 - 22:07:42 PDT)
aneesh cna
[AMBER] dipole autocorrelation functions
(Mon Apr 27 2009 - 23:23:05 PDT)
[AMBER] problem with antechamber
(Tue Apr 07 2009 - 23:32:32 PDT)
[AMBER] calculation of Pi-Pi interaction energy
(Wed Apr 01 2009 - 05:01:51 PDT)
Antonija Tomić
RE: [AMBER] Problems with running two separate jobs in the same time
(Thu Apr 09 2009 - 03:33:03 PDT)
[AMBER] Problems with running two separate jobs in the same time
(Tue Apr 07 2009 - 01:08:53 PDT)
Antonio Morreale
[AMBER] Van der Waals atom types
(Thu Apr 16 2009 - 07:39:14 PDT)
Aravind S
Re: [AMBER] problem with the results in the .out file!
(Wed Apr 01 2009 - 22:49:19 PDT)
Atro Tossavainen
Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so
(Wed Apr 08 2009 - 16:39:30 PDT)
Re: Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so
(Wed Apr 08 2009 - 16:36:53 PDT)
Re: [AMBER] Failures of tests
(Wed Apr 08 2009 - 15:43:08 PDT)
Re: Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so
(Wed Apr 08 2009 - 15:25:54 PDT)
Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so
(Wed Apr 08 2009 - 15:24:52 PDT)
Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so
(Wed Apr 08 2009 - 04:20:27 PDT)
Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so
(Wed Apr 08 2009 - 02:35:17 PDT)
Re: [AMBER] errors while testing
(Tue Apr 07 2009 - 03:18:08 PDT)
Re: [AMBER] ssh and make test.parallel
(Mon Apr 06 2009 - 13:21:07 PDT)
Re: [AMBER] ssh and make test.parallel
(Mon Apr 06 2009 - 03:33:21 PDT)
Re: [AMBER] parallel installation of amber on sun
(Fri Apr 03 2009 - 15:33:52 PDT)
Re: [AMBER] parallel installation of amber on sun
(Fri Apr 03 2009 - 14:40:42 PDT)
Re: [AMBER] parallel installation of amber on sun
(Fri Apr 03 2009 - 02:39:25 PDT)
Re: [AMBER] parallel installation of amber on sun
(Thu Apr 02 2009 - 13:23:05 PDT)
Bala subramanian
Re: [AMBER] basepair
(Tue Apr 14 2009 - 04:09:21 PDT)
Re: [AMBER] How to delete the frames at specific intervals
(Fri Apr 03 2009 - 02:55:35 PDT)
Re: [AMBER] How to find out residence time of water molecules
(Thu Apr 02 2009 - 23:12:18 PDT)
[AMBER] explicit ion with igb=1
(Thu Apr 02 2009 - 06:39:10 PDT)
balaji nagarajan
[AMBER] hbond-error in amber9
(Wed Apr 29 2009 - 19:09:17 PDT)
RE: [AMBER] reg-TMD
(Wed Apr 29 2009 - 18:44:32 PDT)
[AMBER] help_me to know the reason
(Fri Apr 17 2009 - 21:30:07 PDT)
RE: [AMBER] help- regarding - TMD
(Thu Apr 16 2009 - 10:01:39 PDT)
RE: [AMBER] help- regarding - TMD
(Wed Apr 15 2009 - 22:21:26 PDT)
[AMBER] help- regarding - TMD
(Wed Apr 15 2009 - 09:19:59 PDT)
[AMBER] hbond_ptraj_eror
(Tue Apr 14 2009 - 23:53:29 PDT)
[AMBER] problem with explicit solvent in TMD
(Mon Apr 13 2009 - 04:37:21 PDT)
[AMBER] basepair
(Thu Apr 09 2009 - 22:30:57 PDT)
RE: [AMBER] problem in input
(Thu Apr 02 2009 - 13:23:18 PDT)
Barbault Florent
Re: [AMBER] The PDB file was not recognized by Amber, what can i do?
(Tue Apr 28 2009 - 23:56:09 PDT)
Re: [AMBER] The PDB file was not recognized by Amber, what can i do?
(Tue Apr 28 2009 - 16:00:55 PDT)
Re: [AMBER] amber question
(Sun Apr 26 2009 - 01:48:31 PDT)
Beale, John
[AMBER] radius of gyration
(Fri Apr 17 2009 - 04:39:31 PDT)
[AMBER] Contour plot
(Thu Apr 02 2009 - 12:31:22 PDT)
bharat lakhani
[AMBER] how to add charge on metal ions
(Wed Apr 29 2009 - 23:44:46 PDT)
[AMBER] please read this mail
(Sat Apr 18 2009 - 00:38:12 PDT)
[AMBER] please help me out
(Wed Apr 15 2009 - 23:41:08 PDT)
Re: [AMBER] how to add charge in metal ion
(Tue Apr 14 2009 - 05:49:44 PDT)
[AMBER] please help me out
(Wed Apr 08 2009 - 22:10:22 PDT)
[AMBER] please help me out
(Wed Apr 08 2009 - 02:18:41 PDT)
[AMBER] how to add charge in metal ion
(Tue Apr 07 2009 - 02:11:23 PDT)
[AMBER] please help me out
(Thu Apr 02 2009 - 03:13:48 PDT)
Bill Ross
RE: [AMBER] Nonterminal, was not found in name map
(Tue Apr 28 2009 - 22:05:12 PDT)
Re: [AMBER] ANAL problems
(Tue Apr 28 2009 - 13:40:59 PDT)
Re: [AMBER] Restraining counterions?
(Tue Apr 28 2009 - 11:59:52 PDT)
Re: [AMBER] Best rms fit for correlation and covariance analysis
(Tue Apr 28 2009 - 09:57:10 PDT)
Re: [AMBER] Problem with RNA hairpin unwinding in explicit water
(Thu Apr 23 2009 - 10:53:40 PDT)
Re: [AMBER] Creating conditions for biased MD
(Wed Apr 22 2009 - 09:19:20 PDT)
Re: [AMBER] Sander and multiple residues
(Fri Apr 10 2009 - 13:42:14 PDT)
Re: [AMBER] Sander and multiple residues
(Fri Apr 10 2009 - 09:42:36 PDT)
Re: [AMBER] Sander and multiple residues
(Thu Apr 09 2009 - 13:12:10 PDT)
Brent Krueger
Re: [AMBER] CY3 dye parameters
(Sat Apr 25 2009 - 12:33:40 PDT)
Carlos Simmerling
Re: [AMBER] Amber FF and Glycam
(Thu Apr 30 2009 - 11:36:21 PDT)
Re: [AMBER] reg-TMD
(Wed Apr 29 2009 - 04:33:40 PDT)
Re: [AMBER] reg-TMD
(Wed Apr 29 2009 - 03:28:35 PDT)
Re: [AMBER] The PDB file was not recognized by Amber, what can i do?
(Tue Apr 28 2009 - 15:03:57 PDT)
Re: [AMBER] reg-TMD
(Tue Apr 28 2009 - 10:48:18 PDT)
Re: [AMBER] Error with calculation of the potential energy
(Mon Apr 27 2009 - 04:08:47 PDT)
Re: [AMBER] Simulated annealing
(Fri Apr 24 2009 - 08:44:02 PDT)
Re: [AMBER] Simulated annealing
(Fri Apr 24 2009 - 07:49:40 PDT)
Re: [AMBER] error in output file
(Thu Apr 23 2009 - 04:42:02 PDT)
Re: [AMBER] Problem with RNA hairpin unwinding in explicit water
(Wed Apr 22 2009 - 15:53:33 PDT)
Re: [AMBER] Problem with RNA hairpin unwinding in explicit water
(Wed Apr 22 2009 - 15:25:47 PDT)
Re: [AMBER] help regarding step size
(Wed Apr 22 2009 - 04:03:28 PDT)
Re: [AMBER] help regarding step size
(Wed Apr 22 2009 - 03:13:54 PDT)
Re: [AMBER] help- regarding - TMD
(Tue Apr 21 2009 - 16:35:42 PDT)
Re: [AMBER] Set start timestep for mdcrd traj output
(Tue Apr 21 2009 - 16:26:02 PDT)
Re: [AMBER] Creating conditions for biased MD
(Tue Apr 21 2009 - 14:32:09 PDT)
Re: [AMBER] help- regarding - TMD
(Tue Apr 21 2009 - 14:23:23 PDT)
Re: [AMBER] help- regarding - TMD
(Tue Apr 21 2009 - 12:46:41 PDT)
Re: [AMBER] Creating conditions for biased MD
(Tue Apr 21 2009 - 12:44:03 PDT)
Re: [AMBER] Creating conditions for biased MD
(Mon Apr 20 2009 - 11:46:41 PDT)
Re: [AMBER] help- regarding - TMD
(Mon Apr 20 2009 - 08:30:52 PDT)
Re: [AMBER] help- regarding - TMD
(Mon Apr 20 2009 - 08:12:40 PDT)
Re: [AMBER] Atom type error
(Sun Apr 19 2009 - 04:06:07 PDT)
Re: [AMBER] about saltcon
(Sun Apr 19 2009 - 03:49:57 PDT)
Re: [AMBER] Backbone restraint
(Sat Apr 18 2009 - 04:08:39 PDT)
Re: [AMBER] help_me to know the reason
(Sat Apr 18 2009 - 03:53:50 PDT)
Re: [AMBER] Backbone restraint
(Fri Apr 17 2009 - 19:35:26 PDT)
Re: [AMBER] Density in MD simulation
(Fri Apr 17 2009 - 09:10:51 PDT)
Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?
(Wed Apr 15 2009 - 06:33:00 PDT)
Re: [AMBER] problem with explicit solvent in TMD
(Mon Apr 13 2009 - 04:41:41 PDT)
Re: [AMBER] Sander and multiple residues
(Thu Apr 09 2009 - 13:05:23 PDT)
Re: [AMBER] Sander and multiple residues
(Thu Apr 09 2009 - 12:21:56 PDT)
Re: [AMBER] ntwr
(Wed Apr 08 2009 - 15:45:57 PDT)
Re: [AMBER] ntwr
(Wed Apr 08 2009 - 14:47:04 PDT)
Re: [AMBER] A question about SMD force constant
(Tue Apr 07 2009 - 03:32:09 PDT)
Re: Re: [AMBER] sander.MPI parallel run problem
(Mon Apr 06 2009 - 04:02:13 PDT)
Re: [AMBER] sander.MPI parallel run problem
(Mon Apr 06 2009 - 03:09:11 PDT)
Re: [AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule.
(Mon Apr 06 2009 - 03:07:09 PDT)
Re: [AMBER] Error in trajin and rms
(Thu Apr 02 2009 - 12:19:39 PDT)
Re: [AMBER] Averaging simulations
(Thu Apr 02 2009 - 08:24:28 PDT)
Re: [AMBER] explicit ion with igb=1
(Thu Apr 02 2009 - 06:53:54 PDT)
Re: [AMBER] Help: An error happened when I calculate mm/pbsa
(Thu Apr 02 2009 - 04:19:04 PDT)
Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1
(Wed Apr 01 2009 - 04:01:51 PDT)
Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1
(Tue Mar 31 2009 - 19:24:34 PDT)
Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1
(Tue Mar 31 2009 - 18:41:49 PDT)
case
Re: [AMBER] Water-molecules
(Sun Apr 26 2009 - 15:35:36 PDT)
Catein Catherine
RE: [AMBER] ERROR In Restraint file.
(Tue Apr 28 2009 - 16:32:26 PDT)
[AMBER] ERROR In Restraint file.
(Tue Apr 28 2009 - 08:27:18 PDT)
[AMBER] ERROR In Restraint file.
(Tue Apr 28 2009 - 08:12:34 PDT)
chenquan
RE: [AMBER] mean of character in frcmod.ff03
(Wed Apr 15 2009 - 16:36:32 PDT)
[AMBER] mean of character in frcmod.ff03
(Wed Apr 15 2009 - 05:26:38 PDT)
[AMBER] Could not find angle parameter
(Fri Apr 03 2009 - 03:46:47 PDT)
[AMBER] (no subject)
(Fri Apr 03 2009 - 03:12:14 PDT)
Chris Moth
Re: [AMBER] bintraj and amber 10
(Thu Apr 23 2009 - 10:46:44 PDT)
[AMBER] Source of new CYX residue parameters in ff03ua
(Tue Apr 14 2009 - 17:42:33 PDT)
[AMBER] Source of new CYX residue parameters in ff03ua
(Tue Apr 07 2009 - 12:48:46 PDT)
Christopher Materese
[AMBER] uncharged c and n terminal amino acids
(Wed Apr 22 2009 - 11:05:38 PDT)
Cihan Aydin
[AMBER] Best rms fit for correlation and covariance analysis
(Mon Apr 27 2009 - 22:02:14 PDT)
Collins Nganou
[AMBER] Make parallel test faillure
(Thu Apr 30 2009 - 12:36:55 PDT)
[AMBER] (no subject)
(Thu Apr 30 2009 - 12:34:36 PDT)
[AMBER] Request an error
(Thu Apr 30 2009 - 10:41:48 PDT)
[AMBER] Bad value during integer read by sander
(Thu Apr 16 2009 - 08:09:45 PDT)
Dan Kaps
Re: [AMBER] atom types in pdb files
(Mon Apr 13 2009 - 12:29:43 PDT)
[AMBER] atom types in pdb files
(Mon Apr 13 2009 - 07:23:58 PDT)
Re: [AMBER] Sander and multiple residues
(Fri Apr 10 2009 - 10:46:49 PDT)
Re: [AMBER] Sander and multiple residues
(Fri Apr 10 2009 - 08:01:08 PDT)
Re: [AMBER] Sander and multiple residues
(Fri Apr 10 2009 - 05:57:54 PDT)
Re: [AMBER] Sander and multiple residues
(Fri Apr 10 2009 - 05:56:53 PDT)
Re: [AMBER] Sander and multiple residues
(Thu Apr 09 2009 - 13:02:46 PDT)
[AMBER] Sander and multiple residues
(Thu Apr 09 2009 - 11:48:55 PDT)
David A. Case
Re: [AMBER] (no subject)
(Thu Apr 30 2009 - 13:16:35 PDT)
Re: [AMBER] chain restrain x TI
(Thu Apr 30 2009 - 11:01:13 PDT)
Re: [AMBER] Influence about HIS-HIE-HIS-HIP
(Thu Apr 30 2009 - 07:27:02 PDT)
Re: [AMBER] input error in TI calculation
(Wed Apr 29 2009 - 11:48:04 PDT)
Re: [AMBER] (no subject)
(Wed Apr 29 2009 - 10:56:28 PDT)
Re: [AMBER] ERROR In Restraint file.
(Tue Apr 28 2009 - 17:05:23 PDT)
Re: [AMBER] ERROR In Restraint file.
(Tue Apr 28 2009 - 09:17:36 PDT)
Re: [AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing
(Mon Apr 27 2009 - 10:30:55 PDT)
Re: [AMBER] Papers on Amber package usage
(Sun Apr 26 2009 - 05:48:31 PDT)
Re: [AMBER] Unit name with loadMol2 command
(Thu Apr 23 2009 - 15:54:02 PDT)
[AMBER] NAB bug with parmbsc0
(Thu Apr 23 2009 - 09:25:27 PDT)
Re: [AMBER] nmod no run proprely in mmbsa
(Thu Apr 23 2009 - 05:47:44 PDT)
Re: [AMBER] uncharged c and n terminal amino acids
(Wed Apr 22 2009 - 11:16:19 PDT)
Re: [AMBER] atom numbers
(Tue Apr 21 2009 - 10:26:32 PDT)
Re: [AMBER] atom numbers
(Tue Apr 21 2009 - 08:52:22 PDT)
Re: [AMBER] atom numbers
(Tue Apr 21 2009 - 04:54:37 PDT)
Re: [AMBER] Atom type error
(Sun Apr 19 2009 - 10:41:11 PDT)
Re: [AMBER] please read this mail
(Sat Apr 18 2009 - 06:01:08 PDT)
[AMBER] Amber and CHARMM summer school
(Thu Apr 16 2009 - 08:04:18 PDT)
Re: [AMBER] 1-4 vdW, GB MM difference
(Thu Apr 16 2009 - 07:47:55 PDT)
Re: [AMBER] ambertools failed - SMP IA64
(Thu Apr 16 2009 - 07:10:20 PDT)
Re: [AMBER] specification of antechamber AC file format?
(Thu Apr 16 2009 - 05:29:46 PDT)
Re: [AMBER] my FF
(Wed Apr 15 2009 - 05:28:16 PDT)
Re: [AMBER] hpux sander.serial failure info
(Wed Apr 15 2009 - 05:07:45 PDT)
Re: [AMBER] water bonding with protein
(Wed Apr 15 2009 - 04:58:17 PDT)
Re: [AMBER] antechamber and wrong net charge with gasteiger method
(Tue Apr 14 2009 - 11:42:14 PDT)
Re: [AMBER] restrained minimization
(Mon Apr 13 2009 - 19:03:11 PDT)
Re: [AMBER] atom types in pdb files
(Mon Apr 13 2009 - 13:25:04 PDT)
Re: [AMBER] Energy minimisation and NaN
(Mon Apr 13 2009 - 12:28:10 PDT)
Re: [AMBER] Sander and multiple residues
(Fri Apr 10 2009 - 07:03:57 PDT)
Re: [AMBER] RST file
(Fri Apr 10 2009 - 05:21:19 PDT)
Re: [AMBER] igb=0 vs. igb=6 give different answers
(Thu Apr 09 2009 - 19:48:31 PDT)
Re: [AMBER] antechamber problems
(Thu Apr 09 2009 - 11:04:51 PDT)
Re: [AMBER] hpux sander.serial failure info
(Thu Apr 09 2009 - 04:56:51 PDT)
Re: [AMBER] please help me out
(Thu Apr 09 2009 - 04:46:12 PDT)
Re: [AMBER] please help me out
(Wed Apr 08 2009 - 11:10:04 PDT)
Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error
(Tue Apr 07 2009 - 13:41:21 PDT)
Re: [AMBER] prmtop residue format
(Tue Apr 07 2009 - 13:35:40 PDT)
Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error
(Tue Apr 07 2009 - 09:29:18 PDT)
Re: [AMBER] missing violations of the covalent geometry
(Tue Apr 07 2009 - 04:10:42 PDT)
Re: [AMBER] deffision coefficient
(Mon Apr 06 2009 - 19:16:39 PDT)
Re: [AMBER] Do I need to modify the cap residues
(Mon Apr 06 2009 - 11:57:02 PDT)
Re: [AMBER] Amber with AMOEBA force-field
(Mon Apr 06 2009 - 06:00:47 PDT)
Re: [AMBER] Amber with AMOEBA force-field
(Mon Apr 06 2009 - 05:47:11 PDT)
Re: [AMBER] error in MM PBSA
(Sat Apr 04 2009 - 14:16:42 PDT)
Re: [AMBER] constant-pH: appearance of not titrated residues during the Monte Carlo simulation
(Sat Apr 04 2009 - 06:20:28 PDT)
Re: [AMBER] Umbrella test
(Sat Apr 04 2009 - 06:12:13 PDT)
Re: [AMBER] NALA-ALA-CALA peptide with antechamber
(Sat Apr 04 2009 - 06:04:32 PDT)
Re: [AMBER] amber9 serial compilation issues
(Fri Apr 03 2009 - 13:01:02 PDT)
Re: [AMBER] (no subject)
(Fri Apr 03 2009 - 05:17:36 PDT)
Re: [AMBER] please help me out
(Thu Apr 02 2009 - 10:48:10 PDT)
Re: [AMBER] yacc parser
(Thu Apr 02 2009 - 05:03:06 PDT)
Re: [AMBER] ambmol2?
(Wed Apr 01 2009 - 06:19:00 PDT)
Dechang Li
Re: [AMBER] how to plot this kind of map?
(Thu Apr 09 2009 - 01:46:16 PDT)
Re: Re: Re: [AMBER] sander.MPI parallel run problem
(Mon Apr 06 2009 - 04:09:04 PDT)
Re: Re: [AMBER] sander.MPI parallel run problem
(Mon Apr 06 2009 - 03:56:53 PDT)
[AMBER] sander.MPI parallel run problem
(Mon Apr 06 2009 - 00:44:12 PDT)
Dmitri Nilov
Re: [AMBER] Equilibrium bond lengths and angle values
(Tue Apr 28 2009 - 03:56:38 PDT)
[AMBER] Equilibrium bond lengths and angle values
(Fri Apr 24 2009 - 06:19:56 PDT)
Dong Xu
[AMBER] MM-PBSA energy decomposition
(Wed Apr 29 2009 - 19:03:34 PDT)
[AMBER] Amber FF and Glycam
(Wed Apr 29 2009 - 18:42:55 PDT)
[AMBER] restraint constant
(Sat Apr 25 2009 - 15:15:22 PDT)
Re: [AMBER] Disulfide bond
(Tue Apr 21 2009 - 19:41:02 PDT)
[AMBER] Disulfide bond
(Tue Apr 21 2009 - 18:37:46 PDT)
Re: [AMBER] Set start timestep for mdcrd traj output
(Tue Apr 21 2009 - 16:44:50 PDT)
[AMBER] Flexible ring simulation
(Tue Apr 21 2009 - 16:04:55 PDT)
Dr. Debaprasad Giri
Re: [AMBER] problem in installing AMBER10
(Sat Apr 04 2009 - 05:13:46 PDT)
E.M.
[AMBER] ANAL problems
(Tue Apr 28 2009 - 13:12:04 PDT)
Ed Pate
[AMBER] ambmask question
(Mon Apr 06 2009 - 21:36:40 PDT)
[AMBER] ptraj problem
(Fri Apr 03 2009 - 13:13:37 PDT)
Edward M
Re: [AMBER] ANAL problems
(Tue Apr 28 2009 - 16:01:34 PDT)
Farly Walsh
Re: [AMBER] AmberTools compiling error
(Wed Apr 29 2009 - 12:49:27 PDT)
Francesco Pietra
[AMBER] Restraining counterions?
(Tue Apr 28 2009 - 10:32:18 PDT)
Re: [AMBER] Creating conditions for biased MD
(Wed Apr 22 2009 - 11:01:39 PDT)
Re: [AMBER] Creating conditions for biased MD
(Wed Apr 22 2009 - 03:16:11 PDT)
Re: [AMBER] Creating conditions for biased MD
(Tue Apr 21 2009 - 14:49:14 PDT)
Re: [AMBER] Creating conditions for biased MD
(Tue Apr 21 2009 - 14:29:36 PDT)
Re: [AMBER] Creating conditions for biased MD
(Tue Apr 21 2009 - 11:40:35 PDT)
Re: [AMBER] Creating conditions for biased MD
(Mon Apr 20 2009 - 10:31:52 PDT)
Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so
(Sun Apr 19 2009 - 07:36:02 PDT)
Re: Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so
(Wed Apr 08 2009 - 16:20:02 PDT)
Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so
(Wed Apr 08 2009 - 16:17:38 PDT)
Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so
(Wed Apr 08 2009 - 08:23:58 PDT)
Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so
(Wed Apr 08 2009 - 08:14:43 PDT)
Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so
(Wed Apr 08 2009 - 03:03:09 PDT)
Re: [AMBER] ssh and make test.parallel
(Wed Apr 08 2009 - 00:19:36 PDT)
[AMBER] Testing parallel amber10: no libmkl_lapack.so
(Tue Apr 07 2009 - 11:56:25 PDT)
Re: [AMBER] ssh and make test.parallel
(Mon Apr 06 2009 - 07:29:19 PDT)
[AMBER] ssh and make test.parallel
(Mon Apr 06 2009 - 02:58:39 PDT)
Re: [AMBER] amber9 serial compilation issues
(Fri Apr 03 2009 - 15:04:17 PDT)
[AMBER] amber9 serial compilation issues
(Fri Apr 03 2009 - 11:38:12 PDT)
Re: [AMBER] Failure to compile amber9 serial ifort gcc
(Thu Apr 02 2009 - 09:00:46 PDT)
Re: [AMBER] yacc parser
(Thu Apr 02 2009 - 08:37:53 PDT)
Re: [AMBER] Failure to compile amber9 serial ifort gcc
(Thu Apr 02 2009 - 04:16:36 PDT)
[AMBER] Fwd: yacc parser
(Wed Apr 01 2009 - 13:53:01 PDT)
[AMBER] yacc parser
(Wed Apr 01 2009 - 07:58:01 PDT)
[AMBER] Failure to compile amber9 serial ifort gcc
(Wed Apr 01 2009 - 04:04:18 PDT)
FyD
Re: [AMBER] REd program!
(Wed Apr 29 2009 - 06:53:12 PDT)
Re: [AMBER] CY3 dye parameters
(Fri Apr 24 2009 - 23:04:22 PDT)
Re: [AMBER] Equilibrium bond lengths and angle values
(Fri Apr 24 2009 - 14:05:42 PDT)
Re: [AMBER] Amber Sulfate Ion Parameters
(Wed Apr 22 2009 - 23:07:40 PDT)
Re: [AMBER] Amber Sulfate Ion Parameters
(Wed Apr 22 2009 - 22:18:28 PDT)
Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail
(Mon Apr 20 2009 - 07:50:12 PDT)
Re: [AMBER] missing amber force field parameters
(Thu Apr 16 2009 - 02:41:44 PDT)
[AMBER] Release of R.E.D. Server
(Thu Apr 09 2009 - 01:31:30 PDT)
Re: [AMBER] Problem with CAP residues
(Tue Apr 07 2009 - 04:01:35 PDT)
Re: [AMBER] LYN again
(Mon Apr 06 2009 - 07:26:14 PDT)
Re: [AMBER] LYN again
(Sun Apr 05 2009 - 12:24:27 PDT)
Gary Clark
Re: [AMBER] Amber Sulfate Ion Parameters
(Thu Apr 23 2009 - 12:55:24 PDT)
[AMBER] Amber Sulfate Ion Parameters
(Wed Apr 22 2009 - 15:31:00 PDT)
Gert von Helden
[AMBER] polarizable force field for 18-crown-6
(Thu Apr 16 2009 - 10:33:15 PDT)
Giorgos Lamprinidis
Re: [AMBER] mm_pbsa problem
(Wed Apr 01 2009 - 00:36:53 PDT)
Gustavo Seabra
Re: [AMBER] force fields
(Wed Apr 15 2009 - 05:43:49 PDT)
Re: [AMBER] Contour plot
(Thu Apr 02 2009 - 12:47:14 PDT)
Han Ming
Re: [AMBER] fillratio error in mmpbsa
(Wed Apr 01 2009 - 08:06:08 PDT)
Hannes Kopitz
Re: [AMBER] MM-PBSA energy decomposition
(Thu Apr 30 2009 - 03:37:35 PDT)
Hannes Loeffler
Re: [AMBER] How to find out residence time of water molecules
(Fri Apr 03 2009 - 00:31:32 PDT)
Hannes Wallnoefer
[AMBER] input error in TI calculation
(Wed Apr 29 2009 - 08:40:58 PDT)
Re: [AMBER] TI production runs stop after a certain Step number
(Wed Apr 08 2009 - 08:14:32 PDT)
Re: [AMBER] TI production runs stop after a certain Step number
(Wed Apr 08 2009 - 04:48:31 PDT)
[AMBER] TI production runs stop after a certain Step number
(Tue Apr 07 2009 - 04:48:45 PDT)
Helena P M Tossavainen
Re: [AMBER] missing violations of the covalent geometry
(Tue Apr 07 2009 - 05:10:16 PDT)
[AMBER] missing violations of the covalent geometry
(Tue Apr 07 2009 - 02:36:44 PDT)
Hemant Gangwar
Re: [AMBER] error in MM PBSA
(Sat Apr 04 2009 - 10:08:08 PDT)
Hemant Kumar
Re: [AMBER] error in output file
(Thu Apr 23 2009 - 05:20:25 PDT)
[AMBER] parameter for amoeba
(Sat Apr 04 2009 - 04:46:01 PDT)
Hopkins, Robert
RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP
(Wed Apr 01 2009 - 16:10:44 PDT)
Houyang Chen
RE: [AMBER] The PDB file was not recognized by Amber, what can i do?
(Wed Apr 29 2009 - 15:17:51 PDT)
RE: [AMBER] The PDB file was not recognized by Amber, what can i do?
(Tue Apr 28 2009 - 20:42:39 PDT)
[AMBER] The PDB file was not recognized by Amber, what can i do?
(Tue Apr 28 2009 - 15:00:05 PDT)
Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA].
RE: [AMBER] reg-TMD
(Wed Apr 29 2009 - 13:56:07 PDT)
RE: [AMBER] help- regarding - TMD
(Tue Apr 21 2009 - 15:40:36 PDT)
RE: [AMBER] help- regarding - TMD
(Tue Apr 21 2009 - 13:25:15 PDT)
RE: [AMBER] help- regarding - TMD
(Mon Apr 20 2009 - 09:21:06 PDT)
RE: [AMBER] help- regarding - TMD
(Mon Apr 20 2009 - 08:28:30 PDT)
RE: [AMBER] help- regarding - TMD
(Mon Apr 20 2009 - 08:05:38 PDT)
RE: [AMBER] help- regarding - TMD
(Thu Apr 16 2009 - 06:30:22 PDT)
RE: [AMBER] help- regarding - TMD
(Wed Apr 15 2009 - 10:56:07 PDT)
[AMBER] Questions on targeted MD with explicit solvent
(Tue Apr 14 2009 - 06:51:40 PDT)
Hugh Heldenbrand
[AMBER] igb=0 vs. igb=6 give different answers
(Thu Apr 09 2009 - 13:51:02 PDT)
Re: [AMBER] please help me out
(Wed Apr 08 2009 - 08:44:54 PDT)
Ibrahim Moustafa
Re: [AMBER] Density in MD simulation
(Fri Apr 17 2009 - 16:26:46 PDT)
[AMBER] Density in MD simulation
(Fri Apr 17 2009 - 09:09:16 PDT)
iccy liu
RE: [AMBER] Error in trajin and rms
(Thu Apr 02 2009 - 12:19:16 PDT)
[AMBER] long polymer chain and image command in ptraj
(Thu Apr 02 2009 - 12:11:26 PDT)
Ignacio J. General
Re: [AMBER] Partial interactions
(Fri Apr 24 2009 - 10:11:31 PDT)
Re: [AMBER] Partial interactions
(Fri Apr 24 2009 - 07:49:07 PDT)
Re: [AMBER] Partial interactions
(Wed Apr 22 2009 - 12:02:00 PDT)
Re: [AMBER] Partial interactions
(Tue Apr 21 2009 - 07:31:26 PDT)
[AMBER] Partial interactions
(Mon Apr 20 2009 - 14:07:24 PDT)
Re: [AMBER] Thermodynamic Integration and belly
(Mon Apr 13 2009 - 10:26:16 PDT)
[AMBER] Thermodynamic Integration and belly
(Mon Apr 13 2009 - 08:24:15 PDT)
[AMBER] Thermodynamic Integration and belly
(Wed Apr 08 2009 - 12:52:51 PDT)
Ilyas Yildirim
Re: [AMBER] TI production runs stop after a certain Step number
(Tue Apr 07 2009 - 12:08:31 PDT)
Jackie. J. Shen
Re: Re: [AMBER] Backbone restraint
(Mon Apr 20 2009 - 18:12:13 PDT)
[AMBER] A question about SMD force constant
(Mon Apr 06 2009 - 18:40:13 PDT)
Jacopo Sgrignani
[AMBER] calculation of Pi-Pi interaction energy
(Wed Apr 01 2009 - 05:24:28 PDT)
jcmoore.student.umass.edu
[AMBER] CY3 dye parameters
(Thu Apr 23 2009 - 14:42:59 PDT)
Jenny Iskrenova
[AMBER] Negative "number of measurements" in PTRAJ
(Mon Apr 06 2009 - 10:28:59 PDT)
Jia Xu
Re: [AMBER] antechamber problems
(Fri Apr 10 2009 - 07:41:53 PDT)
[AMBER] antechamber problems
(Thu Apr 09 2009 - 10:12:44 PDT)
Jim Parker
[AMBER] Re: install and test Amber 10 parallel on Ubuntu 8.10
(Sat Apr 11 2009 - 21:47:19 PDT)
[AMBER] install and test Amber 10 parallel on Ubuntu 8.10
(Sat Apr 11 2009 - 17:20:25 PDT)
Re: [AMBER] Solved-Amber 1.2 tools test suite failure
(Sat Apr 11 2009 - 12:29:55 PDT)
[AMBER] Amber 1.2 tools test suite failure?
(Sat Apr 11 2009 - 10:41:54 PDT)
Jimmy Heimdal
[AMBER] 1-4 vdW, GB MM difference
(Thu Apr 16 2009 - 04:57:01 PDT)
Jiri Sponer
Re: [AMBER] calculation of Pi-Pi interaction energy
(Wed Apr 01 2009 - 05:38:49 PDT)
john smith
[AMBER] pmemd compilation error
(Mon Apr 27 2009 - 20:30:21 PDT)
Jorgen Simonsen
[AMBER] Regarding syntax for freezing different atoms
(Thu Apr 23 2009 - 05:50:43 PDT)
Josmar R. da Rocha
[AMBER] chain restrain x TI
(Wed Apr 29 2009 - 15:04:52 PDT)
Junmei Wang
Re: [AMBER] ambmol2?
(Tue Mar 31 2009 - 19:41:35 PDT)
Re: [AMBER] ambmol2?
(Tue Mar 31 2009 - 16:08:25 PDT)
Karl Kirschner
Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail
(Thu Apr 23 2009 - 06:54:14 PDT)
Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail
(Thu Apr 23 2009 - 04:43:31 PDT)
Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail
(Tue Apr 21 2009 - 00:24:18 PDT)
Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail
(Mon Apr 20 2009 - 05:27:45 PDT)
Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?
(Wed Apr 15 2009 - 00:07:00 PDT)
Re: [AMBER] long polymer chain and image command in ptraj
(Mon Apr 06 2009 - 01:15:00 PDT)
Re: [AMBER] FF Parameters Transformations ...?
(Mon Apr 06 2009 - 00:39:31 PDT)
Kristina Furse
RE: [AMBER] atom types in pdb files
(Mon Apr 13 2009 - 09:30:05 PDT)
Lachele Foley (Lists)
Re: [AMBER] Amber FF and Glycam
(Thu Apr 30 2009 - 10:16:17 PDT)
Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?
(Fri Apr 17 2009 - 11:13:49 PDT)
liu junjun
Re: [AMBER] parallel problem of QM/MM calculation for AMBER 9
(Tue Apr 28 2009 - 19:18:31 PDT)
[AMBER] parallel problem of QM/MM calculation for AMBER 9
(Tue Apr 28 2009 - 14:53:06 PDT)
lnin_1431.sina.com
[AMBER] how to plot this kind of map?
(Thu Apr 09 2009 - 01:36:45 PDT)
Lucilla Angeli
[AMBER] MM-PBSA: decompose energy error
(Mon Apr 06 2009 - 07:35:58 PDT)
m m
[AMBER] my FF
(Tue Apr 14 2009 - 15:21:38 PDT)
[AMBER] compare MMPBSA result
(Tue Apr 07 2009 - 23:28:06 PDT)
[AMBER] fillratio error in mmpbsa
(Wed Apr 01 2009 - 04:42:45 PDT)
M. L. Dodson
Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so
(Wed Apr 08 2009 - 09:06:09 PDT)
Mannan
[AMBER] How to find out residence time of water molecules
(Thu Apr 02 2009 - 18:52:36 PDT)
[AMBER] How to delete the frames at specific intervals
(Thu Apr 02 2009 - 18:16:49 PDT)
Marek Malý
[AMBER] Mixing of forcefields in case of covaletly bonded systems
(Mon Apr 27 2009 - 05:06:38 PDT)
Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail
(Thu Apr 23 2009 - 07:30:07 PDT)
Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail
(Thu Apr 23 2009 - 06:41:03 PDT)
Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail
(Tue Apr 21 2009 - 19:31:34 PDT)
Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail
(Mon Apr 20 2009 - 20:52:46 PDT)
[AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail
(Mon Apr 20 2009 - 04:52:36 PDT)
Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?
(Thu Apr 16 2009 - 14:25:12 PDT)
Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?
(Tue Apr 14 2009 - 17:40:22 PDT)
Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?
(Tue Apr 14 2009 - 16:18:18 PDT)
[AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?
(Mon Apr 13 2009 - 20:29:17 PDT)
Re: [AMBER] FF Parameters Transformations ...?
(Mon Apr 06 2009 - 13:03:58 PDT)
[AMBER] FF Parameters Transformations ...?
(Wed Apr 01 2009 - 10:29:26 PDT)
Marius Retegan
Re: [AMBER] LYN again
(Mon Apr 06 2009 - 06:55:24 PDT)
[AMBER] LYN again
(Sat Apr 04 2009 - 06:12:09 PDT)
Re: [AMBER] Could not find angle parameter
(Fri Apr 03 2009 - 03:58:47 PDT)
Re: [AMBER] How to create parameter file for unknown residue
(Fri Apr 03 2009 - 03:50:30 PDT)
Re: [AMBER] AmberTools compilation error
(Wed Apr 01 2009 - 13:03:59 PDT)
Mark M Huntress
[AMBER] water bonding with protein
(Tue Apr 14 2009 - 19:55:39 PDT)
[AMBER] force fields
(Wed Apr 08 2009 - 17:23:38 PDT)
Mark Williamson
Re: [AMBER] yacc parser
(Wed Apr 01 2009 - 10:15:56 PDT)
Markus Kaukonen
Re: [AMBER] The PDB file was not recognized by Amber, what can i do?
(Wed Apr 29 2009 - 00:16:30 PDT)
matthew_seetin.urmc.rochester.edu
RE: [AMBER] Problem with RNA hairpin unwinding in explicit water
(Wed Apr 22 2009 - 16:59:02 PDT)
michael bane
[AMBER] make test.serial.QMMM
(Wed Apr 01 2009 - 08:44:51 PDT)
Michael Zimmermann
[AMBER] Using AMBER force fields in NAMD
(Tue Apr 28 2009 - 14:25:56 PDT)
mohamed mohamed
[AMBER] nmod no run proprely in mmbsa
(Thu Apr 23 2009 - 05:20:36 PDT)
Nancy
[AMBER] deffision coefficient
(Mon Apr 06 2009 - 18:18:32 PDT)
[AMBER] deffision
(Sat Apr 04 2009 - 07:30:50 PDT)
[AMBER] a layer of water
(Tue Mar 31 2009 - 18:37:51 PDT)
nandy.physics.iisc.ernet.in
[AMBER] Using smd with fixed atom
(Sun Apr 26 2009 - 07:57:45 PDT)
Naser Alijabbari
Re: [AMBER] bintraj and amber 10
(Sat Apr 25 2009 - 11:47:34 PDT)
Re: [AMBER] bintraj and amber 10
(Thu Apr 23 2009 - 17:37:06 PDT)
Re: [AMBER] bintraj and amber 10
(Wed Apr 22 2009 - 18:05:21 PDT)
[AMBER] bintraj and amber 10
(Tue Apr 21 2009 - 23:31:51 PDT)
[AMBER] Averaging simulations
(Thu Apr 02 2009 - 08:21:41 PDT)
Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1
(Tue Mar 31 2009 - 19:43:28 PDT)
Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1
(Tue Mar 31 2009 - 19:15:13 PDT)
[AMBER] Maxwell-Boltzmann distribution and ig=-1
(Tue Mar 31 2009 - 18:35:43 PDT)
Neha Gandhi
[AMBER] missing amber force field parameters
(Thu Apr 16 2009 - 02:19:57 PDT)
Nicholas Musolino
[AMBER] Unit name with loadMol2 command
(Thu Apr 23 2009 - 12:30:30 PDT)
Re: [AMBER] specification of antechamber AC file format?
(Thu Apr 16 2009 - 06:18:32 PDT)
Re: [AMBER] specification of antechamber AC file format?
(Wed Apr 15 2009 - 15:07:32 PDT)
Re: [AMBER] antechamber problems
(Thu Apr 09 2009 - 11:03:45 PDT)
Re: [AMBER] specification of antechamber AC file format?
(Tue Apr 07 2009 - 12:43:57 PDT)
nicholus bhattacharjee
Re: [AMBER] Atom type error
(Sun Apr 19 2009 - 03:55:37 PDT)
Re: [AMBER] Do I need to modify the cap residues
(Mon Apr 06 2009 - 21:51:22 PDT)
Re: [AMBER] Do I need to modify the cap residues
(Mon Apr 06 2009 - 10:19:41 PDT)
[AMBER] Do I need to modify the cap residues
(Mon Apr 06 2009 - 09:45:20 PDT)
[AMBER] problem with secstruct action command in ptraj
(Mon Apr 06 2009 - 04:49:44 PDT)
[AMBER] How to create parameter file for unknown residue
(Fri Apr 03 2009 - 03:33:03 PDT)
oguz gurbulak
[AMBER] transport properties
(Tue Apr 28 2009 - 07:11:05 PDT)
Re: [AMBER] a layer of water
(Wed Apr 01 2009 - 00:26:46 PDT)
Pansy Patel
RE: [AMBER] Error in trajin and rms
(Thu Apr 02 2009 - 12:25:58 PDT)
[AMBER] Error in trajin and rms
(Thu Apr 02 2009 - 11:58:47 PDT)
Patrick Schopf
Re: [AMBER] Right force fields
(Fri Apr 17 2009 - 06:34:04 PDT)
Re: [AMBER] Right force fields
(Fri Apr 17 2009 - 05:48:14 PDT)
Per Jr. Greisen
Re: [AMBER] Error with calculation of the potential energy
(Mon Apr 27 2009 - 11:57:58 PDT)
Re: [AMBER] Error with calculation of the potential energy
(Mon Apr 27 2009 - 10:11:32 PDT)
[AMBER] Error with calculation of the potential energy
(Mon Apr 27 2009 - 04:03:44 PDT)
Re: [AMBER] Failures of tests
(Thu Apr 09 2009 - 05:52:32 PDT)
Re: [AMBER] Failures of tests
(Wed Apr 08 2009 - 09:17:16 PDT)
[AMBER] Failures of tests
(Wed Apr 08 2009 - 08:41:34 PDT)
Re: [AMBER] errors while testing
(Wed Apr 08 2009 - 04:06:40 PDT)
[AMBER] errors while testing
(Tue Apr 07 2009 - 03:00:19 PDT)
Re: [AMBER] parallel installation of amber on sun
(Fri Apr 03 2009 - 03:22:45 PDT)
Re: [AMBER] parallel installation of amber on sun
(Thu Apr 02 2009 - 13:38:54 PDT)
[AMBER] parallel installation of amber on sun
(Thu Apr 02 2009 - 12:02:47 PDT)
Piotr Cieplak
RE: [AMBER] Using AMBER force fields in NAMD
(Tue Apr 28 2009 - 15:23:15 PDT)
Re: [AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing
(Mon Apr 27 2009 - 12:07:38 PDT)
Re: [AMBER] polarizable force field for 18-crown-6
(Fri Apr 17 2009 - 00:48:03 PDT)
quantum_mania.yahoo.com
Re: [AMBER] Disulfide bond
(Tue Apr 21 2009 - 22:25:45 PDT)
[AMBER] Set start timestep for mdcrd traj output
(Tue Apr 21 2009 - 09:31:45 PDT)
[AMBER] Set start timestep for mdcrd traj output
(Tue Apr 21 2009 - 09:38:53 PDT)
[AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?
(Fri Apr 17 2009 - 10:52:28 PDT)
[AMBER] restrained minimization
(Mon Apr 13 2009 - 17:12:35 PDT)
[AMBER] MMPB(GB)SA on trimer
(Tue Apr 07 2009 - 18:01:39 PDT)
[AMBER] PBSA Radii option
(Tue Apr 07 2009 - 12:31:18 PDT)
R. A.
[AMBER] REd program!
(Tue Apr 28 2009 - 21:37:38 PDT)
Rajesh Raju
Fwd: [AMBER] MM-GBSA Free enegy decomposition
(Tue Apr 28 2009 - 04:28:17 PDT)
[AMBER] MM-GBSA Free enegy decomposition
(Mon Apr 27 2009 - 05:27:23 PDT)
Rausch, Felix
RE: [AMBER] problem in input
(Fri Apr 03 2009 - 01:04:36 PDT)
RE: [AMBER] problem in input
(Thu Apr 02 2009 - 04:08:27 PDT)
Ray Luo
RE: [AMBER] compare MMPBSA result
(Wed Apr 08 2009 - 10:02:41 PDT)
RE: [AMBER] fillratio error in mmpbsa
(Wed Apr 01 2009 - 12:24:20 PDT)
Rilei Yu
[AMBER] Influence about HIS-HIE-HIS-HIP
(Wed Apr 29 2009 - 20:25:48 PDT)
Re: Re: [AMBER] Backbone restraint
(Mon Apr 20 2009 - 18:21:09 PDT)
Re: [AMBER] Backbone restraint
(Fri Apr 17 2009 - 20:29:12 PDT)
[AMBER] Backbone restraint
(Fri Apr 17 2009 - 19:30:38 PDT)
Robert Duke
Re: [AMBER] pmemd compilation error
(Mon Apr 27 2009 - 21:09:15 PDT)
Re: [AMBER] Error with calculation of the potential energy
(Mon Apr 27 2009 - 12:26:06 PDT)
Re: [AMBER] Error with calculation of the potential energy
(Mon Apr 27 2009 - 11:46:43 PDT)
Re: [AMBER] Error with calculation of the potential energy
(Mon Apr 27 2009 - 11:25:14 PDT)
Re: [AMBER] pmemd in amber10 - compile failed in HPC
(Thu Apr 16 2009 - 05:24:45 PDT)
Re: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threader_z_1i_c_1o
(Wed Apr 08 2009 - 06:35:49 PDT)
Re: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threader_z_1i_c_1o
(Wed Apr 08 2009 - 05:13:23 PDT)
Re: [AMBER] pmemd compilation/makefailed-mkl_vml_service_threader_z_1i_c_1o
(Tue Apr 07 2009 - 05:55:00 PDT)
Re: [AMBER] pmemd compilation/make failed-mkl_vml_service_threader_z_1i_c_1o
(Tue Apr 07 2009 - 05:43:36 PDT)
Re: [AMBER] Sander Stalling
(Mon Apr 06 2009 - 09:57:18 PDT)
Re: [AMBER] pmemd compilation/make failed -mkl_vml_service_threader_z_1i_c_1o
(Mon Apr 06 2009 - 07:25:14 PDT)
Ross Walker
RE: [AMBER] Make parallel test faillure
(Thu Apr 30 2009 - 12:48:06 PDT)
RE: [AMBER] The PDB file was not recognized by Amber, what can i do?
(Tue Apr 28 2009 - 20:56:27 PDT)
RE: [AMBER] Nonterminal, was not found in name map
(Tue Apr 28 2009 - 19:49:50 PDT)
RE: [AMBER] parallel problem of QM/MM calculation for AMBER 9
(Tue Apr 28 2009 - 15:24:12 PDT)
RE: [AMBER] Using AMBER force fields in NAMD
(Tue Apr 28 2009 - 15:17:06 PDT)
RE: [AMBER] AmberTools compiling error
(Sun Apr 26 2009 - 18:55:06 PDT)
RE: [AMBER] bintraj and amber 10
(Thu Apr 23 2009 - 06:31:08 PDT)
RE: [AMBER] error in output file
(Thu Apr 23 2009 - 06:28:18 PDT)
RE: [AMBER] Regarding syntax for freezing different atoms
(Thu Apr 23 2009 - 06:24:55 PDT)
RE: [AMBER] Amber Installation problem
(Thu Apr 23 2009 - 06:16:18 PDT)
RE: [AMBER] bintraj and amber 10
(Wed Apr 22 2009 - 03:59:47 PDT)
RE: [AMBER] My step size
(Tue Apr 21 2009 - 04:27:07 PDT)
RE: [AMBER] Atom type error
(Sun Apr 19 2009 - 14:23:38 PDT)
RE: [AMBER] mean of character in frcmod.ff03
(Wed Apr 15 2009 - 07:58:31 PDT)
RE: [AMBER] Source of new CYX residue parameters in ff03ua
(Tue Apr 14 2009 - 21:08:14 PDT)
RE: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?
(Tue Apr 14 2009 - 16:27:37 PDT)
RE: [AMBER] [qm/mm] qmcharge for acidic a.a. in proteins
(Tue Apr 14 2009 - 12:45:06 PDT)
RE: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ?
(Mon Apr 13 2009 - 21:10:38 PDT)
RE: [AMBER] problem with explicit solvent in TMD
(Mon Apr 13 2009 - 08:29:11 PDT)
RE: [AMBER] Solved-Amber 1.2 tools test suite failure
(Sat Apr 11 2009 - 12:51:13 PDT)
RE: [AMBER] Amber 1.2 tools test suite failure?
(Sat Apr 11 2009 - 11:00:45 PDT)
RE: [AMBER] force fields
(Wed Apr 08 2009 - 17:36:05 PDT)
RE: [AMBER] please help me out
(Wed Apr 08 2009 - 08:34:51 PDT)
RE: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threade_z_1i_c_1o
(Wed Apr 08 2009 - 07:53:31 PDT)
RE: [AMBER] how to add charge in metal ion
(Tue Apr 07 2009 - 08:01:14 PDT)
RE: [AMBER] Problems with running two separate jobs in the same time
(Tue Apr 07 2009 - 08:01:14 PDT)
RE: [AMBER] Do I need to modify the cap residues
(Mon Apr 06 2009 - 21:59:37 PDT)
RE: [AMBER] Amber on GPU
(Mon Apr 06 2009 - 18:14:07 PDT)
RE: [AMBER] Do I need to modify the cap residues
(Mon Apr 06 2009 - 10:00:05 PDT)
RE: [AMBER] Sander Stalling
(Mon Apr 06 2009 - 09:58:58 PDT)
RE: [AMBER] Failure to compile amber9 serial ifort gcc
(Thu Apr 02 2009 - 08:45:19 PDT)
RE: [AMBER] Maxwell-Boltzmann distribution and ig=-1
(Tue Mar 31 2009 - 20:52:42 PDT)
Sandro L. Fornili
[AMBER] ptraj and namd charmm dcd
(Wed Apr 01 2009 - 08:59:37 PDT)
sarah genare
[AMBER] run protein with structural Ca+
(Wed Apr 01 2009 - 04:01:24 PDT)
Sasha Buzko
Re: [AMBER] Problem with RNA hairpin unwinding in explicit water
(Fri Apr 24 2009 - 10:20:13 PDT)
Re: [AMBER] Problem with RNA hairpin unwinding in explicit water
(Thu Apr 23 2009 - 10:55:58 PDT)
Re: [AMBER] Problem with RNA hairpin unwinding in explicit water
(Wed Apr 22 2009 - 16:59:14 PDT)
Re: [AMBER] Problem with RNA hairpin unwinding in explicit water
(Wed Apr 22 2009 - 16:10:55 PDT)
Re: [AMBER] Problem with RNA hairpin unwinding in explicit water
(Wed Apr 22 2009 - 15:34:35 PDT)
[AMBER] Problem with RNA hairpin unwinding in explicit water
(Wed Apr 22 2009 - 14:55:58 PDT)
[AMBER] MD on GPU: an existing commercial implementation
(Sat Apr 11 2009 - 17:47:46 PDT)
Re: [AMBER] Amber on GPU
(Thu Apr 09 2009 - 17:54:29 PDT)
Re: [AMBER] Amber on GPU
(Mon Apr 06 2009 - 23:11:24 PDT)
[AMBER] Amber on GPU
(Mon Apr 06 2009 - 17:56:31 PDT)
Seetin, Matthew
RE: [AMBER] Problem with RNA hairpin unwinding in explicit water
(Wed Apr 22 2009 - 15:22:29 PDT)
RE: [AMBER] Failures of tests
(Wed Apr 08 2009 - 08:57:27 PDT)
Seth Hayik
Re: [AMBER] make test.serial.QMMM
(Wed Apr 01 2009 - 10:26:21 PDT)
Siddharth Rastogi
[AMBER] number of waters in first and second solvation shell
(Thu Apr 02 2009 - 04:40:21 PDT)
sikander azam
[AMBER] Water-molecules
(Sun Apr 26 2009 - 06:11:33 PDT)
Sishi Tang
[AMBER] Generate AM1-CM2 charges using antechamber
(Fri Apr 03 2009 - 15:36:46 PDT)
Soni Mufaddal Saifee
Re: [AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule.
(Tue Apr 07 2009 - 21:19:25 PDT)
[AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule.
(Mon Apr 06 2009 - 02:07:51 PDT)
steinbrt.rci.rutgers.edu
Re: [AMBER] Partial interactions
(Fri Apr 24 2009 - 10:48:58 PDT)
Re: [AMBER] Partial interactions
(Fri Apr 24 2009 - 09:20:21 PDT)
Re: [AMBER] Partial interactions
(Wed Apr 22 2009 - 19:55:52 PDT)
Re: [AMBER] Partial interactions
(Tue Apr 21 2009 - 08:17:55 PDT)
Re: [AMBER] Partial interactions
(Mon Apr 20 2009 - 14:47:35 PDT)
Re: [AMBER] Thermodynamic Integration and belly
(Mon Apr 13 2009 - 09:46:19 PDT)
Re: [AMBER] TI production runs stop after a certain Step number
(Wed Apr 08 2009 - 07:35:11 PDT)
Re: [AMBER] TI production runs stop after a certain Step number
(Tue Apr 07 2009 - 07:49:57 PDT)
Steve Seibold
[AMBER] Sander Stalling
(Mon Apr 06 2009 - 09:21:51 PDT)
Sunita Patel
[AMBER] Nonterminal, was not found in name map
(Tue Apr 28 2009 - 17:50:08 PDT)
sychen
[AMBER] [qm/mm] qmcharge for acidic a.a. in proteins
(Tue Apr 14 2009 - 09:33:03 PDT)
Tamara Rogers
[AMBER] per atom energies in sander/pmemd
(Tue Apr 21 2009 - 16:41:27 PDT)
Taufik Al-Sarraj
Re: [AMBER] ambmol2?
(Tue Mar 31 2009 - 19:15:00 PDT)
taufik.alsarraj.utoronto.ca
[AMBER] ptraj (vector and corrplane)
(Fri Apr 10 2009 - 17:45:46 PDT)
Re: [AMBER] ntwr
(Wed Apr 08 2009 - 15:35:57 PDT)
[AMBER] ntwr
(Wed Apr 08 2009 - 14:45:01 PDT)
[AMBER] ptraj randomizeions
(Tue Apr 07 2009 - 16:32:23 PDT)
Re: [AMBER] top2mol2
(Tue Apr 07 2009 - 15:39:34 PDT)
[AMBER] prmtop residue format
(Tue Apr 07 2009 - 13:04:25 PDT)
Re: [AMBER] sequence function
(Mon Apr 06 2009 - 10:06:50 PDT)
[AMBER] sequence function
(Mon Apr 06 2009 - 10:03:20 PDT)
Therese Malliavin
[AMBER] constant-pH: appearance of not titrated residues during the Monte Carlo simulation
(Wed Apr 01 2009 - 02:06:19 PDT)
thirsty
Re: [AMBER] Help: An error happened when I calculate mm/pbsa
(Fri Apr 03 2009 - 00:11:19 PDT)
[AMBER] Help: An error happened when I calculate mm/pbsa
(Thu Apr 02 2009 - 01:12:25 PDT)
Thomas Cheatham
Re: [AMBER] Negative "number of measurements" in PTRAJ
(Tue Apr 07 2009 - 09:57:28 PDT)
Thomas Cheatham III
RE: [AMBER] Using AMBER force fields in NAMD
(Tue Apr 28 2009 - 15:45:15 PDT)
Re: [AMBER] Problem with RNA hairpin unwinding in explicit water
(Wed Apr 22 2009 - 15:56:25 PDT)
Re: [AMBER] ptraj problem
(Fri Apr 03 2009 - 13:23:21 PDT)
Re: [AMBER] ptraj and namd charmm dcd
(Wed Apr 01 2009 - 09:08:51 PDT)
Thomas Exner
[AMBER] Number of LES copies in ptraj
(Tue Apr 21 2009 - 08:28:41 PDT)
Tomasio, Susana
RE: [AMBER] test/amoeba: forrtl: error (78): process killed (SIGTERM)
(Wed Apr 29 2009 - 13:15:02 PDT)
[AMBER] test/amoeba: forrtl: error (78): process killed (SIGTERM)
(Wed Apr 29 2009 - 10:45:36 PDT)
RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error
(Wed Apr 08 2009 - 09:02:48 PDT)
RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error
(Tue Apr 07 2009 - 15:45:57 PDT)
RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error
(Tue Apr 07 2009 - 13:12:19 PDT)
RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error
(Tue Apr 07 2009 - 12:34:26 PDT)
RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error
(Tue Apr 07 2009 - 09:34:57 PDT)
[AMBER] test/amoeba - forrtl: severe (64): input conversion error
(Tue Apr 07 2009 - 08:16:08 PDT)
[AMBER] Problem with CAP residues
(Tue Apr 07 2009 - 03:17:27 PDT)
RE: [AMBER] Amber with AMOEBA force-field
(Mon Apr 06 2009 - 06:40:49 PDT)
RE: [AMBER] Amber with AMOEBA force-field
(Mon Apr 06 2009 - 06:14:22 PDT)
RE: [AMBER] Amber with AMOEBA force-field
(Mon Apr 06 2009 - 05:52:01 PDT)
RE: [AMBER] Amber with AMOEBA force-field
(Mon Apr 06 2009 - 05:49:28 PDT)
[AMBER] Amber with AMOEBA force-field
(Mon Apr 06 2009 - 05:41:18 PDT)
Tommaso Cupido
[AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing
(Mon Apr 27 2009 - 07:10:12 PDT)
valeria.lapietra.unina.it
[AMBER] sulfonamide parameters
(Thu Apr 16 2009 - 08:16:49 PDT)
Vijay Manickam Achari
[AMBER] ambertools failed - SMP IA64
(Thu Apr 16 2009 - 06:17:34 PDT)
[AMBER] pmemd in amber10 - compile failed in HPC
(Thu Apr 16 2009 - 03:13:49 PDT)
RE: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threade_z_1i_c_1o
(Thu Apr 09 2009 - 02:55:53 PDT)
Re: [AMBER] pmemd compilation/makefailed-mkl_vml_service_threader_z_1i_c_1o
(Tue Apr 07 2009 - 23:27:46 PDT)
Re: [AMBER] pmemd compilation/make failed -mkl_vml_service_threader_z_1i_c_1o
(Mon Apr 06 2009 - 21:25:36 PDT)
[AMBER] pmemd compilation/make failed - mkl_vml_service_threader_z_1i_c_1o
(Mon Apr 06 2009 - 00:27:24 PDT)
Vikas Sharma
Re: [AMBER] amber question
(Sun Apr 26 2009 - 02:56:26 PDT)
Re: [AMBER] amber question
(Sun Apr 26 2009 - 02:51:38 PDT)
[AMBER] amber question
(Sat Apr 25 2009 - 23:00:06 PDT)
Re: [AMBER] error in output file
(Thu Apr 23 2009 - 06:55:20 PDT)
Re: [AMBER] error in output file
(Thu Apr 23 2009 - 06:33:49 PDT)
Re: [AMBER] error in output file
(Thu Apr 23 2009 - 04:58:24 PDT)
[AMBER] error in output file
(Thu Apr 23 2009 - 04:39:42 PDT)
Re: [AMBER] help regarding step size
(Wed Apr 22 2009 - 21:40:33 PDT)
Re: [AMBER] help regarding step size
(Wed Apr 22 2009 - 03:50:27 PDT)
[AMBER] help regarding step size
(Wed Apr 22 2009 - 01:57:31 PDT)
Re: [AMBER] My step size
(Tue Apr 21 2009 - 21:49:47 PDT)
Re: [AMBER] atom numbers
(Tue Apr 21 2009 - 11:36:35 PDT)
Re: [AMBER] atom numbers
(Tue Apr 21 2009 - 10:15:07 PDT)
Re: [AMBER] atom numbers
(Tue Apr 21 2009 - 09:58:41 PDT)
Re: [AMBER] atom numbers
(Tue Apr 21 2009 - 08:33:12 PDT)
Re: [AMBER] My step size
(Tue Apr 21 2009 - 08:01:25 PDT)
[AMBER] atom numbers
(Tue Apr 21 2009 - 04:12:27 PDT)
Re: [AMBER] Atom type error
(Mon Apr 20 2009 - 23:55:24 PDT)
[AMBER] My step size
(Mon Apr 20 2009 - 23:50:16 PDT)
Re: [AMBER] Atom type error
(Mon Apr 20 2009 - 03:46:34 PDT)
Re: [AMBER] Atom type error
(Sun Apr 19 2009 - 11:33:36 PDT)
Re: [AMBER] Atom type error
(Sun Apr 19 2009 - 09:50:28 PDT)
Re: [AMBER] Atom type error
(Sun Apr 19 2009 - 09:49:53 PDT)
[AMBER] Atom type error
(Sun Apr 19 2009 - 02:48:01 PDT)
Re: [AMBER] Right force fields
(Fri Apr 17 2009 - 06:14:04 PDT)
[AMBER] Right force fields
(Thu Apr 16 2009 - 23:22:16 PDT)
[AMBER] help regarding force fields
(Thu Apr 16 2009 - 23:06:32 PDT)
[AMBER] chosing complex in amber
(Mon Apr 13 2009 - 22:18:43 PDT)
[AMBER] error saving prmtop and inpcrd files of complex in MM-PBSA
(Mon Apr 13 2009 - 13:11:07 PDT)
[AMBER] MM-PBSA error while running heat.in
(Mon Apr 06 2009 - 02:32:55 PDT)
[AMBER] error in MM PBSA
(Sun Apr 05 2009 - 21:27:21 PDT)
[AMBER] error in MM PBSA
(Sat Apr 04 2009 - 23:09:35 PDT)
[AMBER] error in MM PBSA
(Sat Apr 04 2009 - 10:06:57 PDT)
vivek.viv.sharma.gmail.com
[AMBER] Energy minimisation and NaN
(Mon Apr 13 2009 - 04:55:55 PDT)
waleed zalloum
Re: [AMBER] (no subject)
(Wed Apr 29 2009 - 11:06:44 PDT)
[AMBER] (no subject)
(Wed Apr 29 2009 - 05:15:12 PDT)
Re: [AMBER] Simulated annealing
(Fri Apr 24 2009 - 08:04:47 PDT)
[AMBER] Simulated annealing
(Fri Apr 24 2009 - 07:31:36 PDT)
[AMBER] RST file
(Thu Apr 09 2009 - 07:06:37 PDT)
[AMBER] Counter-ions
(Thu Apr 02 2009 - 03:15:12 PDT)
waleed_zalloum.yahoo.com
[AMBER] Sander
(Mon Apr 06 2009 - 06:17:34 PDT)
Wei Zhang
Re: [AMBER] test/amoeba: forrtl: error (78): process killed (SIGTERM)
(Wed Apr 29 2009 - 11:00:28 PDT)
Re: [AMBER] Disulfide bond
(Wed Apr 22 2009 - 08:00:02 PDT)
Re: [AMBER] Disulfide bond
(Tue Apr 21 2009 - 20:30:36 PDT)
Re: [AMBER] Disulfide bond
(Tue Apr 21 2009 - 18:46:19 PDT)
Re: [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm
(Sun Apr 12 2009 - 06:24:47 PDT)
Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error
(Wed Apr 08 2009 - 08:38:50 PDT)
Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error
(Tue Apr 07 2009 - 11:34:11 PDT)
Re: [AMBER] Amber with AMOEBA force-field
(Mon Apr 06 2009 - 05:57:21 PDT)
Re: [AMBER] Amber with AMOEBA force-field
(Mon Apr 06 2009 - 05:55:59 PDT)
Re: [AMBER] Amber with AMOEBA force-field
(Mon Apr 06 2009 - 05:48:28 PDT)
zgong.hust
[AMBER] about saltcon
(Sat Apr 18 2009 - 19:45:53 PDT)
Zhu, Yong-Liang
[AMBER] number_rec_numbers in mm_pbsa
(Mon Apr 06 2009 - 16:52:06 PDT)
廖青华
回复： [AMBER] number_rec_numbers in mm_pbsa
(Mon Apr 06 2009 - 17:18:54 PDT)
주태성
[AMBER] Install
(Sun Apr 26 2009 - 06:45:45 PDT)
[AMBER] Amber Installation problem
(Thu Apr 23 2009 - 18:35:46 PDT)
[AMBER] Amber Installation problem
(Thu Apr 23 2009 - 06:10:42 PDT)
Last message date
:
Wed May 20 2009 - 13:55:33 PDT
Archived on
: Fri Apr 26 2024 - 05:53:51 PDT
589 messages
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