From: Chris Harrison (charris5_at_gmail.com)
Date: Sun Jul 12 2009 - 18:23:10 CDT
mgssal,
You question is unclear. Please rephrase. The description "off the
protein" is also difficult to understand for those of us unfamiliar with
your protein or why this is a problem for your protein/system.
I infer that you do not want residue 153 "off the protein." If this is the
case you should examine the structures of the trajectory, or at minimum the
final structure, locating the frame in which it becomes "off the protein"
and determine the physical cause (ie favorable interaction between the
residue and ion or water, etc that draws it "off the protein"; or
unfavorable interaction between the residue and some other residue of the
protein that displaces it "off the protein"). The residue would not have
lifted "off the protein" unless it yielded an overall lower, more favorable
energy for the whole system. The reason that has happened must be
determined.
This sounds suspicously like an issue with your system which is in
disagreement with what you expect. I would suggest first determining if the
result is due to a physical or nonphysical cause. Often problems such as
yours have a very logical physical cause.
Chris
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar> Fax: 217-244-6078 On Sun, Jul 12, 2009 at 3:22 AM, mgssal <mgssal_at_gmail.com> wrote: > Hello, > > I am trying to minimize my protein in a water box. The minimization > run seems to run fine, with no errors in the log file; however one of > the residues (#153) seems to be off the rest of the protein at the end > of the run. > > ATOM 136 CA ASN U 152 -9.909 112.197 81.551 1.00 0.00 U > ATOM 137 CA ILE U 153 -8.986 113.903 -23.813 1.00 0.00 U > ATOM 138 CA GLN U 154 -11.491 114.281 77.206 1.00 0.00 U > > The end of the log file is as follows: > ENERGY: 10000 19574.8004 14130.9889 2429.1344 > 62.6588 -639534.6359 75778.8480 0.0000 > 0.0000 0.0000 -527558.2054 0.0000 > -527558.2054 -527558.2054 0.0000 -4169.0182 > -4165.5559 1383393.0000 -4169.0182 -4165.5559 > > WRITING COORDINATES TO DCD FILE AT STEP 10000 > WRITING COORDINATES TO RESTART FILE AT STEP 10000 > FINISHED WRITING RESTART COORDINATES > WRITING VELOCITIES TO RESTART FILE AT STEP 10000 > FINISHED WRITING RESTART VELOCITIES > REINITIALIZING VELOCITIES AT STEP 10000 TO 310 KELVIN. > WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 10000 > WRITING COORDINATES TO OUTPUT FILE AT STEP 10000 > CLOSING COORDINATE DCD FILE > WRITING VELOCITIES TO OUTPUT FILE AT STEP 10000 > ========================================== > WallClock: 83540.904668 CPUTime: 78086.737012 Memory: 425660 kB > Program finished. > > > My conf file pretty much follows the one in the tutorial. Below it > is appended for completeness. > > Thanks, > > --mgssal > > > ############################################################# > ## JOB DESCRIPTION ## > ############################################################# > > # Minimization and Equilibration of > # Ubiquitin in a Water Box > > > ############################################################# > ## ADJUSTABLE PARAMETERS ## > ############################################################# > > structure ./amu_wb.psf > coordinates ./amu_wb.pdb > > set temperature 310 > set outputname amu_wb_eq > > firsttimestep 0 > > > ############################################################# > ## SIMULATION PARAMETERS ## > ############################################################# > > # Input > paraTypeCharmm on > parameters ./par_all27_prot_lipid.inp > temperature $temperature > > > # Force-Field Parameters > exclude scaled1-4 > 1-4scaling 1.0 > cutoff 12. > switching on > switchdist 10. > pairlistdist 13.5 > > > # Integrator Parameters > timestep 2.0 ;# 2fs/step > rigidBonds all ;# needed for 2fs steps > nonbondedFreq 1 > fullElectFrequency 2 > stepspercycle 10 > > > # Constant Temperature Control > langevin on ;# do langevin dynamics > langevinDamping 5 ;# damping coefficient (gamma) of 5/ps > langevinTemp $temperature > langevinHydrogen off ;# don't couple langevin bath to hydrogens > > > # Periodic Boundary Conditions > cellBasisVector1 111. 0. 0. > cellBasisVector2 0. 121. 0. > cellBasisVector3 0. 0 103. > cellOrigin 11. 119. 56 > > wrapAll on > > > # PME (for full-system periodic electrostatics) > PME yes > PMEGridSizeX 120 > PMEGridSizeY 120 > PMEGridSizeZ 108 > #PMEGridSpacing 1.0 > > # Constant Pressure Control (variable volume) > useGroupPressure yes ;# needed for rigidBonds > useFlexibleCell no > useConstantArea no > > langevinPiston on > langevinPistonTarget 1.01325 ;# in bar -> 1 atm > langevinPistonPeriod 100. > langevinPistonDecay 50. > langevinPistonTemp $temperature > > > # Output > outputName $outputname > > restartfreq 500 ;# 500steps = every 1ps > dcdfreq 250 > xstFreq 250 > outputEnergies 100 > outputPressure 100 > > > ############################################################# > ## EXTRA PARAMETERS ## > ############################################################# > > > ############################################################# > ## EXECUTION SCRIPT ## > ############################################################# > > # Minimization > minimize 10000 > reinitvels $temperature > > #run 2500 ;# 5ps > >
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