Fwd: one atom off in the minimization result

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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