Re: Minimization problem of a protein-DNA complex with namd

From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Sun Jul 12 2009 - 19:38:21 CDT

Sudipta,

Maybe NAMD is confused since an atom is interacting directly with its
periodic image due to the cutoff being longer than the periodic
cell. I'd fix the cutoff first (say, reduce it to 12) and set the
margin to 2 and rerun to see if this fixes things.

-Dave

On Jul 12, 2009, at 6:23 PM, Chris Harrison wrote:

> Sudipta,
>
> Your impropers and vdw energies are clearly the first clue,
> suggesting bad contacts and initial geometries. I would suggest
> starting by insuring that you don't have atoms overlapping
> (possessing the same x,y,z coords), likely at position 0.0, 0.0, 0.0.
>
> You also are using a cutoff of 99 and margin of 15. Is there a
> reason for using such large values? The cutoff exceeds the periodic
> box size.
>
>
> 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 Fax: 217-244-6078
>
>
>
>
> On Sun, Jul 12, 2009 at 2:21 AM, sudipta <sudipta.mml_at_gmail.com>
> wrote:
> Hi All,
>
> I want to run a MD simulation of protein-DNA complex by namd.
> So that I have taken coordinates of a protein-DNA complex from PDB
> site. Then I have added the H-atom by AMBER and I have solvated the
> molecule in water manually. I have also rejected those water
> molecules which are hard contact with the complex(i,e any water
> molecules within the 2A from the complex surface are rejected).
> Then I have made a .in file to generate the .psf file of the whole
> system by the psfgen executable. the version of the psfgen
> executable is NAMD_2.6_Linux-i686. The .in file contains the
> topology files of protein and DNA, aliasing of residue and atom,
> delete some atoms, patch of deoxyribose of purine and pyrimidine
> bases, segment name,guesscoord and output file names. I have also
> attached .in file with this mail. Please see it and give feedback
> wheather is it correct or not. After getting this .pdb and .psf
> files I want to minimize the whole system by namd minimization. I
> have also attached the corresponding .conf file. Please see it and
> verify. The minimization is not occuring. In log file, I am not
> getting the errors rather i am getting some warnings which I can't
> understand.
>
>
> TCL: Minimizing for 5000 steps
> Warning: Bad global exclusion count, possible error!
> Warning: Increasing cutoff during minimization may avoid this.
> PRESSURE: 0 nan nan nan nan nan nan nan nan nan
> GPRESSURE: 0 nan nan nan nan nan nan nan nan nan
> ETITLE: TS BOND ANGLE
> DIHED IMPRP ELECT VDW
> BOUNDARY MISC KINETIC
> TOTAL TEMP TOTAL2 TOTAL3
> TEMPAVG PRESSURE GPRESSURE VOLUME
> PRESSAVG GPRESSAVG
>
> ENERGY: 0 475096.5883 38762.7616 1097.8923
> 99999999.9999 -129136.1162 99999999.9999
> 0.0000 0.0000 0.0000 99999999.9999
> 0.0000 99999999.9999 99999999.9999 0.0000
> 99999999.9999 99999999.9999 1000000.0000 99999999.9999
> 99999999.9999
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> INITIAL STEP: 1e-06
> GRADIENT TOLERANCE: nan
> BRACKET: 0 nan nan nan nan
> RESTARTING CONJUGATE GRADIENT ALGORITHM
> INITIAL STEP: 5e-07
> GRADIENT TOLERANCE: nan
> BRACKRESTARTING CONJUGATE GRADIENT ALGORITHM
> INITIAL STEP: 2.5e-07
> GRADIENT TOLERANCE: nan
> BRACKET: 0 nan nan nan nan
> NEW SEARCH DIRECTION
> INITIAL STEP: 1.25e-07
> GRADIENT TOLERANCE: nan
> BRACKET: 0 nan nan nan nan
> ..........................................................
> ...........................................................This is
> repeating
>
> I have tuned some parameters such as cutoff distance,
> cellbravisvector, PBC etc in the .conf file but always I am getting
> same errors. Please tell me what should I do. Awaiting for your
> early reply.
>
> Thanks & regards
> Sudipta
>
>
>
>
>

-- 
David J. Hardy, Ph.D.
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois
dhardy_at_ks.uiuc.edu
http://www.ks.uiuc.edu/~dhardy/

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