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

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Sun Jul 12 2009 - 18:23:40 CDT

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 <http://www.ks.uiuc.edu/%7Echar>
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
>
>
>
>

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