Minimization problem of a protein-DNA complex with namd

From: sudipta (sudipta.mml_at_gmail.com)
Date: Sun Jul 12 2009 - 02:21:36 CDT

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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

• application/octet-stream attachment: pro_dna_new_cc.in

• application/octet-stream attachment: pro_dna_minimization.conf

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