From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Oct 24 2005 - 10:41:05 CDT
Hello,
It appears that a bond is being created that shouldn't exist naturally.
Its possible that a bond has been created between the protein and the heme
group that isn't supposed to be there. The the bonds in the psf file for
the suspicious atoms.
Regards
Brian
On Sun, 23 Oct 2005, Nara Dashdorj wrote:
> Dear NAMD Users:
>
> I am simulation this integral membrane protein that has several
> prosthetic groups. After equilibrating my solvated model, which
> encompasses protein in lipid membrane (~220 000 atoms), I wanted to
> release my protein, but encountered the problem of steric clashes of atoms.
>
> I narrowed down my problem by simulating my protein chains separately in
> vacuum, which resulted in the conclusion of atoms of heme groups are
> clashing with protein subunits. I vissually checked it loading into VMD,
> which indicates several residues are really close to the hemes (within
> ~2 Angstroms). These are not artifact of topology, it is inherent in the
> crystal structure (3.0 Angstrom resolution structure).
>
> These clashes cause huge VDW energy, and simulation produces the
> following log, in which NAMD restarts conjugate gradient algorithm
> repeadetly without any success...
>
> Info: NONZERO IMPRECISION IN COULOMB TABLE: 1.27055e-21 (767)
> 1.48231e-21 (767)
> Info: Entering startup phase 8 with 42778 kB of memory in use.
> Info: Finished startup with 94696 kB of memory in use.
> TCL: Minimizing for 1000 steps
> 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 41796.6193 16153.7223 1893.0569
> 482.6422 781586.9314 99999999.9999 0.0000
> 0.0000 0.0000 99999999.9999 0.0000 99999999.9999
> 99999999.9999 0.0000 -99999999.9999 -99999999.9999
> 2918023.1080 -99999999.9999 -99999999.9999
>
> INITIAL STEP: 1e-06
> GRADIENT TOLERANCE: nan
> BRACKET: 0 0 nan nan nan
> RESTARTING CONJUGATE GRADIENT ALGORITHM
> INITIAL STEP: 2.5e-07
> GRADIENT TOLERANCE: nan
> BRACKET: 0 0 nan nan nan
> RESTARTING CONJUGATE GRADIENT ALGORITHM
> INITIAL STEP: 6.25e-08
> GRADIENT TOLERANCE: nan
> BRACKET: 0 0 nan nan nan
> RESTARTING CONJUGATE GRADIENT ALGORITHM
> INITIAL STEP: 1.5625e-08
> GRADIENT TOLERANCE: nan
> BRACKET: 0 0 nan nan nan
> RESTARTING CONJUGATE GRADIENT ALGORITHM
> INITIAL STEP: 3.90625e-09
> GRADIENT TOLERANCE: nan
> BRACKET: 0 0 nan nan nan
> RESTARTING CONJUGATE GRADIENT ALGORITHM
> INITIAL STEP: 9.76562e-10
>
> To resolve this, I played with minimization options such as minBabyStep,
> minTinyStep, and maximumMove without any success!
>
> Any ideas to resolve this problem is truly appreciated!
>
> --nd
>
************************************************
Brian Bennion, Ph.D.
Bioscience Directorate
Lawrence Livermore National Laboratory
P.O. Box 808, L-448 bennion1_at_llnl.gov
7000 East Avenue phone: (925) 422-5722
Livermore, CA 94550 fax: (925) 424-6605
************************************************
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