From: Nara Dashdorj (dnr_at_physics.purdue.edu)
Date: Mon Oct 24 2005 - 13:09:32 CDT
Brian,
No, there is no bond created that is not suppose to be there, you can
take a look yourself. The pdb code of the protein is 1VF5, there are for
instance heavy atoms of three residues ARG83, TYR34, and LYS208 within
2.6 Ang from the hemes beside the ones that provide ligands.
Thanks, Nara
--------------------------------------------
Naranbaatar Dashdorj
Bioenergetics and Biophotonics
Research Group
Department of Physics
Purdue University
525 Northwestern Avenue
West Lafayette, IN 47906-2036
U.S.A
Phone: (765) 494 8743
Fax: (765) 494 0706
E-mail: dnr_at_physics.purdue.edu
Website: http://www.physics.purdue.edu/~dnr
Brian Bennion wrote:
>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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