Re: Serious Steric Atom Clashes

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Oct 24 2005 - 13:48:23 CDT

The heme residues are not correctly annotated in the psf file. The bonds
are not correct. It appears that some carbon/notrogen atoms are not
right, especially around the heme that is residue 301. One of the
nitrogen atoms has two carbon bonds that straddle the iron atom.

That situtation will never be relaxed with minimization and namd will give
up.

On Mon, 24 Oct 2005, Nara Dashdorj wrote:

> Marcos and Brian:
>
> I am sending the psf and pdb files that are part of my simulation (the
> particular chain causing the problem). Topology tiltes the structure
> around the Fe, which goes away during the minimization, but other than
> that it looks fine to me. The problematic ones are close to the
> phorphyrin ring!
> Please let me know what you think?
>
>
> Thanks, Nara
>
>
> PS: Brain, what is second problem, I did not quite get it?
>
>
>
> Brian Bennion wrote:
>
> >What I am trying to say is that it might be possible that the psf file is
> >messed up and has some extra bonds in it. I would need to see your psf
> >file and pdb file in vmd to make sure no weird bonds were imposed.
> >I can't tell if you are using periodic boundaries in your invacuo test
> >cases, but I would check that a decimal hasn't been misplaced.
> >
> >The two cases above have happened to me before so I keep an eye out for
> >them.
> >
> >Regards
> >Brian
> >
> >
> >
> > On Mon, 24 Oct 2005, Nara Dashdorj wrote:
> >
> >
> >
> >>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.
> >>Any ideas solve this problem?
> >>
> >>Thanks, Nara
> >>
> >>
> >>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
> >>>************************************************
> >>>
> >>>
> >>>
> >>>
> >
> >************************************************
> > 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
> >************************************************
> >
> >
>
>

************************************************
  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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