Re: Serious Steric Atom Clashes

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Oct 24 2005 - 15:01:41 CDT

Hello Nara,

My contention is that the initial states of the heme are so poor, that in
relaxing them to what the topology/parameter files think are natural
positions, the protein is forced to compensate. At 3.0A resolution one
can barely distinguish between bonded heavy atoms.

>From your emails, I assume that this smaller peice that you did
minimmization on worked okay ie, no NAN errors during the conjugate
gradients and completion of the required minimization steps?

Can you send the logfile for that minimzation and the final structure
which has "equilibrated" heme residues?

The problem with heme 301 is not the name. It is the fact that one of the
nitrogen atoms in the porphyrin has an iron atom between it and the two
carbon atoms it is supposed to bound to.

Brian

On Mon, 24 Oct 2005, Nara Dashdorj wrote:

>
> There are several type of hemes, so I had to came with names depending
> on ligand nature. I told you about the iron ligand (in the middle) that
> relaxes if I just do short simulation, I do not know why topology does
> that, but I did not really pay attention to it, since it goes nicely to
> natural position.
>
> Regards to the problme, I am talking about nonbonded VDW, which is
> caused by the non-liganded residues within the van der waals distance?
> Would patched residue cause the problem?
>
> The heme 301, what is wrong with that?
>
> Nara
>
> Marcos Sotomayor wrote:
>
> >
> >
> > Yeap, something is wrong with the bonding of your heme. Create a
> > representation "not protein" and display it in "licorice". You will se
> > inmmediatly that something is wrong in the middle.
> >
> > Marcos
> >
> > On Mon, 24 Oct 2005, Brian Bennion wrote:
> >
> >> 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
> >> ************************************************
> >>
>

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