[MMTK] Reading a coordinated CYS from a PDB file

Konrad Hinsen hinsen at cnrs-orleans.fr
Tue Oct 14 06:19:12 UTC 2008


On 13.10.2008, at 22:55, Jose Borreguero wrote:

> I have four CYS coordinated to a Fe atom in a PDB file which I want  
> to read. Because of the coordination, all the CYS lack the H_gamma.  
> When I read the pdb file:
>
> universe = InfiniteUniverse()
> conf = PDBConfiguration(mypdb)
> universe.addObject(conf.createAll())
> t = Trajectory(universe, nc_file, "w", "hello", block_size = 1)
>
> I see that  universe._atoms contains the H_gamma atoms for the CYS.  
> So, my question is: does my "universe" contain four extra ghost  
> atoms (one H_gamma for each of my four CYS) ?

Yes. MMTK's database definition for CYS contains the H_gamma, so they  
will be there. If they are missing in the PDB file, MMTK will  
estimate positions for them, as it does for other missing hydrogen  
atoms.

A quick-and-dirty way to get CYS without the H_gamma is to change CYS  
in your PDB files to CYX. You will then get the residues that are  
normally involved in disulfide bonds, but without the bonds, as your  
sulfurs are unlikely to be close enough for forming S-S bonds (MMTK  
uses a cutoff of 2.5 Angstrom). Note however that the force field  
parameters for CYX are probably quite different from what you would  
need in your case. But then, the Fe is difficult to handle by  
empirical force fields anyway.

Konrad.
--
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr
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