Hi Tom--
>
> So I have generated two separate PSFs and PDBs using python scripts
> with appropriate atom deletions (for the protein, where the metal will
> bind) and for the metal ion, but i cannot figure out how to unite the
> two into a single structure. I guess the problem is two-fold, first
> specifying that the metal is part of the protein structure, but also
> specifying to which atoms in the protein the metal is bound, but also
> specifying bond lengths/angles/dihedrals that I used to do explicitly
> as part of the xplor script in the old days.
>
There are two approaches for incorporating metals- one is with
explicit covalent terms (bonds, bond angles, impropers), and the other
using distance restraints for bond-info only. You can choose. Given
what you've done already the easiest approach is to do
protocol.initStruct('file1.psf')
protocol.initStruct('file2.psf',erase=False)
protocol.initCoords('file1.pdb')
protocol.initCoords('file2.pdb')
and then use distance restraints to tie the ion in place.
If you have a pretty good idea of the metal center's geometry, you
will probably get a more accurate result if you regenerate a PSF using
patch statements along the lines of
eginput/PSF_generation/isopeptide.py
In the Xplor-NIH distribution. This approach will require the patch
and associated parameters.
best regards--
Charles
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