Hello Carl--
>
> Based on answers from the mailing list and examples, I modified a topology
> file and parameter file for incorporating the two Zn.
> Upon running the file (see below) I can successfully generate the psf-file
> and a pdb-file. However, in the pdb-file, the Zn2+ and some N and C-terminal
> residues gets coordinates -9999.9. I have tried fixing that by running
> fixupCovalentGeom in the script, which causes the script to fail, saying
> missing atoms.
>
Please see the example in eginput/PSF_generation/addAtoms.py in the
Xplor-NIH distribution. From your description, it seems that you
missed calling protocol.addUnknownAtoms().
best regards--
Charles
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--
Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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