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
-- Charles Schwieters email: [email protected] www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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