Hello Charles Thanks. That solved it and I can successfully start the docking. I had to change names for the atom types to get the addunknownatoms to recognize them.
Best regards Carl 23 apr 2013 kl. 17:39 skrev "Charles Schwieters" <charles at schwieters.org>: > > 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: Charles at Schwieters.org > www: http://schwieters.org/cds > phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt >
