[MMTK] Problems reading PDB with Proline

Anna Gorska gvalchca.agr at gmail.com
Tue Jul 15 08:22:00 UTC 2014

Dear MMTK community,
I would like to read-in a PDB containing both protein and nucleic acids. 
I managed to change the names of atoms in nucleotides so the MMTK reads them fine, but encountered some problems in protein chains reading.

The MMTK seems to expect that for all nitrogen atoms there will be at least one hydrogen in the structure:

IOError: Atom HN1 of PDB residue PRO not found in residue Pro of object .Pro2

When in fact this is a structure I have:

Best Regards,
Anna Gorska

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://starship.python.net/pipermail/mmtk/attachments/20140715/a8f1048a/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: PastedGraphic-3.png
Type: image/png
Size: 16577 bytes
Desc: not available
URL: <http://starship.python.net/pipermail/mmtk/attachments/20140715/a8f1048a/attachment.png>

More information about the mmtk mailing list