[MMTK] Cant read full-atom RNA PDB file

Konrad Hinsen research at khinsen.fastmail.net
Tue Jul 15 10:28:22 UTC 2014

Anna Gorska writes:

 > 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

The message says the contrary: Your PDB file contains an atom called
"HN1" and MMTK doesn't find any such atom in its definition of a
proline residue. So the question is: what do you want MMTK to do with
that atom called HN1?

In general, MMTK makes no general assumptions at all about atoms and
bonds. The chemical database (under MMTK/Database) contains the
definitions of residues and molecules that MMTK applies. You can
replace these by your own if the built-in ones don't fit your needs.
For more information, see the manual:


Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen

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