[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:

  http://dirac.cnrs-orleans.fr/Manuals/MMTK/mmtk.html#the-chemical-database

Konrad.
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
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E-Mail: research AT khinsen DOT fastmail DOT net
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