[MMTK] Cant read full-atom RNA PDB file

Konrad Hinsen research at khinsen.fastmail.net
Wed Jul 9 16:19:23 UTC 2014


Anna Gorska writes:

 > It works only if I let MMTK guess positions of my hydrogens, but when I try to read
 > it full this is the error I get:
 > 
 > IOError: Atom H5' of PDB residue RG not found in residue RG5 of object C.RG5_1
 > 
 > As if the Charmm naming scheme is storage to MMTK or it was lacking
 > the data for 3/ 5 ters of RNA,

There are 3-ter and 5-ter forms for all nucleic acids, but it is well
possible that some naming variants are missing in the MMTK database.

The 5-ter ribose has atoms 1H5' and 2H5', the two hydrogens bound to
C5', but no plain H5'. There's also H5T for the hydrogen bound to O5.

You can add alternative names to the MMTK database. Look for the
file MMTK/Database/Groups/ribose_5ter.

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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