[MMTK] Cant read full-atom RNA PDB file

Anna Gorska gvalchca.agr at gmail.com
Thu Jul 10 13:02:37 UTC 2014

Dear Konrad,

Thanks for your quick answer!
But the problem is still there.

First, I understand that adding another item (“H5'“: "1H5") in the pdb_alternative dictionary should solve the problem.

Second, what is the difference between files:
ribose_5ter_3ter and ribose_5ter,
should I change both ?

Did I understand you correctly ?


> 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
> -- 
> ---------------------------------------------------------------------
> 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
> http://dirac.cnrs-orleans.fr/~hinsen/
> ORCID: http://orcid.org/0000-0003-0330-9428
> Twitter: @khinsen
> ---------------------------------------------------------------------

More information about the mmtk mailing list