[MMTK] Problems with loading some PDF files

Konrad Hinsen research at khinsen.fastmail.net
Thu Oct 13 10:06:22 UTC 2011


On 12 Oct, 2011, at 20:58 , Новиков Глеб wrote:

> When I've tried to load this structure to the MMTK i've obtained error message 
> 
> IOError: Atom H of PDB residue VAL not found in residue Val of object .Val45

Welcome to the wonderful world of PDB files! It's the most abused file format in molecular modeling, so problems like this are unfortunately common.

However, if I run the following three-line script:

from MMTK import *
from MMTK.Proteins import Protein
p = Protein('glycinR.pdb')

I don't get the error message you see. Could you please post your script for comparison?

This is not to say that my script runs fine. It crashes on the last residue of your structure:

	Atom OC1 of PDB residue ILE not found in residue Ile of object .Ile348

There is indeed no OC1 in ILE, so I am as clueless as MMTK ;-)

> How I can add this atoms to MMTK database ? Or it'll be also also very comfortable that it'd be an apperation wich modify PDB to the suitable form ( e.g gromacs deleate all hydrogens and then build it at once)

You can delete all hydrogens if you first construct a PDBConfiguration object (from MMTK.PDB) and then call its method deleteHydrogens(). Then you can call createPeptideChains() which adds new hydrogen atoms.

Konrad.
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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
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