[MMTK] Creating universe with heme in PDB file

Konrad Hinsen research at khinsen.fastmail.net
Fri Jan 20 11:52:07 UTC 2012

Hyuntae Na writes:

 > Could you help me to make a universe that has a protein with a heme
 > that is connected to the protein. I use 1A6G for my study. The pdb
 > file has a protein and a heme, and they are connected together. If
 > I use "MMTK.Proteins.Protein (pdbFile)" to generate a protein
 > structure, it remove water and heme, but take only protein part. I
 > need a molecule of the pdb file, where both protein and heme are
 > connected as described in the pdb file. Can you help me to generate
 > it?

That is unfortunately a bit tricky. MMTK wants a petide chain to be
a sequence of amino acids. If there's anything bound to an amino acid,
you have to define a special amino acid that includes the ligand.

 > setResidueConfiguration
 >     pdbmap[0] + ' of object ' + object.fullName())
 > IOError: Atom NA of PDB residue HEM not found in residue HEM of object heme

The group definition HEM in the MMTK database is for unbound heme in
myoglobin. I think that's the one called heme-b but I am not sure.
There are various hemes with slight differences in the chemical
structure, so you have to find out which one you need, and then make a
database definition for it.

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

More information about the mmtk mailing list