[MMTK] applyto with c_terminus=1 protein structure

Konrad Hinsen research at khinsen.fastmail.net
Thu Mar 24 17:03:01 UTC 2011


On 24/3/11 16:13 , ra.biehl wrote:

> I have a sequence of proteins structures with the same content but
> different atom positions from an MD run as a pdb file with model
> sections 1 to 200
>
> I can load the individual configurations with
>
>  >conf1 = PDBConfiguration('xx001')
>  >chain=conf1.peptide_chains[0].createPeptideChain(c_terminus=1)
>  >universe.addObject(chain)
> and i can work with the universe
>
> to change only the coordinates to a second configuration
>  >conf2 = PDBConfiguration('xx002')
>  >conf2.applyTo(universe[0])
> i get the message
>  >Warning: 3231 atom(s) were not assigned (new) positions.

It would be useful to know to what "3231 atoms" corresponds in your system.

One explanation might be that your PDB files lack hydrogen atoms, which 
MMTK adds when constructing a peptide chain. In that case, your system 
should have a total of 3231 hydrogen atoms added.

If 3231 atoms is your total system size, then either something is wrong 
with your PDB files, or with MMTK. Could you send a small test case?

> using
>  >chain=conf1.createAll()
> IOError: Atom O1 of PDB residue LYS not found in residue Lys of object
> .Lys415
> because i cannot tell create all about the c_terminus

That's what createPeptideChain is for: you must do some more work, but 
you get the chance to provide more options. createAll() calls 
createPeptideChains, so ultimately this is the same operation.

Konrad.
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
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E-Mail: research at  khinsen dot fastmail dot net
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