[gmx-users] Re: gmx-users digest, Vol 1 #417 - 2 msgs

Marc Saric marc.saric at mpi-dortmund.mpg.de
Mon Sep 30 12:16:08 CEST 2002

gmx-users-request at gromacs.org wrote:

> I have a collection of pieces of protein in one pdb file
> (obtained by taking all atoms closer than xx au from iron and
> not breaking any amino acids.)
> However, pdb2gmx only set correct termini (NH3+ or COO- in my case)
> to aminoacids that are at the beginning and in the end of the pdb file,

This might be due to the fact, that there are no "TER" records inserted 
and/or all residues have the same chain-ID (but I'm not totaly shure).

> and termini (of protein fractions) sitting in the middle of the
> pdb file are lef untouched (which is incorrect).

Of course.

> Question: Has someone coded a program that puts different pieces of
> protein in different pdb files or solved this problem by some other means?
> (Did not find this in the manual or FAQ).
> Or do I have to do it myself (breaking the protein by hand to various pdb
> files is too much for me).

You simply could start with adding "TER"-Records after all 
non-consecutive residue-Ids.
This could also be done in a script. I have something similar which 
relies on Python 1.5.2 (might also work in 2.x) and Scientific-Python 
2.0 and does something similar for CNS (a X-Ray-Package).

It might need some adjustment to work for GROMACS, but I could send it 
to you if you want.

It eats a PDB-file and outputs another PDB-File with correct TER-Records.
Bye,  Marc Saric

Max-Planck-Institut fuer molekulare Physiologie
Otto-Hahn-Str.11  44227 Dortmund  phone:0231/133-2168

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