[gmx-users] topology

[Anton Feenstra]

prasad wrote:

> Dear Gromacs users and developers,
> 
> I have 2 polypeptide chains in one protein, I have also chlorophyls and  an
> individual FE ion(non heme) in that.
> In .pdb LINK records it is mensioned that  the FE ion has a  link with
> Histidin's of A and B chains(polypeptide chain identifiers) of the protein
> and also other amino acids.
> when we create the topology file for the protein pdb2gmx create 2 individual
> itp files for 2 chains and 1 itp file for the HETATOMS.
> But the FE is having link with both the chains( A and B). not only FE, the
> MG of my heteroatom also has link with one residue of one of the protein
> monomer. i didnot understand how to tell to gromacs about the link between
> FE and monomer residues. So, how to write the topology for that? I will be
> very much grateful to you if some one can suggest me...

pdb2gmx reads building block topologies (mainly amino acid residues) from
a "residue topology database", or .rtp. First off, you'll need to write your
own .rtp entry for chlorophyll (I don't believe it is already in the standard
files). Read the manual for how to do this.

Then, using the file 'specbonds.dat' (also described in the manual, else you
can search the list archives), you can tell pdb2gmx to add bonds between iron
and appropriate residues in both monomers.

Finally, when running pdb2gmx, you have to tell it to treat both chains as
one molecule, by using the '-merge' flag (it may be named slightly different).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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