[gmx-users] topology

prasad prasad.gajula at uos.de
Tue Feb 10 17:03:01 CET 2004

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...
Thanks in advance

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