[gmx-users] Creating custom position restraints for a multi-chain protein

[Kolmus, Elizabeth K.]

Hello,


I am attempting to create my own set of position restraints for a protein with 4 chains. However, this fails when I attempt to run the files through grompp. Here is the workflow:


gmx make_ndx -f protein.pdb -o chain-n.ndx (for n = 1-4)

    del 0-9

    r x-y | r z-w & chain n

    name 0 ChainN

    q


gmx genrestr -f protein.pdb -n chain-n.ndx -o posre_Protein_chain_N.itp


When I take the resulting .itp files and try to pre-process with them, I get the following error:

Program gmx, VERSION 5.0.5
Source code file: /usr/local/gromacs-5.0.5/src/gromacs/gmxpreprocess/toppush.c, line: 1806

Fatal error:
[ file posre_Protein_chain_B.itp, line 699 ]:
Atom index (6413) in position_restraints out of bounds (1-6412).
This probably means that you have inserted topology section "position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.


The issue is not actually with where the section is placed. It is placed in the correct file - topol_Protein_chain_B.itp . However, topol_Protein_chain_B.itp numbers atoms from 1-6412, and posre_Protein_chain_B.itp begins at atom 5512, as per the protein.pdb atom numbering. How can I renumber the atoms in posre_Protein_chain_B.itp (and the other two files) in an intelligent way?


Thanks,

Elizabeth


PS I am sure this would be a trivial problem if I knew awk or perl, but I don't yet.