[gmx-users] generating topology for artificial residues

Grange Hermitage ghermitage at y7mail.com
Wed Jul 9 12:15:37 CEST 2008

Hi all,
What approach to use to generate a topology file for peptides which include artificial residues such as serine with its sidechain extended by two carbons to double bond with another such residue i.e.
Also I need to generate a topology for another type of artificial peptide which includes beta-3 residues (C inserted in mainchain between CA and C ).
Say I want to use a force field other than the 2 supported by the PRODRG2..5 server.
I have tried to defining ff*.rtp residue definitions, but .top generated by pdb2top are missing defaults essential for grompp (gb_ gd_). The residue definitions have only [ atom ] specifications, allowing the other sections to default as per the manual.

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