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.
CA-CB-OG-C1-C3=C4-C2-OG-CB-CA
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.
thanks,
Grange.
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