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<DIV>Hi all,</DIV>
<DIV> </DIV>
<DIV>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.</DIV>
<DIV>CA-CB-OG-C1-C3=C4-C2-OG-CB-CA</DIV>
<DIV> </DIV>
<DIV>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 ).</DIV>
<DIV> </DIV>
<DIV>Say I want to use a force field other than the 2 supported by the PRODRG2.5 server.</DIV>
<DIV> </DIV>
<DIV>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.</DIV>
<DIV> </DIV>
<DIV>thanks,</DIV>
<DIV> Grange.</DIV>
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<DIV> </DIV></DIV></div><br>
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