Dear Astrid Maaß;
The atoms of the planes including aromatic rings and sp2 atoms in a
ligand, are often out of plane.
Checked by parmchk as in the manual 4.1.2 (p.72) before generating top and
crd files, a frcmod file will be written out for the missing parameters. A
frcmod file will be used as in tutorials.
Best Regards.
Kazuo Koyano
Center for Collaborative Research, The University of Tokyo
4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, JAPAN
Tel; 03-5452-6587 Fax; 03-5452-6545
E-mail koyano.fsis.iis.u-tokyo.ac.jp
URL: http://www.fsis.iis..u-tokyo.ac.jp/
>
> I would like to model ligands in complex with a protein. Thus I
> converted the ligand.mol2 files into *.prepi files with antechamber (no
> problems). However, generating prmtop and prmcrd-files with leap fails,
> if e.g. aromatic rings are present in the ligand; error messages tell
> that very often angle parameters and sp2 improper torsion parameters are
> missing in the gaff.dat (version of Feb. 2002). Is a newer version of
> the gaff.dat available or any other help?
>
> Thanks in advance,
>
> Astrid Maaß
>
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Received on Fri Sep 12 2003 - 11:53:00 PDT
