Re: [AMBER] Parametrizing a peptide ligand

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Fri, 20 May 2011 13:18:26 +0200

Dear Gustavo,

> Thank you very much, I'll try that. Just one thing: I understand that
> R.E.D can help with the charges, but what about the
> bonds/angles/dihedrals? Can I combine R.E.D. results to, say,
> antechamber's to get those?

- Equilibrium values for bond & angles: they could come from X-ray structures.
- FF cst for bond & angle: we always adapt them from GAFF or from
rules from the original Cornell et al. FF
- We always re-fit/check key dihedrals from GAFF.

In your case, the key dihedrals are those of the peptide bond or for
aromatic systems. right? See for instance the F-87 project in R.E.DD.B.:
http://q4md-forcefieldtools.org/REDDB/projects/F-87/
http://q4md-forcefieldtools.org/REDDB/projects/F-87/script1.ff
http://q4md-forcefieldtools.org/REDDB/projects/F-87/script3.ff

More generally, my feeling is that these basic rules should be
followed if you use R.E.D. _OR_ Antechamber.

regards, Francois





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Received on Fri May 20 2011 - 04:30:03 PDT
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