OK, I'll try that.
Thanks a lot!
Gustavo.
On Fri, May 20, 2011 at 8:18 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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 - 12:30:02 PDT
