AMBER Archive (2006)

Subject: Re: AMBER: modeling a non-standard molecule.

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Wed Mar 08 2006 - 15:27:10 CST

Thanks Bill for the reply. I have checked the atom types and the bonds
and they are correct. But I can not find the missing parameters in
gaff or ff99 files. Is there a way to get them (like using similar
paramters for atoms that are similar enough or something similar to
using parmcheck)??

thanks
Nitin
On 08/03/06, Bill Ross <ross_at_cgl.ucsf.edu> wrote:
> > ... when I put the molecule in the protein
> > and try to crate the prmtop and inpcrd file, it gives me a bunch of
> > warnings for missing parameters (inlcuding bond lengths, angles and
> > finally torsions). I think most of these warnings come from the new
> > bonds that I make between the molecule and the residues on either
> > side.
>
> Assuming the correct atoms are bonded AND of the correct type,
> you will need to add the necessary parameters. Make sure the
> bonds and types are correct first however!
>
> Bill
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