AMBER Archive (2006)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Mar 08 2006 - 15:47:50 CST

> 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)??

I haven't really used amber since gaff came along. In my experience
failing that you'd need to base it on comparisons or derive your
own, depending on how sensitive your results are likely to be to
the level of effort. There is an appendix to the amber7 manual on
parameter development.

Bill
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