AMBER Archive (2008)

Subject: Re: AMBER: question - gaff and leaprc.ff03ua

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Nov 19 2008 - 09:08:02 CST

On Wed, Nov 19, 2008, oguz gurbulak wrote:
>
> I want to do a geometric optimization in order to find the new xyz
> cordinates of my molecule and after that evaluate the partial charges of
> my molecule before using gaff or leaprc.ff03ua in xleap . Is ?t necessary
> to do all these operations when using gaff or leaprc.ff03ua ?

Depends. It's always a good idea to have a good structure to start with, so
geometry optimization should not hurt. The bcc charge scheme will
automatically optimize the geometry (at the AM1 level), so you don't strictly
need to do it yourself. If you are looking for RESP charges, you will surely
need an optimized geometry.

...dac

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