AMBER Archive (2009)

Subject: Re: [AMBER] Gaff compatible with ff899.SB

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Dec 21 2009 - 09:32:40 CST

there is no problem- the difference in case for the atom types doesn't
affect the interactions. they are both designed to use the same functional
form.
having said that, you should make sure to use the "bsc0" DNA parameter
update, not just ff99SB. search the archives for more information.

On Mon, Dec 21, 2009 at 10:03 AM, Pol Boudard <boudardp_at_averell.umh.ac.be>wrote:

> Dear members,
>
>
>
> I read that gaff force field is compatible with the macromolecular force
> fields like ff99.SB.
>
>
>
> Atom types are lower case for Gaff and upper case for ff99.SB. How could
> the non-bonded interactions be taking into account between a polymer
> parameterized with Gaff and DNA parameterized with ff99.SB? How do these
> two force fields "understand" each other in terms of electrostatic and
> Van der Waals interactions?
>
>
>
> Thank you,
>
>
>
> Pol Boudard
>
>
>
> University of Mons - Belgium
>
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