AMBER Archive (2009)

Subject: Re: [AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide

From: Dongshan Wei (dswei0523_at_gmail.com)
Date: Thu Dec 10 2009 - 18:14:12 CST

Hi Ross,

Thanks for your reply. So is it safe to use the ff03 force field from
Amber10 not Amber8 ?

Dongshan

On Thu, Dec 10, 2009 at 7:02 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Hi Dong,
>
> > Do you notice the difference of Amber ff03 force field between Amber8
> > and
> > Amber10 for dipeptide ACE-ALA-NME? I found the charges of atoms from
> > ACE and
> > NME terminals are different in Amber8 ff03 and Amber10 ff03 force
> > fields but
> > the charges of atoms from ALA unit are same. The detailed charges for
> > all
> > atoms in Ala2 dipeptide are shown as follows:
>
> Yes the original incarnation of the FF03 force field use the FF94 charges
> for the N and C termini. This was later updated to FF03 charges for the N
> and C termini to be consistent with the rest of the force field. Yong Duan
> can comment more on the effect this has since it is not clear to me how
> this
> effects the results. The original published information for FF03 I assume
> used FF94 charges for the termini.
>
> Also note bugfix.10 for AMBER 8 which addresses some issues with ACE and
> NME
> in FF03 - make sure you have applied this. Also bugfix.19.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
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-- 
-----------------------------------------------------------------------------------
Dr. Dongshan Wei
Department of Chemistry
Boston University
Boston, MA, 02215
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