AMBER Archive (2009)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Dec 10 2009 - 18:02:16 CST

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

/\
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|\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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