AMBER Archive (2006)

Subject: Re: AMBER: failed to save prm and xyz using ff96

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Wed Mar 01 2006 - 14:51:09 CST

Can yuo recommend any of the papers discussing the problems of parm96?

Thanks,

Joseph

On Tue, 28 Feb 2006, Carlos Simmerling wrote:

> I would also add my opinion that unless you have a very good reason,
> you should not be using parm96. It has some serious problems
> that have been documented in the literature.
>
> Ross Walker wrote:
>
> >Dear Abd
> >
> >
> >
> >>using the ff03, it perfectly works.
> >>
> >>Below are the steps that i did in the xleap:-
> >>
> >>
> >>
> >>>source leaprc.ff96
> >>>
> >>>
> >>For atom: .R<Zn 389>.A<ZN1 1> Could not find type: Zn
> >>For atom: .R<C0 390>.A<CA1 1> Could not find type: C0
> >>
> >>
> >
> >Check the force field data files in $AMBERHOME/dat/leap/parm
> >
> >In there you will find parm96.dat which defines all of the atom types in the
> >FF96 force field. If you check parm99.dat and frcmod.FF03 you will see the
> >parameters for the FF03 force field. Note, in the parm96.dat file there is
> >no Zn atom type defined and so you need to provide this. Calcium is defined
> >as C0 but only it's mass is provided, there are no van der Waals parameters
> >and so this atom type is not recognised either.
> >
> >Compare this to the parm99.dat file where mass and VDW parameters are
> >provided for both Zn and C0. This is why FF03 (which is based on parm99.dat)
> >works but FF96 does not. The solution, assuming that you want to model the
> >Ca and Zn as simply ions is to use the parameters from the FF03 force field.
> >Although you will need to make this clear in any write-up of your work so
> >that other researchers are aware of exactly which parameters you used and
> >can reproduce things.
> >
> >To do this you need to create an frcmod file with the parameters from the
> >FF03 force field and then load this frcmod file into Leap.
> >
> >The following tutorial has an example frcmod file in it.
> >http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/index.htm
> >
> >All the best
> >Ross
> >
> >/\
> >\/
> >|\oss Walker
> >
> >| Department of Molecular Biology TPC15 |
> >| The Scripps Research Institute |
> >| Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> >| http://www.rosswalker.co.uk | PGP Key available on request |
> >
> >Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> >be read every day, and should not be used for urgent or sensitive issues.
> >
> >
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Joseph Nachman				Department of Biochemistry
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tel: +1 416 978-5510			Toronto, Ontario M5S 1A8
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