AMBER Archive (2006)

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

From: Ross Walker (
Date: Tue Feb 28 2006 - 10:31:41 CST

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.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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