AMBER Archive (2006)

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

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Tue Feb 28 2006 - 11:24:23 CST

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 |
>
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