AMBER Archive (2006)

Subject: AMBER: How to develop charge for my deprotonated glycine

From: Jianzhong Liu (zhong_at_udel.edu)
Date: Tue Feb 28 2006 - 13:58:31 CST

Dear amber users,

I just want to run a simulation about deprotonated glycine. How can I
develop the charge for it by using RESP?

thanks,

Jianzhong Liu
Chemistry & Biochemistry
University of Delaware
Newark, DE 19716
Tel: 302-831-3522(O)
---------------------------------------
             Vita Brevis, Ars Longa
----- Original Message -----
From: "Ross Walker" <ross_at_rosswalker.co.uk>
To: <amber_at_scripps.edu>
Sent: Tuesday, February 28, 2006 11:31 AM
Subject: RE: AMBER: failed to save prm and xyz using ff96

> 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
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>
>
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