AMBER Archive (2006)

Subject: Re: AMBER: where to set bondi radii for halogens

From: Giulio Rastelli (rastelli.giulio_at_unimo.it)
Date: Fri Oct 27 2006 - 16:10:32 CDT

Dear David,
sorry, I meant bromine and not chlorine.
The chlorine works fine (rad=1.7). It is the bromine
that resports 1.5.
I run the sustiva example, and the radii are assigned
correctly to F and Cl.
Are bromine (and iodine?) bondi radii correctly included
in unitio.c?
Thanks a lot for your help
Giulio

Scrive "David A. Case" <case_at_scripps.edu>:

> On Fri, Oct 27, 2e006, Giulio Rastelli wrote:
>
> > I am running a MM-PB/GBSA calculation using amber9
> > on a protein-ligand complex whose topology was
> > built with leap with default mbondi radii, using
> > amber atom types for the protein and gaff types
> > for the ligand. The ligand contains one chlorine
> > and one fluorine atom. I noticed that in the RADII
> > flag in the topology, the two halogens are assigned a value
> > of 1.5, which seems to be the default when radii are
> > not parameterized.
>
> > Is there a way in unitio.c file in leap to tell
> > that the radii should be Cl=1.75 and F=1.47, in
> > each session pertaining to different igb options?
>
> This sounds like a bug. The code in unitio.c looks like it should be
> giving non-default radii for fluorine and chlorine. (Note that the mbondi
> value of fluorine 1.5, the same as the default, but you should be getting
> a radius of 1.7 for chlorine.)
>
> One test you can make: go to $AMBERHOME/test/antechamber/sustiva, and use
> the sustiva.mol2.save and frcmod.save files as input into LEaP. If you save
> the prmtop file, you should see that the radius for the chlorine atom is 1.7
> --anyway, that is what I get. So, see if that works for you.
>
> You can certainly change the values that are assigned, either by editing
> untio.c or by just editing the prmtop file once it is created.
>
> [It could be that the mm-pbsa script is over-riding the prmtop values in some
> fashion, but I would need to see more details.]
>
> ...regards....dac
>
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---------------------------------------
Prof. Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Università di Modena e Reggio Emilia
Via Campi 183, 41100 Modena - ITALY
---------------------------------------
tel 0039-059-2055145
fax 0039-059-2055131
www.scifar.unimore.it/on-line/Home/Gruppidiricerca/Prof.GiulioRastelli.html

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