AMBER Archive (2006)

Subject: AMBER: where to set bondi radii for halogens

From: Giulio Rastelli (rastelli.giulio_at_unimo.it)
Date: Fri Oct 27 2006 - 11:59:00 CDT

Dear all,
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. I know that halide radii have not been
tested, but I am wondering if a choice other than 1.5
would be more appropriate.
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?
Without setting these radi for the halogens, GB
calculation in sander does not complain, but
I'm afraid that wrong radii are used, and cannot
evaluate the impact on the results.
Also, I noticed that in $AMBERHOME/dat/antechamber/RADIUS.dat
the radii for halogens are present, and I wonder if leap
points to this file.
Thanks a lot for your help
Giulio 

-- 

Prof. Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Facolta' di Bioscienze e Biotecnologie
Universita' 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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