AMBER Archive (2004)

Subject: Re: AMBER: continue for No radius for F atom in MM_PBSA

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Sun Oct 24 2004 - 15:06:15 CDT

Xiao He wrote:
>
> Dear Amber users,
>
> I find in mm_pbsa/mm_pbsa_calceneent.pm
>
> # This implementation uses bondi radii
>
> # Parameters: $pdb,$pqr,$r_mol
> my $pdb = shift;
> my $pqr = shift;
> my $r_mol = shift;
>
> # Bondi radii + 1.4A and probe radius of 0.0A yields SAS
> # Bondi radii + 0.0A and probe radius of 1.4A yields molecular surface
> # Bondi radii + 0.0A and probe radius of 0.0A yields vdW surface
> my %exp_rad = (
> "N" => 1.550 + 1.400,
> "H" => 1.200 + 1.400,
> "C" => 1.700 + 1.400,
> "O" => 1.500 + 1.400,
> "P" => 1.800 + 1.400,
> "S" => 1.800 + 1.400,
> "FE" => 1.300 + 1.400,
> "Na+" => 1.200 + 1.400,
> "Cl-" => 1.700 + 1.400,
> "MG" => 1.180 + 1.400,
> );
>
> print " Generate PQR\n";
> make_pqr_file($pdb,$pqr,\%exp_rad);
> }
>
> Who can give me the radius of F,Cl,Br,or the reference paper?

See J Phys Chem 1964, 68, 441 or e.g.
http://www.casper.organ.su.se/reference/bondi.pdf.

Best regards

Holger

> Thanks in advance!I appreciate.
>
> 　　　　　　　　Xiao He
> 　　　　　　　　hx_at_itcc.nju.edu.cn
> 　　　　　　　　　　2004-10-24
>
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Juniorprofessur fuer Molekulare Bioinformatik

J. W. Goethe-Universitaet
Fachbereich Biologie und Informatik
Institut fuer Mikrobiologie
Marie-Curie-Str. 9
60439 Frankfurt/Main

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29826
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.uni-frankfurt.de/~hgohlke
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