AMBER Archive (2003)

Subject: Re: AMBER: mm_pbsa and antechamber

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Mon Nov 24 2003 - 13:37:02 CST

"Rajendra P. OJHA" schrieb:
>
> Dear All,
> In MM_PBSA atomtype of the molecule and the
> corresponding .siz and .crg files are required. How
> to create the .crg, .siz and atomtype files for the
> molecule.

One way to generate .crg and .siz files is to write a pdb file using the
"trajout" command in ptraj with the "dumpq" option (which results in
having charges and radii in the B-factor/occupancy columns of the pdb
file) and then to adapt the format of the file to the one used as input
by delphi. Please note that you need to specify the appropriate
dielectric radii beforhand when generating the prmtop file with leap
(see the leap command "set default PBradii ...").

Best regards

Holger

> Thanking you,
> Ojha
>
> =====
> Professor R. P. Ojha DDU Gorakhpur University
> Biophysics Unit Gorakhpur - 273 009,INDIA
> Department of Physics Phone:91-551-202167;321473
> Fax :91-551-340459
> Email : rp_ojha_at_yahoo.com
>
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke

J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Germany                         

Tel.:  (+49) 69-798-29503; Fax: (+49) 69-798-29826
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.rz.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++

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