AMBER Archive (2004)

Subject: Re: AMBER: PB in mm-pbsa

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Sun Feb 29 2004 - 08:02:29 CST

Sue Heavner schrieb:
>
> Dear Amber Users,
> I am using delphi through mm-pbsa to perform free energy calculations.
> Can anyone tell me how to setup the mm-pbsa.in file so that the PB
> calculations are performed with the non-linear eqn. to include salt
> effects? I see it used in the literature (JACS, Vol. 120. No. 37, 1998
> pp 9402-9409; J Biomol. Struct. Dyn., Vol. 16. No. 2, 1998 pp 265-280)
> this way.

In the @DELPHI section of the mm_pbsa.in file, you may add further
variables which are passed directly to the delphi input file. Hence, set
LINIT to 0 and add NONIT with some value > 0 and delphi should use the
non-linear PB equation.

Best regards

Holger

> Thanks in advance for your help.
> Sue Heavner
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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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