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.bioinformatik.uni-frankfurt.de
URL: http://www.rz.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++
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Received on Sun Feb 29 2004 - 14:53:00 PST
