AMBER Archive (2007)

Subject: Re: Re: AMBER: parse radii

From: AYTUG TUNCEL (ATUNCEL_at_ku.edu.tr)
Date: Mon Apr 09 2007 - 03:02:59 CDT

Thanks Holger,

I used the command "set default pbradii parse", but it gave me the following message,

gbparm value must be 'bondi', 'amber6', 'mbondi', 'pbamber', or 'mbondi2'
usage: set <container> <parameter> <object>
     or: set default <parameter> <value>

Is there something I am missing? Thanks in advance.

Aytug

-----Original Message-----
From: Holger Gohlke <gohlke_at_bioinformatik.uni-frankfurt.de>
To: amber_at_scripps.edu
Date: Wed, 4 Apr 2007 11:24:17 +0200
Subject: Re: AMBER: parse radii

Am Mittwoch, 4. April 2007 11:10 schrieb AYTUG TUNCEL:
> Hi all,
>
> Is it possible to use parse radii in mm_pbsa calculations without Delphi in
> Amber8 ? Thanks in advance.

Yes, you can do so by generating a prmtop file via leap using the "set default
pbradii parse" option and running mm_pbsa with the pbsa module (PROC=2),
setting RADIOPT=0 and using this prmtop file. Make sure the SURFTEN/SURFOFF
values and PRBRAD are according to what they should be when using the PARSE
radii.

Best regards

Holger

>
> Aytug
>
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Juniorprofessor fuer Molekulare Bioinformatik

J.W. Goethe-Universitaet
Fachbereich Biowissenschaften
Institut für Zellbiologie und Neurowissenschaft
Max-von-Laue-Str. 9
60438 Frankfurt/Main
Germany

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29527
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++
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