AMBER: mm-gbsa

From: Oliver Hucke <ohucke.u.washington.edu>
Date: Tue, 17 Aug 2004 16:59:21 -0700

Dear all,

I am trying to analyse a trajectory of a bromine containing organic
molecule with mm-gbsa.
First the mm_pbsa.pl script terminated with the message in the log file:

   No radius found for BR ...

I then added a radius to the %exp_rad hash in mm_pbsa_calceneent.pm, and
the script ran fine.

Further I noticed messages like the following in the log file:

     Doing 1 for MM GAS
No values for MM_GAS existing -> Skipping

My questions are:
------------------
o What do these messages in the mm_pbsa log script mean?
o Is it correct to simply add missing radii to the %exp_rad hash in
mm_pbsa_calceneent.pm?
o I suppose the radii in the prmtop file are used for the GB part of the
analysis whereas the radii in %exp_rad are used in the SA part?

Thanks in advance,
Oliver

-- 
_______________________________________________________________
Oliver Hucke, Dr.
                               Health Sciences Building - K418C
University of Washington      1959 NE Pacific St.
Dept. of Biochemistry         phone: (206) 685 7046
Box 357742                    fax  : (206) 685 7002
Seattle, WA 98195-7742        email: ohucke.u.washington.edu
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Received on Thu Aug 19 2004 - 00:53:02 PDT