AMBER Archive (2002)

Subject: Re: mm_pbsa output error

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Mon Sep 23 2002 - 23:21:30 CDT

Dear Mike,

the first three "uninitialized values" result from a missing "surface
area" value in com/rec.all.out (1st snapshot), the other lines from the
"nan" values for EGB.
Just to make sure in the latter case - did you choose the proper GB
radii in leap for the GB model you want to use later on in sander? Have
a look at "set default PBradii ..." in the leap manual.
I cannot see why the surface calc. for the first snapshot fails - there
are no log files etc. You might want to comment the lines which remove
log files in the functions "calc_MM_GB_SAS" and "calc_ms" in mm_pbsa.pl.

The statement that PB entries are overwritten is not important in that
case (it was put in for future functionality).

I hope that helps - best regards

Holger

> We seem to be having trouble running mm_pbsa in Amber7. The simulation
> proceeds as expected creating output files for the ligand, receptor,
> and complex. However, an error message is output before the
> statistics.out file is created. The run ends with this error:
>
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1234.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1202.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1202.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1323.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1323.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1323.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1323.
> No data for 0+0 GB GB 0
>
> I am unsure what to make of this. Upon looking at the *rec.all.out
> file as well as the *com.all.out file there seems to be something wrong
> with EGB field in several of the steps. For some of the snapshots the
> EGB result is 'nan' while in others it produces the expected value.
> Could our output errors have something to do with this value? Does
> anybody know what this might indicate? The log file says that the
> entries for PB must be overwritten but I'm not sure where they come
> from. Any information that could be provided will be extremely
> helpful. Relevant files can be found at:
> http://filebox.vt.edu/users/mimurra3/mm_pbsa/
>
> thank you,
>
> Mike
>
> -------------------------------
> Michael Murray
> Dept. of Biochemistry
> 201 Engel Hall
> Virginia Polytechnic Institute and State University
> Blacksburg, VA 24061-0308 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++