AMBER Archive (2008)

Subject: AMBER: mmpbsa molsurf.c error

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Sep 03 2008 - 18:56:59 CDT

I checked out the AMBER mailing list about this problem but did not
find a solution. I tried the suggestions given in the following page, but
did not work.

http://amber.ch.ic.ac.uk/archive/200605/0068.html

So, let me explain the problem. I have a system which I decomposed to
complex/ligand/receptor. I am trying to use mmpbsa approach to get the
binding free energies following the tutorial # 3. Normally, I have over
200 structures to analyze, but for one or two structures I am getting the
following error:

molsurf: molsurf.c:1063: is_buried: Assertion `sarg1 >= 0.0' failed.

So, I am trying to understand what the problem is with this particular
structure. I followed David Case's suggestion to print out the
radius/sarg1/probe_diam/etc. values prior to the error by including

-------------------------
  if(sarg1 <0) {
    fprintf(stderr,"%8.3f %8.3f %8.3f %8.3f %8.3f\n", sarg1, ai->rad, aj->rad, probe_diam, d_ij);
  }
-------------------------

When I re-run mm_pbsa.pl script, I am getting the following error:

-------------------------
  -0.000 2.950 3.100 0.000 6.050
molsurf: molsurf.c:1063: is_buried: Assertion
`sarg1 >= 0.0' failed.
Aborted
  -0.000 2.950 3.100 0.000 6.050
molsurf: molsurf.c:1063: is_buried: Assertion
`sarg1 >= 0.0' failed.
Aborted
-------------------------

The structure looks pretty normal, and the printed out value for sarg1
should not create any problem with the mm_pbsa.pl script (it is 0.0), yet
the script gives an error. I created a -pqr file using ambpdb and checked
out that structure (and the values). They look pretty normal. Also, when I
used molsurf on this .pqr file, I did not get any error message. So, I
am clueless at this point on what is causing the problem in MMPBSA
module. Any help is greatly appreciated. Thanks. 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Physics        -                              =
  = University of Rochester      -                              =
  = 585-275-6766 (office)        - 585-267-5644 (home)          =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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