AMBER Archive (2004)

Subject: Re: AMBER: question about molsurf

From: Chris Page (chris.page_at_cancer.org.uk)
Date: Thu Nov 25 2004 - 12:45:28 CST

> On Fri, Oct 15, 2004, Xiao He wrote:
>
> > The error in molsurf during the mm_pbsa program:
> > molsurf: molsurf.c:1055: is_buried: Assertion `sarg1 >= 0.0' failed.

> I am assuming that you looked at line 1055 of molsurf.c before asking
> the question, so I won't repeat what you already know.

Having just had the same problem, I think I've found a small bug in the
code, whereby on lines 6007 and 6012, the subscript to xvertex is out of
range. Changing this from xvertex[4] to xvertex[3] (which I'm guessing is
what the author intended...) certainly cured the assertion failure in my
case, and otherwise produces sensible numbers (ie. exactly the same as
before, for the 99% of my structures that were not afflicted by the
failure). But perhaps someone with a better understanding of how the
program works could tell me if this hack is reasonable?

cheers,
Chris

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