AMBER Archive (2004)

Subject: Re: AMBER: question about molsurf

From: David A. Case (
Date: Fri Oct 15 2004 - 10:28:10 CDT

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.

Something is bad about the radii, probe diameter, or geometry of your
molecule. I don't recall having seen this assertion failure before. You
probably should add a line like the following right before line 1055:

   if( sarg1 < 0.0 )
      printf( %8.3f %8.3f %8.3f %8.3f\n", ai->rad, aj->rad, probe_diam, d_ij);

That might be a first start at figuring out what is going wrong; unless, of
course, you know that there is something unusal about the problem you are
dealing with.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to