AMBER Archive (2006)

Subject: Re: AMBER: molsurf.c error

From: David A. Case (
Date: Fri May 05 2006 - 12:34:32 CDT

On Fri, May 05, 2006, Miguel Ferreira wrote:
> I added the line above in the molsurf.c file following the line 1055:
> if( sarg1 < 0.0 )
> printf( %8.3f %8.3f %8.3f %8.3f\n", ai->rad, aj->rad, probe_diam,
> d_ij);
> I donīt know exactly what would be expected to obtain with this change but
> I did not see any difference in my output files. I just added the line...

Your earlier runs had the message about failing the sarg1 > 0 test, but these
don't. So something else must have changed. The above suggestion was to try
to get more info about the failure.

> After create pqr files for complex, ligand and protein, I ran molsurf in
> each of them. The results were:
> -- > molsurf complex.pqr 1.4
> 15504 atoms read
> WARNING: 4 cusps intersection: not trimmed (surface area will be slightly
> overestimated
> I am confused with these results. What the warnings mean?

You can ignore those warnings.

> Isnīt it strange
> that running molsurf alone, the ligand surface area can be computed but not
> when running the mm_pbsa script?

This is a question for the mm-pbsa gurus, like Holger or Ray. But please
check to be sure that the same molsurf executable is being run from the
command line as from the script. (For example, check the result of typing
"which molsurf".)


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