AMBER Archive (2008)

Subject: Re: AMBER: mmpbsa molsurf.c error

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Sep 17 2008 - 07:10:40 CDT

On Thu, Sep 04, 2008, Ilyas Yildirim wrote:

> I think there is some kind of a bug in MMPBSA's approach on calculating
> the molecular surface. The problem looks to be related to rounding of
> numbers.
>
> In molsurf.c file, sarg1 is calculated as follows:
>
> ------------------
> sarg1 = (ai->rad + aj->rad + probe_diam) * (ai->rad + aj->rad +
> probe_diam) - d_ij * d_ij;
> -----------------
>
> When I print out the values of sarg1, ai, aj, probe_diam, and d_ij I get
> the following values respectively (as well as the error message):
>
> ------------------
> -0.0000000000000002949029909 2.9500000000000001776356839
> 3.1000000000000000888178420 0.0000000000000000000000000
> 6.0500000000000007105427358
> molsurf: molsurf.c:1075: is_buried: Assertion `sarg1 >= 0.0' failed.

I've updated molsurf.c in Amber11 (in both src/nab and src/mm_pbsa);
please test.

[We need to avoid the duplcation of this code at some point.]

...dac

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