AMBER Archive (2008)

Subject: Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error

From: David A. Case (
Date: Mon Jun 02 2008 - 18:23:46 CDT

On Thu, May 29, 2008, Kateryna Miroshnychenko wrote:

> Funny, but it does work, at least in my particular case. Don't know why ;)
> But you are right of course, the sarg should be equaled to zero before sqrt.
> See below the last variant of molsurf modification. Please find attached the
> pqr file, that caused the problem. (sarg1 = -3.66e-16)

Your pqr file is flawed: it looks like you have *diameters* and not radii in
the final column of the pqr file. I'm not sure how you prepared this file
(maybe there is a bug somewhere else?) but you need to divide the final column
numbers by a factor of two.

...good luck...dac

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