Re: [AMBER-Developers] Another sleap complaint - Assertion failed

From: Scott Brozell <>
Date: Thu, 18 Mar 2010 01:04:08 -0400


On Wed, Mar 17, 2010 at 03:24:52PM -0400, Ben Roberts wrote:
> sleap seems to not like residues with spurious TER cards in them.
> Specifically, I just tried to run it on such a file, and got a major
> complaint from an ASSERT:
> [gtkleap]$ source 1FWJ_middle.leaprc
> loadamberprep 1FWJ_chg2.prep
> model = loadpdb BPR-20100317-002_stripped.pdb
> Warning: there is an atom H in residue GLY567 which does not exist in the model 9!
> This atom will not be created.
> Assertion failed: (srcpos.size() > 0), function impose, file geometry.cpp, line 99.
> Abort trap
> My sources tell me that even if sleap is entitled to just stop in such
> a case, an assertion indicates that a serious error has been triggered.
> Can an sleap developer elaborate?

assertions are used to validate the assumptions for a particular piece
of code. The one triggered is a precondition in the language here:

Basically function
numvec impose( std::vector< numvec > srcpos, ...
is checking that it is being fed an xyz position vector.
Apparently, something higher up in the call chain is not handling
the spurious ter card situation.

Wei will probably quickly fix this input situation.

> My input is available for inspection at

no workie:
You don't have permission to access /roberts/files/BPR-20100317-002/ on this server.


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Received on Wed Mar 17 2010 - 22:30:02 PDT
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