[AMBER-Developers] Another sleap complaint - Assertion failed

From: Ben Roberts <roberts.qtp.ufl.edu>
Date: Wed, 17 Mar 2010 15:24:52 -0400


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?

My input is available for inspection at

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Received on Wed Mar 17 2010 - 12:30:02 PDT
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