VMD-L Mailing List

From: Bryan Roessler (roessler_at_uab.edu)
Date: Fri Feb 02 2018 - 04:09:33 CST

Hello,

I have a short engineered protein fragment that is correctly ordered and
numbered with resids and nums (701, 702, 703, 704, 705) in the original
pdb, however when I run autopsf on the original pdb the resulting
*_autopsf_formatted.pdb places the residues in the wrong order (702, 703,
704, 701, 705). This results in peptide bonds being generated between
non-consecutive residues. Thus the carboxyl in residue 701 ends up bound to
the amino in residue 705 even though they are at opposite ends of the
peptide. I have tried renumbering the residues from 1 to no avail. The only
oddity in my peptide is that residues 701 and 705 are non-standard and use
custom topologies, with the correct DECL and BOND +N for residue 701 and -C
for residue 705.

Thanks,
Bryan

*Bryan Roessler | Researcher*
UAB | The University of Alabama at Birmingham
*uab.edu/cmdb <http://uab.edu/cmdb>*
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