[AMBER] hydrogen bonding facility in ptraj

From: Beale, John <John.Beale.stlcop.edu>
Date: Fri, 4 Mar 2011 07:38:11 -0600

I am using ptraj to extract the hydrogen bonding information for a 72-residue protein. The part of the output that lists the hydrogen bonds is fine, as it is identifying all of the hydrogen bonds that I can pick by hand. The problem is with the reporting of the occupancies. The hbond program is reporting that all of the occupancies are 100% (and sometimes it reports 200% or 300%). Clearly there is something wrong, but I haven't been able to troubleshoot this. I am attaching my ptraj hbond script. Can someone tell me what might be wrong; why are my occupancies so out of line? Does my script look OK?



John M. Beale, Jr., Ph.D.
Professor of Medicinal Chemistry and Pharmacognosy
Saint Louis College of Pharmacy
4588 Parkview Place
Saint Louis, Missouri 63110
Cell: 314-315-0409
FAX: 314-446-8460

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Received on Fri Mar 04 2011 - 06:00:03 PST
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