[gmx-users] question about gmx do_dssp

Justin Lemkul jalemkul at vt.edu
Sun Aug 6 02:33:44 CEST 2017

On 8/5/17 8:12 PM, Mark Abraham wrote:
> Hi,
> I'd start by checking if that last residue is a normal one...

The check_oo() function in gmx_do_dssp.cpp looks like it will not work correclty 
for CHARMM, because it does not identify CHARMM termini, thereby ignoring the 
C-terminus.  It looks for O, O1, or OC1 (which actually doesn't appear to be 
used by any force field).  CHARMM uses OT1/OT2 for COO- termini, so a check for 
OT1 needs to be added.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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