[gmx-users] DSSP

Justin Lemkul jalemkul at vt.edu
Thu May 25 20:59:39 CEST 2017

On 5/25/17 12:08 PM, Mariusz Wierzbowski wrote:
> Hi,
> I would like to analyze secondary structure elements for my protein. I want to
> do it with do_dssp command in gromacs. I am using gromacs on a plgrid platform.
> The problem is that an error occurs:
> Fatal error: DSSP executable (/opt/dssp/bin/dssp) does not exist (use setenv DSSP).
> On other forums I have read about setting the environment with setenv or export
> but I think that these solutions are for programs on local system.

do_dssp is just a wrapper that calls the dssp program.  do_dssp always needs to 
know where the dssp binary is and it does that by assuming it is in 
/usr/local/bin/dssp unless you specify otherwise with an environment variable. 
That's true no matter what kind of computer you're running on.



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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