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 DSSP 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 -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
