[gmx-users] result of do_dssp

Justin Lemkul jalemkul at vt.edu
Tue Jan 7 03:34:41 CET 2014

On 1/6/14, 6:51 PM, Nur Syafiqah Abdul Ghani wrote:
> Dear All,
> I'm running an analysis of secondary structure by using do_dssp
> program in GROMACS. The problem that i had was the result..I dont know
> how to read the result..Its because there were amount for each of
> alpha helix,beta sheet and so on but when i'm comparing others works,
> their paper just showed the percentage of each helices and sheet.
> Correct me if i'm wrong..When i read the result of do_dssp,below of
> the result stated the percentage and is that the amount that i should
> take??

That percentage considers all frames of the trajectory, which may or may not be 
appropriate in all cases.

> In addition,after run do_dssp they will create the .xpm picture
> right?but after convert the file format,mine can't be opened and
> read.May i know why?

You should be able to open the .xpm file in a program like Gimp, but if you want 
legends and time stamps all properly interpreted, that's what xpm2ps is for.  It 
produces an EPS file that can be opened by just about everything.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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