[gmx-users] Secondary structure of peptides

Justin Lemkul jalemkul at vt.edu
Wed May 9 02:44:16 CEST 2018

On 5/7/18 10:57 PM, m g wrote:
> Dera Justin,I tried to obtained .eps file for my peptides with this command "gmx xpm2ps -f ss.xpm -o ss.eps -bx 1 -by 30", but unfortunately I can't obtained a good .eps file that show me the secondary structure.  I tried another value for -bx and -by flags, but they can't gave me a good figure. Basically,how should I choose values for -bx and -by flag? Would you please help me?Best regards,Ganj

You need to calculate a conversion factor that converts the ratio of (# 
of frames/# residues) to something legible. You may be better off using 
an .m2p file, which gives you lots of options for tweaking the output.




Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list