[gmx-users] Secondary structure of peptides

[Justin Lemkul]

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.

http://manual.gromacs.org/documentation/current/user-guide/file-formats.html#m2p

-Justin

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

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