[gmx-users] DSSP regardin

Mateusz Bieniek bieniekmat at gmail.com
Sat Mar 16 17:57:00 CET 2019

Hi Rahul,

I've run into a similar issue a year ago. It is possible to configure gmx
with the extra configuration file (as described in the documentation) to
get this right.

However, I found it to be archaic and wrote my own quick DSSP visualiser in

I am planning to improve the code and release it with the next paper, but
for now I attach the simple one.

Note that not all dssp letters/secondary structures have been added, so you
might need to add more colors:
colors = {
    coil_char: "#FFFFFF",
    bsheet_char: "#FF0000",
    bbridge_char: "#000000",
    bend_char: "#008000",
    turn_char: "#FFFF00",
    three_helix_char: "#808080",

Hope this helps, Mat

On Fri, 15 Mar 2019 at 17:06, RAHUL SURESH <drrahulsuresh at gmail.com> wrote:

> Hi Users.
> I have Performed dssp for 1000ns simulation. On converting the xpm to eps,
> the axis are not visible to any extent. I have tried with different values
> and I couldn't obtain a good image. Can anyone pass possible  suitable
> commands for long simulations to obtain a satisfactory image?
> --
> *Regards,*
> *Rahul *
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