[gmx-users] contact analysis between the all backbone of same protein

[soumadwip ghosh]

Hi,

You can obtain the backbone atom contacts in the same protein using the gmx
mdmat command.

gmx mdmat -f *.trr/xtc -s *.tpr -n index.ndx -mean dm.xpm -t 0.5 (the -t
option is because you want the protein contacts within 0.5 nm I guess).
When prompted, select the correct group from index file. It will ask you
for the group only once.

Then post process the .xpm file into an eps file using,

gmx xpm2ps -f dm.xpm -o dm.eps -rainbow red
One can view the .eps file in eps viewer and convert it into a .png or
.tiff file.


Best of luck!

Soumadwip Ghosh
Post Doctoral Research Associate
Dept of Molecular Imaging & Therapy
City of Hope National Medical Center
Duarte, CA - 91010
United States