From: Ashar Malik (
Date: Tue Jan 09 2018 - 00:48:54 CST

To visualize a NAMD trajectory you need to load a PSF (structure file). Is
the disulfide bond defined in the psf? If yes VMD should render it. And
since you know which two residues interact to form a disulfide bond you can
zoom into those.

However "looking" is not a good way. You should get the distance between
the atoms forming the disulphide bond in all frames and graph that trend.

If you are new to VMD and can't get the distance between two atoms have a
look at the archive.

I am not familiar with how martni coarse grains systems. A quick search
shows system prep requiring extra flags to set up disulphide bonds but I am
not sure how that scales to simulating with NAMD. I am not sure how
residues are coarse grained. Depending on that your selection of atoms
between which you choose to observe distance may vary. If Martini retains
Sulpher while coarse graining, it would be straightforward, otherwise you
may have to measure the bond implicitly.

On Jan 9, 2018 7:27 PM, "Shahee Islam" <> wrote:

I have made coarse grained protein accoring to residue base coarse grained
tutorial using martini force field and simulated the system in namd.My
question is as my proteins contain disulfide bond ,how can i see those
disulfide bond bond in the protein,because i am not able to see those
disulfide bond in vmd.

Thanking you
Shahee Islam
University of calcutta