From: Souvik Sinha (
Date: Tue Jan 09 2018 - 02:05:47 CST

You can not see the 'bond' unless it is defined in the psf itself. It seems
you did not consider defining the disulphide bond during the initial
modeling and that is why you are not seeing it now.

On Tue, Jan 9, 2018 at 12:51 PM, Shahee Islam <>

> the sulfur atoms are in the bead but still the bond between the two beads
> containing the sulfur atoms are not showing in the vmd.
> On Tue, Jan 9, 2018 at 12:18 PM, Ashar Malik <> wrote:
>> 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:
>> Hi
>> 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

Souvik Sinha
Research Fellow
Bioinformatics Centre (SGD LAB)
Bose Institute
Contact: 033 25693275