VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 09 2018 - 11:25:28 CST

Hi,
  When loading files that explicitly enumerate bonds, such as PSF files,
VMD will not try and do any additional "bond guessing". So, if the PSF
doesn't explicitly include a disulfide bond, VMD will not display it,
end of story... VMD also doesn't currently have any particular knowledge
about martini CG bead naming conventions, so it would not be able to guess
the existence of a disulfide bond in the case that a PSF file was not used.

It is conceivable that we could teach VMD to recognize martini CG structures
and automatically guess things like disulfide bonds, but it's not in our
current work plan so for the time being one has to work around this limitation.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 09, 2018 at 01:35:47PM +0530, Souvik Sinha wrote:
> 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
> <[1]shaheeislam726_at_gmail.com> wrote:
>
> 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 <[2]asharjm_at_gmail.com>
> 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.Â
> 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.Â
> If you are new to VMD and can't get the distance between two atoms
> have a look at the archive.Â
> 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. Â
> On Jan 9, 2018 7:27 PM, "Shahee Islam" <[3]shaheeislam726_at_gmail.com>
> 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
>
> References
>
> Visible links
> 1. mailto:shaheeislam726_at_gmail.com
> 2. mailto:asharjm_at_gmail.com
> 3. mailto:shaheeislam726_at_gmail.com 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/