Re: fix disulfide bridge in coarse grain MD

From: Fotis Baltoumas (
Date: Wed Oct 19 2016 - 12:36:11 CDT


Are you using the NAMD-formatted Martini parameters provided by the
Martini NAMD tutorial of the TCBG website? If so, there should be no
problem, since there is a "DISU" patch in the protein topology file:

! disulfide bond
BOND 1C5c 2C5c

located in the "" file.

So, basically do what you would do for an all-atom system. If you use
the AutoPSF GUI, just use the Patch submenu and define the disulfide
bond. If you work through the Tcl scripts provided by the tutorial, you
may have to edit the one generating the initial PSF for the protein
(i.e. prior to applying the secondary structure information) and include
lines for your disulfide bonds.

In both cases, be careful not to apply the AUTOgenerate function for the
angles and dihedrals, since that is incompatible with the NAMD/Martini

Hope I helped,

Fotis Baltoumas

On 10/19/2016 07:54 PM, Deng, Jinxia (Nancy) wrote:
> Hi All,
> I am attempting to some coarse grain(CG) MD for a peptide with
> disulfide bond.
> I have no problem to fix this in atomic model by “DISU patch” in vmd
> script, but have no idea how to fix the CG model.
> So wonder whether anyone can share some script or advise me how to…
> Greatly appreciated for any input.
> Thanks,
> Nancy

Fotis A. Baltoumas
Phd Candidate, Bioinformatics Postgraduate Programme
Department of Cell Biology and Biophysics
Faculty of Biology, University of Athens
Panepistimiopolis, Athens 157 01, GREECE
email :

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