[gmx-users] How to create S-S bond

[Justin A. Lemkul]

Quoting kinshuk at chem.iitb.ac.in:

> Dear sir,
>   I want to create S-S bond between two cys in a peptide chain
> irrespective of
>  the conformation of the peptide. I tried this using an option -ss as flag
> in pdb2gmx but it failed to create S-S bond. since, S-S ditance was more
> in free cysSH cysSH, but i want to bring them together to form S-S bond.
> Plz tell me so that i could  solve my problem?

http://wiki.gromacs.org/index.php/specbond.dat

It would probably be best to place a copy of this file in the working directory,
and leave the system-level specbond.dat alone so your changes don't affect
anything other than this particular setup.

-Justin

>
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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