Re: forming disulfide after equilibrating system

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Dec 23 2006 - 12:55:40 CST

You need to apply a DISU patch using psfgen. You can do this with
your equilibrated structure, assuming the two cysteines are not too
far apart. You will first need a pdb for this final structure.

The problem is, to run psfgen, you need a pdb for each segment.
AutoPSF in vmd should do it automatically for you. The topology file
should explain how to apply the disulfide patch (probably DISU
seg:res1 seg:res2 but check to be sure).

After applying the patch, be sure to minimize the resulting
structure. Let us know if there are any problems.

On Dec 22, 2006, at 5:24 PM, dora guzman wrote:

> I hope someone can help me with this:
>
> I have equilibrated my protein in reduced form (free cysteines),
> but I'm wondering if there is a way to covalently restrain the
> atoms to form a disulfide bridge at this point? Or do I need to
> start from scratch? I'd like to perform SMD on both the oxidized
> and reduced forms of the protein.
>
> Thanks in advance!
>
> -dora

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:19:58 CST