Re: How to link two proteins

From: Peter Freddolino (
Date: Wed May 16 2007 - 07:25:26 CDT

Hi Olivier,
your best bet is to define a patch in the topology file, and then apply
it to the appropriate residues. You can use the DISU patch as a model,
and then put in the appropriate atoms from your two residues to replace
those involved in a disulfide bond.

olivier walker wrote:
> Hi all,
> I'm working on a dual domain protein. The two proteins are linked together by
> a glycine (for chain A) and the side chain of a lysine (for chain B). The
> original pdb file has a connect word that define this link.
> I was wondering how to keep this link during Molecular dynamics. Is it better
> to define a patch in the topology file or to define a new residue?
> I must confess I really don't know how to do it because It's just a matter of
> linking two residues that are not linked in the sequence.
> Thanks in advance for any help,
> Olivier

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