From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed May 16 2007 - 07:25:26 CDT
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,
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:40 CST