[gmx-users] intra-chain peptide bond

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 30 14:04:26 CET 2010

Semin Lee wrote:
> Dear Gromacs Users:
> I was wondering if there is a way to introduce an intra-chain peptide 
> bond between side chains of LYS1 and GLU30 of Pin1 WW domain (PDB ID: 
> 1I6C, Model 1). I'm trying to check if additional stability can be 
> acquired from cyclisation using MD simulation.
> The distance between NZ of LYS1 and CD of GLU30 is 3.3A. How can I make 
> them to be close enough to form a peptide bond, and even if I manage to 
> get them close enough, how can I actually introduce a peptide bond? 
> Should I add modified residue information to somewhere?

You will need to:

1. Make custom residues in the .rtp file of the force field of interest (i.e., 
LYS with only one proton, GLU without the terminal O).
2. Modify specbond.dat to add the inter-residue bond.


> Thanks in advance!
> Best regards,
> Semin


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list