[gmx-users] intra-chain peptide bond

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 30 14:06:32 CET 2010

Justin A. Lemkul wrote:
> 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).

...and the relevant .hdb file to include your custom LYS residue, if needed.


> 2. Modify specbond.dat to add the inter-residue bond.
> -Justin
>> 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


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