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.
-Justin
Thanks in advance!
Best regards,
Semin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
