[gmx-users] Creating cyclic peptides

[Easton J.W.]

Hi,


I'm trying to create a cyclic hexapeptide using pdb2gmx. I want to be able to do this using either an AMBER or CHARMM forcefield.


Initially I have been following the instructions in this link,


https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-September/074609.html


However this will not work using an AMBER forcefield... I've attempted to search for an answer to this but I haven't been able to find anything. I have seen a few mentions of using "specbond.dat", however very few details on how to do this.


I'm fairly new to using GROMACS and so any help or advice that you can give would be appreciated


Kind regards,


James Easton
PhD Student, Tavassoli Group, Essex Group
School of Chemistry, University of Southampton