[gmx-users] Creating cyclic peptides

Easton J.W. jwe1g13 at soton.ac.uk
Tue Oct 17 16:54:41 CEST 2017

Thanks Justin,

Is there anyway of getting it to work using an AMBER forcefield as well?

Kind regards,


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: 17 October 2017 15:46:27
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Creating cyclic peptides

On 10/17/17 10:13 AM, Easton J.W. wrote:
> 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

pdb2gmx doesn't like to deal with cyclic peptides. You can probably make
it work but the easier approach (if you want to use the CHARMM force
field) is to build the topology with the online CHARMM-GUI server.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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