[gmx-users] Creating cyclic peptides

[Justin Lemkul]

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

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

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