[gmx-users] Creating cyclic peptides

[Easton J.W.]

Dear Maud,


Thanks, I will give that a try,


Regards,


James

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Maud Jusot <Maud.Jusot at impmc.upmc.fr>
Sent: 17 October 2017 16:10:42
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Creating cyclic peptides

Dear James,

If you want to use an Amber force field, you can create the topology in
the amber format with AmberTool and then convert it to the gromacs
format using Acpype tool
(http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder). It works for
cyclic peptides.

Best regards,

Maud

Le 17/10/2017 à 16:54, Easton J.W. a écrit :
> Thanks Justin,
>
>
> Is there anyway of getting it to work using an AMBER forcefield as well?
>
>
> Kind regards,
>
>
> James
>
> ________________________________
> 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
>
> --
> ==================================================
>
> 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
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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