[gmx-users] Creating cyclic peptides

[Alan]

Please, get it here

svn checkout
http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/stable/ccpn/python/acpype
acpype

Interestingly, but Google code still holds the correct information too:

https://code.google.com/archive/p/acpype/

On 17 October 2017 at 16:19, Easton J.W. <jwe1g13 at soton.ac.uk> wrote:

> 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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Alan Wilter SOUSA da SILVA, DSc
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