[gmx-users] pyroglutamate in gromos53a6

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Nov 22 18:17:40 CET 2011

Hi Henry,

That would be a bit of a wild west approach. A better approximation
would be taking the charges from the backbone amide group, as it is
just an amide with on either side aliphatic carbons. Doing it properly
is a bit more involved, as for the G53a6 FF you need to choose
parameters giving the right free enthalpy of solvation.



On Tue, Nov 22, 2011 at 5:10 PM, Henry Hocking <H.G.Hocking at uu.nl> wrote:
> Dear all,
> Where can I find gromos53a6.ff parameters for pyroglutamate (PCA/ PGLU/ PGA)
> ?
> Alternatively, given that I have them in amber99.ff and oplsaa.ff is there a
> way I could adapt these to gromos53a6.ff?
> Can I use, for example, the gromos53a6.ff atom types from glutamine,
> add/remove appropriate bonds / angles / impropers and then take the
> corresponding charge values from my amber99.ff/aminoacid.rtp file. I assume
> that what I've just suggested is the cowboy method and that in reality it is
> not that straightforward, right?
> Kind regards,
> Henry
> --------------------------------------------------------
> Henry Hocking, PhD
> Utrecht University
> Bijvoet Center for Biomolecular Research
> Padualaan 8
> 3584 CH Utrecht, The Netherlands
> Phone: +31-30-2532875
> Fax: +31-30-253 7623
> E-mail: H.G.Hocking at uu.nl
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

More information about the gromacs.org_gmx-users mailing list