[gmx-users] Creating topology for Cu-containing enzyme,

[João M. Damas]

Hi Francesca,

Please contact me directly.

Best,
João

On Fri, Aug 12, 2016 at 8:23 AM, Francesca Lønstad Bleken <
FrancescaL.Bleken at sintef.no> wrote:

> Hi,
>
> Thank you Joao, Justin and Marlon for your answers.
>
> Joao, I have been looking at your article the last days as it explains
> very well what you have done, particularly in the Supplementary info, so
> I am very happy that you answered this thread. Would it be possible for me
> to look at your specbond.dat, .rtp and .itp files so that I better can
> ensure that I am doing things the right way?
> Your system is very similar to mine, so I think I would learn a lot from
> looking at your setup. I hope this is not an inappropriate request, I will
> of course acknowledge you help if this work comes to a publication.
>
> Best regards,
> Francesca
>
>
>
> Date: Thu, 11 Aug 2016 15:40:30 +0100
>
> From: Jo?o M. Damas <jmdamas at itqb.unl.pt<mailto:jmdamas at itqb.unl.pt>>
>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org<mailto:
> gmx-users at gromacs.org>>
>
> Subject: Re: [gmx-users] Creating topology for Cu-containing enzyme,
>
>                 GROMOS96 force field.
>
> Message-ID:
>
>                 <CAN8VxHy3rJZ=s-2D1QE+HGH7wVNNQ1tYoQA16AfWnuwbv-
> f75Q at mail.gmail.com<mailto:CAN8VxHy3rJZ=s-2D1QE+HGH7wVNNQ1tYoQA16AfWnuwbv-
> f75Q at mail.gmail.com>>
>
> Content-Type: text/plain; charset=UTF-8
>
>
>
> Hi Francesca,
>
>
>
> For previous works on copper proteins (
>
> http://pubs.acs.org/doi/abs/10.1021/ct500196e), I have used specbond.dat
> as
>
> Marlon suggested for coppers bound to the protein. For coppers bound to a
>
> co-factor, I would assume you are building an .itp for the co-factor, so I
>
> would include them directly on that .itp file.
>
>
>
> Best,
>
> Jo?o
>
>
>
> On Wed, Aug 10, 2016 at 8:26 PM, Francesca L?nstad Bleken <
>
> FrancescaL.Bleken at sintef.no<mailto:FrancescaL.Bleken at sintef.no>> wrote:
>
>
>
> I am interested in a metalloenzyme with Cu and I have found several studies
>
> > in the literature on systems similar to mine using GROMACS and the Gromos
>
> > force field. I see that GROMOS contains parameters for Cu, and I intend
> to
>
> > keep the Cu-protein distances for the ligand atoms fixated during MD (as
> I
>
> > see most of the previous papers have done). However, I do not understand
>
> > how to prepare the topology for the cofactors with Cu, and none of the
>
> > papers discuss this. pdb2gmx does not recognize it and the PRODRG server
>
> > suggested in the excellent tutorial on protein-ligand system does not
>
> > recognize Cu.
>
> > Do you have a suggestion for how to proceed with creating the topology
>
> > including Cu (in one case) and Cu-containing (another case) co-factors?
>
> > Direction towards tutorials that I might have missed are also
> appreciated.
>
> >
>
> > Kind regards,
>
> > Francesca
>
> > --
>
> > Gromacs Users mailing list
>
> >
>
> > * Please search the archive at http://www.gromacs.org/Support
>
> > /Mailing_Lists/GMX-Users_List before posting!
>
> >
>
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> >
>
> > * For (un)subscribe requests visit
>
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>
> > send a mail to gmx-users-request at gromacs.org<mailto:gmx-users-request@
> gromacs.org>.
>
> >
>
> ?
>
> --
>
> Jo?o M. Damas
>
> PhD Student
>
> Protein Modelling Group
>
> ITQB-UNL, Oeiras, Portugal
>
> Tel:+351-214469613
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613