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

Francesca Lønstad Bleken FrancescaL.Bleken at sintef.no
Fri Aug 12 09:23:19 CEST 2016


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,

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.


                <CAN8VxHy3rJZ=s-2D1QE+HGH7wVNNQ1tYoQA16AfWnuwbv-f75Q at mail.gmail.com<mailto:CAN8VxHy3rJZ=s-2D1QE+HGH7wVNNQ1tYoQA16AfWnuwbv-f75Q at mail.gmail.com>>

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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.



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

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Jo?o M. Damas

PhD Student

Protein Modelling Group

ITQB-UNL, Oeiras, Portugal


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