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 <jmda...@itqb.unl.pt<mailto:jmda...@itqb.unl.pt>> To: Discussion list for GROMACS users <gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>> Subject: Re: [gmx-users] Creating topology for Cu-containing enzyme, GROMOS96 force field. Message-ID: <CAN8VxHy3rJZ=s-2d1qe+hgh7wvnnq1tyoqa16afwnuwbv-f...@mail.gmail.com<mailto:CAN8VxHy3rJZ=s-2d1qe+hgh7wvnnq1tyoqa16afwnuwbv-f...@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.ble...@sintef.no<mailto:francescal.ble...@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-requ...@gromacs.org<mailto:gmx-users-requ...@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-requ...@gromacs.org.