Thankx for the reply ... Can you refer some papers which can be helpful for me to do MD simulation of proteins with ions ... It will be of great help.. I searched the gromacs user list but couldn't get much material..
On Thu, Feb 17, 2011 at 12:32 AM, Ran Friedman <ran.fried...@lnu.se> wrote: > Hi, > > There are methodological difficulties in simulating multivalent ions > together with proteins. Check the mailing list for a discussion and > reference. This is not an > issue of Gromacs but of dealing with protein-ion interactions using a > classical non-polarisable force field. Check the literature. > > Ran. > > Message: 3 > Date: Wed, 16 Feb 2011 20:14:07 -0800 > From: bharat gupta <bharat.85.m...@gmail.com> > Subject: [gmx-users] RE: simulation of a metal binding sites > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <aanlktin06ut6+wrfpz4a79fq9g-galmk35uxecph+...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I have incorporated some metal binding sites(zinc ion) in my protein. Now I > want to see whether that region binds to zinc ions or not and what is the > effect of ion binding to the topology of the protein .. Can this be done > using gromacs and how ?? > > Regards > > -- > Bharat > Ph.D. Candidate > Room No. : 7202A, 2nd Floor > Biomolecular Engineering Laboratory > Division of Chemical Engineering and Polymer Science > Pusan National University > Busan -609735 > South Korea > Lab phone no. - +82-51-510-3680, +82-51-583-8343 > Mobile no. - 010-5818-3680 > E-mail : monu46...@yahoo.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/c1c1ccc7/attachment-0001.html > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com
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