Hi Sonali, First of all, you'll have to find a force field that supports tyrosinate and serinate. These aren't generally considered titratable and are consequently not in the list for interactive selections with pdb2gmx. Once you've found a suitable force field, you'll have to set the protonation states by renaming the residues. Such simulations are advanced, requiring a thorough knowledge of simulations and force fields. Do check http://www.gromacs.org/Documentation/How-tos/Parameterization if you haven't done so.
Hope it helps, Tsjerk On Mon, Sep 27, 2010 at 8:49 AM, sonali dhindwal < sonali11dhind...@yahoo.co.in> wrote: > Thanks Kass for the help. > > I want to specifically protonate one of the lysine near the active site and > deprotonate Tyr and Ser. It will be kind if you can please help me to know > how to select that specific residue number. > > Regards > -- > Sonali Dhindwal > > > --- On *Mon, 27/9/10, Itamar Kass <itamar.k...@monash.edu>* wrote: > > > From: Itamar Kass <itamar.k...@monash.edu> > Subject: Re: [gmx-users] Query regarding protonation and deprotonation of > some residues > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Monday, 27 September, 2010, 10:07 AM > > > Hi, > > You need to define the protonation sate vie pdb2gmx. > > pdb2gmx -tyr -lys > > On 27/09/10 2:34 PM, sonali dhindwal wrote: > > Hello All, > > I came through this research article, in which author has selectively > deprotonated and protonated some of the residues to simulate the condition > for electrostatic interaction with the substrate while carrying out > molecular dynamics simulation. > > It will be appreciable, if you could help me regarding the same, how to > deprotonate Tyr and Ser residue and protonate Lysine residue of the protein > while preparing the protein topology to be used for molecular dynamics > simulation in Gromacs. > > Thanks and Regards. > > -- > Sonali Dhindwal > > > -- > > > "In theory, there is no difference between theory and practice. But, in > practice, there is." - Jan L.A. van de Snepscheut > > =========================================== > | Itamar Kass, Ph.D. > | Postdoctoral Research Fellow > | > | Department of Biochemistry and Molecular Biology > | Building 77 Clayton Campus > | Wellington Road > | Monash University, > | Victoria 3800 > | Australia > | > | Tel: +61 3 9902 9376 > | Fax: +61 3 9902 9500 > | E-mail: itamar.k...@monash.edu <http://mc/compose?to=itamar.k...@monash.edu> > ============================================ > > > -----Inline Attachment Follows----- > > -- > gmx-users mailing list > gmx-users@gromacs.org<http://mc/compose?to=gmx-us...@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<http://mc/compose?to=gmx-users-requ...@gromacs.org> > . > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > 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 > -- 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
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