Dear Neeru Sharma, I know off hand from years of work with Mg-GTP sites, they are realativly rigid/staritforward. If the bonds arn't present with occupied GTP, or Mg at the beggining, you should equilabrate your starting structures more. Unless your looking at the GTP binding to Mg in which case, the Mg bonds should at least be present. Mg wont leave the site under norm conditions, unless the protein is unfolded (or recycled in cell biological or biochemical terms), or outcompeted with a higher affine ion.
> Can anyone suggest me what parameters or pull_geometry shall I use, to > perform the same. Any suggestion is welcome! Thats too experiment specific to say, without knowing what your trying to look at. Grüess Stephan Watkins -------- Original-Nachricht -------- > Datum: Thu, 28 Jun 2012 23:30:38 +0530 > Von: neeru sharma <neeru.bioi...@gmail.com> > An: gmx-users@gromacs.org > Betreff: [gmx-users] Regarding umbrella sampling simulations along H-bonds > Dear Gromacs Users, > > I am simulating a system containing Protein-Mg-GTP complex. > > I intend to perform the umbrella sampling on the system to calculate > PMF and to perform wham analysis. > I have generated a series of conformations for the umbrella sampling. > My main consideration is towards the 2 H-bonds: one between Protein > and MG and other one between protein and GTP. Both of these bonds were > absent during the start of the simulation but formed when the > simulation was completed. > > Can anyone suggest me what parameters or pull_geometry shall I use, to > perform the same. Any suggestion is welcome! > > > -- > Thanks and regards, > Neeru > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
