Dear Stephan Watkins, Thanks for your response. I would again like to specify my query to my main concerns. My main query lies for the 2 H-bonds: one between Protein and MG and other one between protein and GTP.
1) I have 2 configurations of my system. In the initial state: Prot-Mg-GTP complex (Without 2 hbonds ) and final state: Prot-Mg-GTP complex (With 2 hbonds ) I was looking, if there is some way to perform umbrella sampling and then perform WHAM analysis or to calculate PMF for this system, which would also be based these 2 Hbonds ? 2) Also, I have the trajectory traversing the formation of these Hbonds during the course of simulation. Can I use this trajectory to perform some analysis based on these H bonds in terms of free energy, PMF or energy barrier needed to reach to the final state? But as far as I understand, gromacs takes electrostatic energy term into consideration and there is no such specific treatment for H-bonds in terms of energy calculation. 3) One more thing, can I use pull code in my case where one atom (of the protein and connected to rest of the protein too) forms a H-bond with Mg and another atom with GTP ? 4) Or is there any better way to calculate some kind of energy barrier or PMF needed to form these 2 H-bonds along the simulation length? Any suggestion is welcome. Thanks, Neeru 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
