Hi Justin Thanks a lot. What is the purpose of adding 100mM NaCl. Is it mimicking physiological condition. Shahid Nayeem
On Tue, Apr 19, 2011 at 5:47 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > shahid nayeem wrote: >> >> Hi Justin >> I went through your tutorial of umbrella sampling. Please clarify that >> while generating configuration one requires index.ndx of certain >> residue. These residue are from the restrained chain or from the chain >> on which pulling force is to be applied in order to separate the >> chain. why two groups are created. Does index.ndx should contain all >> residue from the chain which has to move or few are sufficient. > > Do what is appropriate for your system. The reasons for the restraints I > used are described in my paper that I link from the tutorial. I certainly > hope you've read it to understand the methodology. Thus you do not > necessarily have to apply the exact methodology to get a sensible result. > > You need two groups - a reference group and a group to which the pulling > force is applied. Maybe your reference group (whatever it is) needs to be > restrained to avoid structural deformation, maybe it doesn't. Whether or > not an index file is necessary also depends on how you set up the reference > and pulled groups. If they are default groups, then you don't need an index > file, but if they are some subset of existing groups, then yes, you need a > custom index file, just like any other Gromacs operation. > > -Justin > >> Shahid Nayeem >> >> On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: >>> >>> shahid nayeem wrote: >>>> >>>> Dear All >>>> I have some protein complex pdb after docking two monomers. The >>>> scoring of these docked structure are not true representative of >>>> binding affinity. I want calculate the binding affinity affinity of >>>> these docked pdb. Can anyone suggest me, how should I proceed. >>>> Shahid Nayeem >>> >>> Calculating a PMF is a common approach. >>> >>> http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force >>> >>> -Justin >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> 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 >>> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 > -- 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