Justin A. Lemkul
jalemkul at vt.edu
Tue Apr 19 14:17:26 CEST 2011
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.
> Shahid Nayeem
> On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul <jalemkul at 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.
>> 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
>> gmx-users mailing list gmx-users at gromacs.org
>> 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-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users