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
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========================================
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
========================================
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