[gmx-users] Protein Solvent Dynamics - Coordinates for docking

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 21 16:07:18 CEST 2009

ram bio wrote:
> Dear Justin,
> Thanks for the suggestion and advice.
> As i have used a modelled protein and want to obtain the lowest energy
> configuration of the protein by doing dynamics, i want to collect the
> structure (coordinates in pdb) representing average of all the
> frames/configurations produced in MD and also the lowest energy
> configuration structure (coordinates in PDB) produced during the
> simulation, which can be used for docking. Please help how to obtain
> the average structure as well as the lowest energy configuration
> structure.

Average structures are not always meaningful (or even physically-relevant):


You can get average structures from, i.e. g_cluster -cl, if you want.  As for 
the lowest energy structure, analyze potential energy, and dump out the frame 
corresponding to the lowest point.  Hopefully you saved coordinates and energies 
at the same interval :)  The potential energy will correspond to that of the 
system, but hopefully it should give some indication of the lowest energy 
configuration.  I don't know anything about your system, but it will also depend 
on how much the energy fluctuates as to how relevant this structure might be, 
and how different it might be from an "average."

If your structure comes from some model you built, realize that 1 ns is an 
exceptionally short time frame, especially given the capabilities of modern 
hardware and the speed of the GROMACS code.  You may want to consider running a 
bit longer to ensure that you really have a stable system.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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