[gmx-users] Extra paramter to watch for mutants activity in MD run

Mark Abraham Mark.Abraham at anu.edu.au
Mon Feb 20 05:52:48 CET 2006

raja wrote:
> Dear All,
>      I have simulated a protein whose experimental mutants activity is
>      known. For that protein, the mutant residues lies far away from the
>      active site are contributing to its enhanced activity. But how
>      these residues from far end of active site showing effect on
>      catalytic activity is unknown. Now I have completed simulating that
>      protein in wild type condition for 2ns and further look forward to
>      monitor some parameter say for example the distance between the
>      mutant residues and the set of active site residues and more. Hope
>      it will help me to get some insight for rationalization of the
>      mutants of interest. Now I look forward some extra parameter from
>      your end, which I can monitor from MD run so that I can better
>      rationalize the mutants’ activity.

This type of decision on how to analyze simulation results is a core 
scientific one. Anyone who thinks that in general is easy or trivial 
doesn't understand how complex these systems can be. You are the only 
person who has some understanding of the existing knowledge about the 
behaviour of your protein system. For that reason, you need to make the 
judgement. You need to find out what kinds of analyses have been done in 
the past on other systems and assess their applicability for your 
system. You can get some clues from the capabilities of gromacs utility 
programs (read the manual), by reading relevant scientific literature, 
or paying someone to be your consultant :-)


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