[gmx-users] Insight for my EM output analysis

[raja]

Hi all,

Energy minimization of two proteins, two are same protein but differing
in form in which it is available in PDB (ligand bound and bare active
site). There are no different in secondary structure extension between
these two proteins according to experimental structure. When I minimize
these two proteins using Gromacs minimization engine, a part of the
secondary structure in protein with bound ligand is lost (here secondary
structure is referring a Helix), coincidently that is the region of
interest for my study. That is, the mutant variant at that position
having a role in substrate conversion effect. I repeated the protocol of
minimization with more rigorous using more stringent parameter set but
there is no effect. This is really adding more interest to my work. I
feel that I got result even before the most rigorous part of real MD
itself. Is it really some thing to be existed about? And is it something
that Gromacs engine had found out, the imperfection in crystallographic
solved structure. Kindly   share similar experience, one had in this
list, would be so interesting to hear and feel good about my on going
work.

With regards,
B.Nataraj
-- 
  raja
  raja_28 at fastmail.us

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