[gmx-users] compare simulations between wt and mutate protein

spitaleri.andrea at hsr.it spitaleri.andrea at hsr.it
Mon Apr 2 22:50:22 CEST 2007

Hi all,
I am performing a MD study using as starting point a protein whose
structure has been determined by nmr. the md of wild type has show few
structural changes of some sidechains after 20ns. Afterfwards, using the
same starting point but mutating a PRO to LEU, I have perfomed a similar
MD. The structural behaviour of the mutate protein is a bit different
(fair enough) from the wt. However, I was wondering whether it should be
more fair perform a MD for the mutate protein using the as starting
point the equilibrated structure (after 20ns) of the wt. 
Second, performing different MD on the wt and the mutate protein, how
may compare properly the results (a part of rmsd, energies, sas, hbond,
etc..)? Is it logic to perform a PCA on the energies values? Any
suggestion are welcome.

Thanks in advance



Andrea Spitaleri PhD
Dulbecco Telethon Institute 
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)

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