[gmx-users] how to deal with the initial structure?

Xavier Periole x.periole at chem.rug.nl
Tue Aug 24 10:43:18 CEST 2004

hj zou wrote:

>Dear GROMACS users,
>       I'm performing a long-timescale simulation on a protein-ligand complex.And now I wanna compare the differences between apo- and holo- system.However,no crystal structure of apoprotein is available so far.So I wanna delete the ligand of holo-protein,take it as the initial structure of apoprotein and then perform a long-time simulation.Can anyone tell me whether it's reasonable or not? Any other suggestions?
>      Thank you in advance.
>Best regards
Because you do not have and a priori don't know the structure of the
you are going to have to decide when the simulation is of the apo will be in
the apo state !!! You can wait the equilibration of the rmsd but you
will never be
sure it is the apo protein structure you are sampling. If there is an
even small
conformational change you may never see it.
On the other hand you can try to collect all the information of the apo
in the literatrure and compare to your "aopo"-protein.



   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole

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