[gmx-users] Re:rather theoretical question

[alexander yakovenko]

Dear D. Egorov 
If C1 and C2 is a X-ray structures it is not possiable to reproduce structures (I  
have never found it). But you may found position, when the dynamics 
simulations are similar. Calculate near 1.2ns of dynamic for both complexes, 
link trajectories into one file,  make  index group of your ligand and binding 
sites residues and make clustering for this group to linked trajectory. You can 
found some clusteres, which contain frames from trajectory 1 and trajectory 2 
(time less 1.2 ns and time more 1.2 ns) in one cluster. This work at my protein 
of near 300 residues. 
 
 
Alexander Yakovenko 
Institute of Molecular Biology & Genetic of NAS of Ukraine 
03143 
acad.Zabolotnogo str. 150 
Kiev 
Ukraine 
______________________________________________ 
E-mail: yakovenko_a at ukr.net 
 
>Dear Gromacs users, could anybody answer next question. 
> 
>Suppose, we have two different conformations of the same enzyme-cofactor  
>complex,say, C1 and C2. Further, conformations of ligand binding sites 
>and ligands themselves are also different for these C1 and C2 states.  
>Then we place,say, ligand in conformation from C2 to binding site of C1  
>( with previously deleted C1 ligand ). How is it reasonable  to wait 
>that MD convert C2 ligand conformation to right for receptor C1 state  
>and reproduce right ligand fit. What complications may occur here.