15 Aug
2003
15 Aug
'03
2:52 a.m.
Dear Modeller users !
I am trying to model a protein with a Ca binding site, using 7 well aligned structural templates. Some of these structures contain a Ca atom in the homologue position. I read in the documentation that you could introduce hetero atoms and water using a syntax like ASFDGSFA/--WW--W- , but I could not get a hand on a concrete example.
Also, if I introduced such a site, would Modeller take the electrostatic interaction between the Ca and the side chain atoms into account in the simulated annealing part? Or would it just place the hetero atoms in the equivalent position?
Thank you very much for any suggestion,
Kind regards,
Karsten
--
Karsten Suhre
Information Genomique & Structurale
CNRS
F-13402 Marseille