<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META content="text/html; charset=koi8-r" http-equiv=Content-Type>
<META content="MSHTML 5.00.2614.3500" name=GENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=#ffffff>
<DIV><FONT face="Arial Cyr" size=2>Dear Gromacs users, could anybody answer next
question.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face="Arial Cyr" size=2>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 ). </FONT><FONT face="Arial Cyr"
size=2>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.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face="Arial Cyr" size=2>Thanks for your attention to my
problem.</FONT></DIV>
<DIV><FONT face="Arial Cyr" size=2>D. Egorov</FONT></DIV></BODY></HTML>