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<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Hello, Dear </SPAN><FONT
face="Times New Roman"><SPAN style="FONT-SIZE: 10pt">gmx-users,</SPAN><SPAN
style="FONT-FAMILY: 'Arial Unicode MS'"><?xml:namespace prefix = o ns =
"urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></FONT></P>
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face="Times New Roman"></FONT> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt"><FONT face="Times New Roman">I have a question about
g_lie. I embedded a membrane protein-ligand complex in the lipid bilayer
and performed the usual MD simulation. I wish that I could use
the resulting energy file to estimate the ligand binding affinity.
So the "solvents" here include the water, lipid bilayer
and ion. Then how can I calculate the Elj and Eqq at its
unbound state? </FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT
face="Times New Roman"></FONT> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt"><FONT face="Times New Roman">Can someone help me to
clarify the procedure to calculate the linear interaction energy?<SPAN
style="mso-spacerun: yes"> </SPAN><o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt"><FONT face="Times New Roman">Is the following steps
right?<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt"><SPAN style="mso-spacerun: yes"><FONT
face="Times New Roman"></FONT></SPAN></SPAN> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt"><FONT face="Times New Roman">Perform the usual MD
simulation the solvated protein-ligand complex </FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt"><FONT face="Times New Roman">Perform another MD
simulation for free ligand and water. (If so, are there any specific
requirements for the solvent system here? Do they have to be the same as the
"solvent" system in the above step?) </FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt"><FONT face="Times New Roman">Calculate the average
value of LJ and Coulomb interaction energies between free ligand and water
as the input for Elj and Eqq<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT
face="Times New Roman"></FONT> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt"><FONT face="Times New Roman">Thanks a lot!<SPAN
style="mso-spacerun: yes"> </SPAN><o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT
face="Times New Roman"></FONT> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt"><FONT face="Times New Roman">Jerry
Song</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt"><FONT face="Times New Roman">Department of
Chemistry<o:p></o:p></FONT></SPAN></P><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: 'Times New Roman'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA">Rensselaer
Polytechnic Institute</SPAN></FONT></DIV></BODY></HTML>