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<DIV><FONT face=Arial size=2>Hi there,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I would like to suggest the
following useful additions to the GROMACS package related to NMR
refinement:</FONT></DIV>
<DIV><FONT face=Arial size=2>When the dihedral angle restraints have been
implemented it would be good to have a g_dihed function that prints the
violations for dihedrals. A similar function would be very useful as well for
the orientational restraints (orire, g_orire) (It's not clear to me how this is
done currently). <FONT face=Arial size=2>For the orientational restraints the
following measure of fit is often used in the NMR community and would be good to
have implemented: </FONT></FONT></DIV>
<DIV><FONT face=Arial size=2> </DIV>
<DIV><FONT face=Arial size=2>Q = rms (D-experimental - D-calculated) / rms
(D-experimental)</FONT></DIV>
<DIV>(Cornilescu Q-factor, <EM><FONT face="Times New Roman">Cornilescu et al.
</FONT><FONT size=2><FONT face="Times New Roman">J. Am. Chem. Soc.
</FONT></FONT></EM><B><FONT size=2><FONT face="Times New Roman">1998,
</FONT></B></FONT><I><FONT size=2><FONT face="Times New Roman">120,
</FONT></I></FONT><FONT face="Times New Roman"><FONT size=2>6836</FONT><FONT
size=2>-</FONT><FONT size=2>6837</FONT></FONT><FONT face="Times New Roman"><FONT
size=2>)</FONT></FONT></DIV>
<DIV> </DIV>
<DIV>It also might be useful to have these types of restraints handled in
g_energy with the -viol option. </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>thanks in advance!</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Chris</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>PS I remember noticing sometime ago that g_energy
-viol does not show any lower-bound violations of distance restraints. Probably
a small bug.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>PPS If you are interested: I'd be happy to
contribute all the NMR refinement protocols that I am currently developing to
the GROMACS community once they're all finished.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
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