<div>OK,</div><div>but for some AMBER dihedral the same goal has been obtained using an X for i and l atoms, </div><div>like:</div><div>X FE SS X 9 0.00 0.0 4</div><div><br></div><div>Why the same approach wasn't used for OPLSAA?</div>
<div><br></div><div><br></div><br><div class="gmail_quote">Il giorno 21 marzo 2012 11:35, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> ha scritto:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb"><div class="h5"><br>
<br>
francesco oteri wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs users,<br>
I am working on a program that need topology parsing. I am using the OPLSAA forcefield and I noticed that in ffbonded.itp file belonging to this force field there are these strange lines:<br>
<br>
[ dihedraltypes ]<br>
; i j k l func coefficients<br>
; Added DvdS for Quartz simulations<br>
SI OS 1 0.000 3.766 3<br>
SI OH 1 0.000 3.766 3<br>
<br>
<br>
If it describes dihedral definition, how is possible having only two atom types?<br>
<br>
</blockquote>
<br></div></div>
Those are the central two atoms in the dihedral, i.e. atoms j and k in the i-j-k-l notation for a dihedral.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<span class="HOEnZb"><font color="#888888"><br>
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>Cordiali saluti, Dr.Oteri Francesco<br>