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On 21/03/2012 10:17 PM, francesco oteri wrote:
<blockquote
cite="mid:CAFQcp-MSiHiLeWqabr1wWHqA+L9Vym18_ujPHKt7HDaRAnG+pg@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
Assuming Justin's right, then either approach could have been used.
The .itp file parsing works by finding which of a large number of
scanf strings match a given line, so having two ways to do the same
thing is no big deal. You could argue that not needing to recognise
later that X means "any atom type" is more efficient, and also that
the more terse description is less clear to the user. Life ==
trade-offs :)<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAFQcp-MSiHiLeWqabr1wWHqA+L9Vym18_ujPHKt7HDaRAnG+pg@mail.gmail.com"
type="cite">
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<div class="gmail_quote">Il giorno 21 marzo 2012 11:35, Justin A.
Lemkul <span dir="ltr"><<a moz-do-not-send="true"
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>
========================================<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 moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<span class="HOEnZb"><font
color="#888888"><br>
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</div>
<br>
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<div><br>
</div>
-- <br>
Cordiali saluti, Dr.Oteri Francesco<br>
<br>
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