<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">It is normal to have combinations of negative and positive values for the barrier heights. Those are just the best coefficients to reproduce some QM rotational energy curve during the parameterization. The negative periodicities are a convention from AMBER. They simply indicate that the dihedral angle potential has more than one term. For your example below:<br><br><p class="yiv896062293MsoNormal" style=""><span style="font-size:10pt;" lang="PT-BR">O2-P
-OS-CP<span style=""> </span>1<span style=""> </span>0.10<span style=""> </span>0.0<span style=""> </span>-3.<span style=""> </span>Dimethyl phosphate</span></p>
<p class="yiv896062293MsoNormal" style=""><span style="font-size:10pt;" lang="PT-BR"><span style=""> </span></span><span style="font-size:10pt;">1<span style=""> </span>-0.50<span style=""> </span>0.0<span style=""> </span>-2.</span></p>
<p class="yiv896062293MsoNormal" style=""><span style="font-size:10pt;"><span style="">
</span>1<span style=""> </span>0.10<span style="">
</span>0.0<span style=""> </span>1</span></p><br>-3, -2 and 1 signify V3, V2 and V1 terms, respectively. Once a positive value is reached, terms for the O2-P-OS-CP potential have been completely accounted for.<br><br>Hope that helps.<br>Austin-<br><br><br>--- On <b>Tue, 7/19/11, Mark Abraham <i><Mark.Abraham@anu.edu.au></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Mark Abraham <Mark.Abraham@anu.edu.au><br>Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format.<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Tuesday, July 19, 2011, 7:08 AM<br><br><div id="yiv896062293">
On 19/07/2011 11:56 PM, sa wrote:
<blockquote type="cite">
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<p class="yiv896062293MsoNormal"><span style="font-size:10pt;
font-family:Arial;" lang="EN-US">Dear
GROMCS users, </span></p>
<p class="yiv896062293MsoNormal"><span style="font-size:10pt;
font-family:Arial;" lang="EN-US"> </span></p>
<p class="yiv896062293MsoNormal"><span style="font-size:10pt;
font-family:Arial;" lang="EN-US">I
am trying to convert some GLYCAM parameters in GROMACS format.
For this
purpose, I am using the latest GLYCAM parameters downloaded
from the RJ. Woods’
website and the examples given in the acpype code (here for
the dihedral angles) : <br>
</span></p>
<p class="yiv896062293MsoNormal"><br>
</p>
<p class="yiv896062293MsoNormal"><a rel="nofollow" target="_blank" href="http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9&r=9&redir=1">http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9&r=9&redir=1</a><br>
</p>
<p class="yiv896062293MsoNormal"><br>
<span style="font-size:10pt;font-family:Arial;" lang="EN-US"></span></p>
<pre><span style="" lang="EN-GB">-------------------
<span class="yiv896062293str"># dihedral idivf barrier hight/2 kcal/mol phase degrees periodicity comments</span></span></pre>
<pre><span class="yiv896062293str"><span style="" lang="EN-GB"> X -ca-ca-X 4 14.500* 180.000 2.000 intrpol.bsd.on C6H6</span></span><span style="" lang="EN-GB">
<span class="yiv896062293str">* to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in topolbuild, why?) = 30.334 or 15.167 kJ/mol</span>
<span class="yiv896062293str"># X -CA-CA-X 4 14.50 180.0 2. </span></span><span class="yiv896062293str"><span style="" lang="PT-BR">intrpol.bsd.on C6H6 (from parm99.dat)</span></span><span style="" lang="PT-BR">
<span class="yiv896062293str"># X-CA-CA-X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; intrpol.bsd.on C6H6</span>
-----------</span></pre>
<pre><span style="" lang="PT-BR"> </span></pre>
<pre><span style="" lang="EN-GB">I have no problems with the parameters for proteins. But, in case of the GLYCAM parameters, I am a little confused
about the conversion of dihedral force constants (DFC), especially when the DFC and the periodicity values are < 0 for example
for this torsion:
</span></pre>
<p class="yiv896062293MsoNormal" style=""><span style="font-size:10pt;" lang="PT-BR">O2-P
-OS-CP<span style=""> </span>1<span style=""> </span>0.10<span style=""> </span>0.0<span style=""> </span>-3.<span style=""> </span>Dimethyl phosphate</span></p>
<p class="yiv896062293MsoNormal" style=""><span style="font-size:10pt;" lang="PT-BR"><span style=""> </span></span><span style="font-size:10pt;">1<span style=""> </span>-0.50<span style=""> </span>0.0<span style=""> </span>-2.</span></p>
<p class="yiv896062293MsoNormal" style=""><span style="font-size:10pt;"><span style="">
</span>1<span style=""> </span>0.10<span style="">
</span>0.0<span style=""> </span>1</span></p>
</blockquote>
<br>
Where only a positive value makes sense, sometimes people use
negative values to indicate some special functional form. This can
be easier to code. Regardless, you'll have to check out the GLYCAM
documentation and see what is meant, before you can address how to
convert it into a GROMACS format. Obviously the contents of parts of
chapter 4 and 5 of the manual will be important.<br>
<br>
Mark<br>
</div><br>-----Inline Attachment Follows-----<br><br><div class="plainMail">-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a></div></blockquote></td></tr></table>