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On 19/07/2011 11:56 PM, sa wrote:
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<p class="MsoNormal"><span style="font-size: 10pt; font-family:
Arial;" lang="EN-US">Dear
GROMCS users, </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family:
Arial;" lang="EN-US"> </span></p>
<p class="MsoNormal"><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="MsoNormal"><br>
</p>
<p class="MsoNormal"><a moz-do-not-send="true"
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="MsoNormal"><br>
<span style="font-size: 10pt; font-family: Arial;" lang="EN-US"></span></p>
<pre><span style="" lang="EN-GB">-------------------
<span class="str"># dihedral idivf barrier hight/2 kcal/mol phase degrees periodicity comments</span></span></pre>
<pre><span class="str"><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="str">* 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="str"># X -CA-CA-X 4 14.50 180.0 2. </span></span><span class="str"><span style="" lang="PT-BR">intrpol.bsd.on C6H6 (from parm99.dat)</span></span><span style="" lang="PT-BR">
<span class="str"># 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="MsoNormal" style=""><span style="font-size: 10pt;
font-family: "Courier New";" 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="MsoNormal" style=""><span style="font-size: 10pt;
font-family: "Courier New";" lang="PT-BR"><span
style=""> </span></span><span
style="font-size: 10pt; font-family: "Courier New";">1<span
style=""> </span>-0.50<span style=""> </span>0.0<span
style=""> </span>-2.</span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt;
font-family: "Courier New";"><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>
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