<div dir="ltr"><div class="gmail_default" style="font-family:georgia,serif">Hello-



<p class="">I’m trying to use CHIMERA to model the hexameric hydrogen
bonding of isophthalic acid. I’m just an organic chemist, not a computational
chemist. The PDB2PQR subroutine is returning the reply “Error encountered: No
heavy atoms found!”. Here is sequentially what I have done:</p>

<p class="" style="margin-left:36pt"><span style="mso-fareast-font-family:&quot;Times New Roman&quot;"><span style="mso-list:Ignore">1.<span style="font:7pt &quot;Times New Roman&quot;">     </span></span></span>A
pdb file of isophthalic acid hexamer was imported.</p>

<p class="" style="margin-left:36pt"><span style="mso-fareast-font-family:&quot;Times New Roman&quot;"><span style="mso-list:Ignore">2.<span style="font:7pt &quot;Times New Roman&quot;">     </span></span></span>The
covalent bond lengths and angles were set to realistic ones.</p>

<p class="" style="margin-left:36pt"><span style="mso-fareast-font-family:&quot;Times New Roman&quot;"><span style="mso-list:Ignore">3.<span style="font:7pt &quot;Times New Roman&quot;">     </span></span></span>The
names of the concerned atoms were defined in the Build Structure/Modify
Structure/Change Modified Residue’s name box, as described in the User Guide
(i.e., <span style="mso-fareast-font-family:&quot;Times New Roman&quot;">Cac, O2, O3 and
H)</span></p>

<p class="" style="margin-left:36pt"><span style="mso-fareast-font-family:&quot;Times New Roman&quot;"><span style="mso-list:Ignore">4.<span style="font:7pt &quot;Times New Roman&quot;">     </span></span></span><span style="mso-fareast-font-family:&quot;Times New Roman&quot;">The default limits of 3.4 Å
and 30° were used</span></p>

<p class="" style="margin-left:36pt"><span style="mso-fareast-font-family:&quot;Times New Roman&quot;"><span style="mso-list:Ignore">5.<span style="font:7pt &quot;Times New Roman&quot;">     </span></span></span><span style="mso-fareast-font-family:&quot;Times New Roman&quot;">The AMBER force field was
chosen.</span></p>

<p class=""> </p>

<p class="MsoNormal"><span lang="DE">Thanks very much</span></p>

<p class="MsoNormal"><span lang="DE"> </span></p>

<p class="MsoNormal"><span lang="DE">Fenton</span></p>

<p class="MsoNormal"><span lang="DE">(PS – I’m a private person, not associated
with either academia nor industry)</span></p>





</div><br>-- <br><div class="gmail_signature"><div dir="ltr"><span style="font-family:georgia,serif"><font size="2">Dr. Fenton
Heirtzler<br>Phone: +1-301-312-5145<br>On<a href="http://www.linkedin.com/in/fentonhorgchem/" target="_blank"><span style="color:blue">
LinkedIn</span></a><br>Skype: fentonheirtzler<br>Supporter of the <a href="http://www.350.org/" target="_blank"><span style="color:blue">International
Day of Climate Action</span></a><span lang="DE"></span>





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