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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Good morning, Dear Professor,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">My name is Zhenjiao Du, from Kansas State University.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">I am employing molecular docking for peptide screening and need to build peptide ligands for docking screening. I used to generate ligand by VMD and then energy minimized
by molecular dynamics simulation, but the final conformation is not that matchable to the crystallography results. Chimera generated ligands perform a better job.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">I find Chimera provides amazing ligand energy minimization protocols, but there is no any resource for the scripts based ligand generation and minimization since I might
need to generate thousands of peptide ligands for virtual screening. I find Chimera also supports python programming.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Could you please provide me some information for the ligand generation by Chimera based on python scripts? I really appreciate it.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">I am looking forward to your reply.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Sincerely,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black">Zhenjiao Du<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black">Vice president of CAFS Student Committee</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black">Ph.D. student, Cereal Chemistry
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black">Grain Science & Industry</span><span style="color:black">,
</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black">Kansas State University</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black">150A Waters Hall</span><span style="color:black">,
</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black">Manhattan, KS 66502<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black">Pronouns: He/His</span><span style="color:black"><o:p></o:p></span></p>
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