<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:"Malgun Gothic";
panose-1:2 11 5 3 2 0 0 2 0 4;}
@font-face
{font-family:"\@Malgun Gothic";}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
{mso-style-priority:34;
margin-top:0in;
margin-right:0in;
margin-bottom:0in;
margin-left:.5in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Calibri",sans-serif;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Arial",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri",sans-serif;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:950550384;
mso-list-type:hybrid;
mso-list-template-ids:-89070976 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l0:level1
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level2
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level3
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level4
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level5
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level6
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level7
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level8
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level9
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
ol
{margin-bottom:0in;}
ul
{margin-bottom:0in;}
--></style>
</head>
<body lang="EN-US" link="#0563C1" vlink="#954F72">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Dear,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">I am trying to publish our structure and modeling done by CHIMERA.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">My questions are<o:p></o:p></span></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1"><span style="font-family:"Arial",sans-serif">What is the default option for distance for selecting residues around ligand (e.g., XX A around ligand).<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1"><span style="font-family:"Arial",sans-serif">Any time scale for simulation?<o:p></o:p></span></li></ol>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Here is my method description. Any suggestion, related citation, and help would be appreciated.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">“~. Residues within
<span style="background:yellow;mso-highlight:yellow">XX</span> A of the ligand was selected for simulation.
</span><span style="font-size:11.0pt;font-family:"Arial",sans-serif">The model was then subjected to energy minimization using the AMBER ff14SB protein force field in the Chimera package (34).”</span><span style="font-family:"Arial",sans-serif"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">In-Kwon<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;mso-fareast-language:EN-US">In-Kwon Kim, Ph.D.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;mso-fareast-language:EN-US">Assistant Professor<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;mso-fareast-language:EN-US">Department of Chemistry<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;mso-fareast-language:EN-US">University of Cincinnati</span><o:p></o:p></p>
</div>
</body>
</html>