<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Zehra,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera does not include any explicit parameterization of FAD. If necessary, it estimates parameters on the fly. If you are doing a serious simulation you would want the most accurate parameters you can obtain, so perhaps you could ask for help on the AMBER mailing list (<a href="http://ambermd.org/MailingLists.php" class="">http://ambermd.org/MailingLists.php</a>). That said, there is a parameterization for FAD at this site: <a href="http://amber.manchester.ac.uk/" class="">AMBER parameter database</a>, though I don't know if its protonation state matches what you need.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 20, 2021, at 8:59 AM, Zehra GÜNEŞ via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Dear all,<div class=""><br class=""></div><div class="">I am working on a research protein that contains FAD. I have tried to prepare it for simulation but unfortunately I have neither trajectory nor parameter file of FAD. Would it be possible to share with me these files if you have?</div><div class=""><br class=""></div><div class="">Thanks in advance,</div><div class=""><br class=""></div><div class="">Zehra Güneş </div></div>
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