<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Chimera relies on the no-longer-supported Amber program <i class="">sleap</i> to add the ions, and that program was using an old leaprc (leaprc.ff02.r1) that in turn used an old ions file (ions03.lib) that had a very limited set of ions. I have now switched to a newer leaprc for <i class="">sleap</i> (leaprc.ff14SB) and consequently newer ions lib (atomic_ions.lib) with <i class="">many</i> more ion types available, including Ca2+.<div class=""><br class=""></div><div class="">So, if you get the next daily build you should be able to add Ca2+ ions.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><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>
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<br class=""><div><blockquote type="cite" class=""><div class="">On Feb 16, 2016, at 7:43 AM, manan <<a href="mailto:manan782@gmail.com" class="">manan782@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""> Chimera allows users to add ions to a given structure using Amber tools. This option has a predecided set of ions. Is it possible to add ions other than those mentioned in the add ions option. For example,Ca2+ is not included in the list, so is it possible to add Ca2+ ions?<div class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature">Manan Desai<div class="">Research Student</div><div class="">Department of Biochemistry
</div><div class="">The Institute of Science<br class="">15 Madame Cama Road,<br class="">Mumbai-400 032<br class="">India<br class=""><br class=""></div></div>
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