<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="">Hi Michał,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>You can write a prmtop for any open structure in Chimera using the Write Prmtop tool (in the Amber category). Now, that tool is designed to work with normal organic molecules, whereas your “molecule” is a linear chain of 10 boron atoms, so you are going to have to set partial charges and GAFF atom types “by hand” before running Write Prmtop instead of letting Chimera try to figure them out (which ultimately won’t work). So, you need to execute these two commands before running the tool</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>setattr a charge 0</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>setattr a gaffType c3</div><div class=""><br class=""></div><div class="">Then you can run the tool. You’ll get a dialog complaining about incompatibilities with the force field. Just ignore it (i.e. click “Continue Anyway” on the dialog). Then you will be able to write a prmtop that you can use with your DCD file.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></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 class=""><br class=""></div></div>
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P.S. If your didn’t mean for the boron atoms to form a chain, you should use HETATM instead of ATOM records in your PDB file.</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 22, 2016, at 7:31 AM, Michał Kadlof <<a href="mailto:m.kadlof@cent.uw.edu.pl" class="">m.kadlof@cent.uw.edu.pl</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="gmail_default" style="font-family:monospace,monospace">Is there any way to read dcd trajectory from openMM simulation?<br class="">Example in attachment.<br class=""><br class=""></div><div class="gmail_default" style="font-family:monospace,monospace">OpenMM does not produce psf or prmtop files :(<br class=""></div><div class="gmail_default" style="font-family:monospace,monospace"><br class=""><br clear="all" class=""></div><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><span style="font-family:monospace,monospace" class="">--<br class="">pozdrawiam serdecznie<br class="">Michał Kadlof <<a href="mailto:m.kadlof@cent.uw.edu.pl" target="_blank" class="">m.kadlof@cent.uw.edu.pl</a>></span><br class=""></div></div></div></div></div></div>
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