<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Srigouri,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The black frames are typically symptomatic of a system that "blew up", i.e. some atoms were not correctly parameterized and consequently wound up directly on top of one another during the simulation, which results in an infinite energy and immediately thereafter coordinates that go to infinity; hence the black frames.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera and the Molecular Modeling Toolkit (MMTK) that it employs can always correctly parameterize standard amino and nucleic acids (and water), so it would be other molecules in your system that are producing the parameterization problem. If these other molecules are not important to your reason for running the simulation, you could simply delete them before beginning the entire MD process.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>If they are important, then you would have to use a more expert-level simulation package in order to develop the proper set of parameters and run your simulation -- which will be quite challenging. Some example simulation packages include Amber, Gromacs, Namd, Charmm, and OpenMM.</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><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Dec 26, 2021, at 8:48 AM, Sri Oruganty 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="">Hello,<div class=""><br class=""></div><div class="">I am a senior in high school, and I was interested in learning about proteins and mutations. I download Chimera to run MD simulations on a specific protein, but not all the frames are loading. After the frame number gets to a certain point (i.e. 14) every subsequent frame is completely blank. Why is this happening? <br clear="all" class=""><div class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><font face="verdana, sans-serif" style="background-color:rgb(255,255,255)" color="#9900ff" class="">Best regards,</font><div class=""><font face="verdana, sans-serif" style="background-color:rgb(255,255,255)" color="#9900ff" class="">Srigouri Oruganty</font></div><div class=""><font face="verdana, sans-serif" style="background-color:rgb(255,255,255)" color="#9900ff" class="">Pronouns: She, her, hers</font></div><div class=""><a href="mailto:sri.oruganty@gmail.com" target="_blank" class=""><font face="verdana, sans-serif" style="background-color:rgb(255,255,255)" color="#9900ff" class="">sri.oruganty@gmail.com</font></a></div><div class=""><font face="verdana, sans-serif" style="background-color:rgb(255,255,255)" color="#9900ff" class="">(610)-207-6325</font></div><div class=""><br class=""></div></div></div></div></div></div>
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