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Thank you for the reply! <div><div><br></div><div>I do not need many specifities. I only need to imagine what could be the change. </div><div><br></div><div>Can I please have any more information or any website where I can learn the steps to perform local minimization/ count steric clashes/H bonding in Chimera?</div><div>I do not know where to start from.</div><div><span style="-webkit-text-size-adjust: auto;"> I would highly appreciate any clue. </span></div><div><br></div><div>Thank you! </div><div><br></div><div>Kloe<br><br><a href="https://overview.mail.yahoo.com/?.src=iOS">Sent from Yahoo Mail for iPhone</a><br><br><p class="yahoo-quoted-begin" style="font-size: 15px; color: #715FFA; padding-top: 15px; margin-top: 0">On Friday, December 21, 2018, 9:59 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:</p><blockquote class="iosymail"><div dir="ltr">Hi Kloe,<br></div><div dir="ltr">Chimera does not calculate free energies or thermodynamic stabilities, sorry. This generally requires much more extensive modeling, such as long dynamics simulations with a dedicated package like AMBER, Gromacs, etc. Other, more empirical programs (i.e. easier to use and shorter calculations) also exist for estimating the effects on stability of mutations, but I don’t have specific knowledge or recommendations in that area.<br></div><div dir="ltr"><br></div><div dir="ltr">What you can do with Chimera is simple first-order assessments of amino acid mutations or modifications of ligands, by simply counting up H-bonds and steric clashes, or performing small local minimizations, and using your own chemical intuition. I hope this clarifies the situation,<br></div><div dir="ltr">Elaine<br></div><div dir="ltr">-----<br></div><div dir="ltr">Elaine C. Meng, Ph.D. <br></div><div dir="ltr">UCSF Chimera(X) team<br></div><div dir="ltr">Department of Pharmaceutical Chemistry<br></div><div dir="ltr">University of California, San Francisco<br></div><div dir="ltr"><br></div><div dir="ltr">> On Dec 21, 2018, at 10:42 AM, kloe brathon <<a ymailto="mailto:kloebrathon@yahoo.com" href="mailto:kloebrathon@yahoo.com">kloebrathon@yahoo.com</a>> wrote:<br></div><div dir="ltr">> <br></div><div dir="ltr">> Dear Chimera Users,<br></div><div dir="ltr">> I am studying on a protein and its interactions with its ligands and I want to explore what would be the effect on protein thermodynamic stability if some parameters were changed such as addition, removal of hydrogen bonds or other forces. Any idea on how to do that? I am new on this. <br></div><div dir="ltr">> Thank you on advance!<br></div><div dir="ltr">> Kloe <br></div><div dir="ltr"><br></div><div dir="ltr">_______________________________________________<br></div><div dir="ltr">Chimera-users mailing list: <a ymailto="mailto:Chimera-users@cgl.ucsf.edu" href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br></div><div dir="ltr">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div><blockquote></blockquote></blockquote></div></div>
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