<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="">O and H are exceptions because of the peculiar interactions between them: as you mentioned the values of the radii are reported (no need to hunt around for them).<div class="">Moreover, the fact that their value is different from the standard covalent radii is mainly attributable to the electrostatic functional form (different form may need slightly different covalent radii to get the correct hydrogen bonding properties). All this is again explained in both paper mentioned.</div><div class=""><br class=""><div class="">For all other elements covalent radii are more than enough.</div><div class="">Of course, depending on your system, you may need to tune them (get some experiencing and this will be a natural step).</div><div class=""><br class=""></div><div class=""><br class=""><div class=""><div><blockquote type="cite" class=""><div class="">On 25 Mar 2015, at 20:21, Joshua Carr <<a href="mailto:jkenne...@gmail.com" class="">jkenne...@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello,<div class=""><br class=""></div><div class="">Does that mean the MM radii are the same for all MM_KIND's for the same element? I'm concerned because based on JCTC 1, 1176 (2005), it seems that the appropriate radius can vary somewhat substantially for the same element in different bonding environments. That paper lists 1.2 A (for O) and 0.44 A (for H) as the appropriate radii for water (which add up to substantially more than the OH bond length). Meanwhile, a table of covalent radii (e.g. from the Cambridge Structural Database, <a href="http://en.wikipedia.org/wiki/Covalent_radius" class="">http://en.wikipedia.org/wiki/Covalent_radius</a>) lists 0.66 A for O and 0.31 A for H, almost a factor of 2 different for O. Moreover, the radii ought to vary for different bonding environments. Although JCP 116, 6941 (2002) indicates that there is some tolerance for a range of values, it is certainly possible to mess up the calculation by using bad values.</div><div class=""><br class=""></div><div class="">The best I can think to do now is use 1.2 A and 0.44 A for water, and use values from the Cambridge Structural Database for all the protein atoms. Is that reasonable? I feel this is probably not that big a deal, but I'm new to QM/MM and am trying to ensure I don't make an error that will be difficult to control for.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class=""><br class=""></div><div class="">Josh</div><div class=""><br class=""></div><div class="">On Wednesday, March 25, 2015 at 10:48:44 AM UTC-5, Teo wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div style="word-wrap:break-word" class=""><div class="">MM radii are just covalent radii (it’s very well explained in few papers).</div><div class="">Find a table with covalent radii and you’ll have solved your problem (that’s what the mentioned script was doing)...</div><div class=""><br class=""></div><div class="">Teo</div><div class=""><br class=""></div><div class=""><blockquote type="cite" class=""><div class="">On 25 Mar 2015, at 15:29, Joshua Carr <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="s3IVn9qJM9kJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;" class="">jken...@gmail.com</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class="">I am having the same problem! I need to define radii for some new atom types, and I have no idea how to do so. Someone help, please!<div class=""><br class=""></div><div class="">Josh Carr<br class=""><br class="">On Thursday, March 12, 2015 at 8:34:33 AM UTC-5, Kristof wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">Hi all, <br class="">I am trying to set up a QMMM simulation, for which I will need the covalent radii for the electrostatic coupling.<br class="">I found some old mails in this list that mentioned a "<a href="http://covalent_radii.pl/" rel="nofollow" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fcovalent_radii.pl%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNHZl2l-dTTwkXDzWLxFusy8ySeHag';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fcovalent_radii.pl%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNHZl2l-dTTwkXDzWLxFusy8ySeHag';return true;" class="">covalent_radii.pl</a>" script that is supposed to yield those. It is supposed to be in the files section of this group.<br class="">However, I cannot find it (I can't find the files section for that matter), can someone please help me out?<br class=""><br class="">Best,<br class="">Kristof<br class=""></div></blockquote></div></div><div class=""><br class=""></div>
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