<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 Eric,<div class=""><br class=""></div><div class="">Thank you very much. I tried the new script on residues 126 and 127 of the attached PDB file. Both ligands are indole. </div><div class=""><br class=""></div><div class="">The Reply Log returns</div><div class=""><br class=""></div><div class=""><div class="">#0 center of mass: 29.5741 29.9514 29.7281, radius of gyration: 3010.778</div><div class="">#0 center of mass: 29.5741 29.9514 29.7281, radius of gyration: 3010.778</div><div class=""><br class=""></div><div class="">This looks unrealistic and seems to be off by at least 3 orders of magnitude. </div><div class=""><br class=""></div><div class="">I used the following script based on AmberTools15</div><div class=""><br class=""></div><div class=""><div class="">parm cmplx_solv.prmtop</div><div class="">trajin prod_0-100ns.nc</div><div class="">radgyr :126&!(@H=) out RoG.dat mass nomax</div><div class="">run</div></div><div class=""><br class=""></div><div class="">I get a radius of gyrations with mean ~ 1.8 angstrom. <b class="">See snapshot attached.</b></div><div class=""><br class=""></div><div class="">For easy reference, the AmberTools15 manual states (<b class="">p.586</b>)</div><div class=""><br class=""></div><div class=""><b class="">radgyr | rog</b><br class=""><br class=""><b class="">radgyr</b> [name>] [<mask>] [out <filename>] [mass] [nomax] [tensor] </div><div class=""><br class=""></div><div class=""><b class="">[<name>]</b> Data set name.<br class=""><b class="">[<mask>]</b> Atoms to calculate radius of gyration for; default all atoms. [out <filename>] Write data to <filename>.<br class=""><br class=""><b class="">[mass] </b>Mass-weight radius of gyration.<br class=""><b class="">[nomax]</b> Do not calculate maximum radius of gyration.<br class=""><b class="">[tensor]</b> Calculate radius of gyration tensor, output format ’XX YY ZZ XY XZ YZ’. Data Sets Created:<br class=""><b class=""><br class=""></b></div><div class=""><b class="">Data Sets Created:<br class=""></b></div><div class=""><b class=""><br class=""></b></div><div class=""><b class=""><name></b> Radius of gyration in Ang.<br class=""><b class=""><name></b>[Max] Max radius of gyration in Ang.<br class=""><b class=""><name></b>[Tensor] Radius of gyration tensor; format ’XX YY ZZ XY XZ YZ’.<br class=""><br class="">Calculate the radius of gyration of specified atoms. For example, to calculate only the mass-weighted radius of gyration (not the maximum) of the non-hydrogen atoms of residues 4 to 10 and print the results to “RoG.dat”:<br class=""><br class=""><div class=""> radgyr :4-10&!(@H=) out RoG.dat mass nomax</div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""></div></div></body></html>