Hi, <div>I agree it could be very useful. You can insert the bond hand-coding it in the topology, but you need also to generate angle and dihedral. </div><div>This is very boring and error prone.</div><div><br></div><div>Francesco<br>
<br><div class="gmail_quote">Il giorno 08 marzo 2012 12:32, Ehud Schreiber <span dir="ltr"><<a href="mailto:schreib@compugen.co.il">schreib@compugen.co.il</a>></span> ha scritto:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-US" link="blue" vlink="purple"><div><p class="MsoNormal">Hi,<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">The mechanism for specifying special bonds for the pdb2gmx program, using the specbond.dat file (manual section 5.6.7), seems to me not general enough. The characteristic length of the bond is specifiable, but the range of lengths for which a bond is assumed is hardcoded as +-10% of the characteristic length. I, for example, am perturbing structures using the Concoord method, and lengths of disulfide bonds sometimes vary by more than 10%.<u></u><u></u></p>
<p class="MsoNormal">I therefore suggest that two values would be added at the end of the line declaring a special bond, specifying the minimum and maximum lengths. These two values would be optional, so as not to break the existing arrangement, which would remain as the default. This should not require more than a few extra lines of code and would be, in my opinion, very useful.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">What do you say?<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Thanks,<u></u><u></u></p><p class="MsoNormal">Ehud Schreiber.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p></div></div><br>--<br>
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