<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hello Ahir,<div><span class="Apple-tab-span" style="white-space:pre"> </span>I think you are going to have to use Help->Report a Bug in Chimera and attach your structure file because I cannot reproduce your problem. When I open 1bw9 and minimize it in the daily build using all the defaults (except #conjugate gradient steps = 0) it works. If I then try again, deleting the B chain and allowing only atoms within 5 angstroms of the PPY residue to move, it also works. So it's something specific to your version of the structure or your version of Chimera…</div><div><br></div><div>--Eric</div><div><div><br> Eric Pettersen<br> UCSF Computer Graphics Lab<br> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a><br><br></div><div><div>On Aug 13, 2014, at 8:36 AM, Ahir Pushpanath <<a href="mailto:ahir29@gmail.com">ahir29@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div>Hey there, whenever I try to do a minimisation of a ligand in presence of protein, with a few residues selected as flexible , rest held as rigid, I get past the adding hydrogen box, but it always has a error saying it cant calculate partial charge for the first N-terminal residue, N atom , for example. If I try and delete that residue, it just moves up and says it cant do it for the second one. The PDB file seems fine, and I have opened in Discovery studio and seen it has partial charges assigned fine. Can you enlighten me on what maybe going wrong? I am using the latest build of Chimera.</div>
<div> </div><div>PDB is 1BW9 chain A (only one conformation chosen in multiple conformation residue positions).</div><div>The ligand is the PPY inside.</div><div>the flexible residues are all those 5A away apart from NAD.<br clear="all">
<br>-- <br></div><div dir="ltr"><div>Dr. Ahir Pushpanath<b> PhD.</b><br>Senior Biologist,<br></div>Johnson Matthey.<br><div><br><br></div></div>
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