<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Mar 18, 2013, at 3:34 AM, Elisabeth Ortega wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div>Dear Chimera dev. Team,<br><br><br></div><div>I'm trying to do the same as JD. The message that I receive is when I try to minimize is "Element Pt (atom #0.1.A@PT1) is not currently supported".</div></div></blockquote><div><br></div>This means that the platinum atom does not have a "gaffType" attribute assigned. This attribute should have been assigned by AddCharge. If you are assigning the charges yourself, you need to assign some gaffType to the platinum (I guess I suggest: setattr a gaffType Pt Pt).</div><div><br><blockquote type="cite"><div dir="ltr"><div>As Mr Pettersen told me before, I defined the parameters of PT in heme-iron.frcmod file in ../bin/amber/dat/leap/parms and I also defined the "pt" atom in the MMTK Database. Then I added the charges without the covalent bond between the PT and its neighbours and finally I try to minimize with and without the bonds. Nothing happens.<br></div></div></blockquote><div><br></div>What does "nothing happens mean exactly? Does no minimization occur? Does a minimization occur but no atoms move?</div><div><br></div><div>--Eric</div><div><br><blockquote type="cite"><div dir="ltr"><div>
Probably I'm modifying the wrong files... <br><br></div><div>Then, I have other question to you regarding the IDAM Type. When I minimize, the N3 atoms become N3+. How can I change it?<br><br><br></div><div>Thank you so much for your time and your patience. <br>
</div><br clear="all"><br>-- <br><font><span style="font-family:trebuchet ms,sans-serif">Elisabeth Ortega Carrasco, Ph.D. Student</span><br style="font-family:trebuchet ms,sans-serif"><span style="font-family:trebuchet ms,sans-serif">
Molecular Modelling of Transition Metal Systems Group</span><br style="font-family:trebuchet ms,sans-serif"><span style="font-family:trebuchet ms,sans-serif">
Lab. C7/153, Chemistry Department</span><br style="font-family:trebuchet ms,sans-serif"><span style="font-family:trebuchet ms,sans-serif">
Universitat Autonoma de Barcelona</span><br style="font-family:trebuchet ms,sans-serif"><br style="font-family:trebuchet ms,sans-serif"><span style="font-family:trebuchet ms,sans-serif">
Tel.: +34935812857</span></font>
<font><br style="font-family:trebuchet ms,sans-serif"><span style="font-family:trebuchet ms,sans-serif">
email.: </span><a style="font-family:trebuchet ms,sans-serif" href="mailto:ortega.elisabeth@qf.uab.cat" target="_blank">ortega.elisabeth@qf.uab.cat</a></font>
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