<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Yes, if you use the 1.6.1 release of Chimera, GTP is treated as a "standard" residue in that Chimera knows what the charges are for each atom without having to call antechamber to compute them (that computation typically fails with highly negatively charged molecules like GTP).<div><br></div><div>--Eric</div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 16px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div></div></div><div><br><div><div>On May 17, 2012, at 12:50 PM, Scott Brozell wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi,<br><br>On Wed, May 16, 2012 at 03:22:11PM +0530, Mary Varughese wrote:<br><blockquote type="cite">I have to include the cofactor GTP as part of my receptor protein and dock<br></blockquote><blockquote type="cite">with a ligand. But chimera is not allowing to prepare rec_charged.mol2 file<br></blockquote><blockquote type="cite">since it fails at finding amibcc charge method for GTP residue. Then i<br></blockquote><blockquote type="cite">separately prepared the mol2 file for GTP (using gtp.prep and gtp.frcmod)<br></blockquote><blockquote type="cite">and after performing dockprep on the receptor i opened the GTP.mol2 file in<br></blockquote><blockquote type="cite">the same window and write the mol2 file. but again at grid generation it<br></blockquote><blockquote type="cite">fails "Reading in coordinates of receptor.<br></blockquote><blockquote type="cite">WARNING assign_vdw_labels: Atom valence violated for 1SA0.pdb (combined)<br></blockquote><blockquote type="cite">**** GTP 848 C8 13145.<br></blockquote><blockquote type="cite">Error reading in receptor."<br></blockquote><br>Which version of chimera are you using ?<br>There was some recent activity for GTP but using Gasteiger charges:<br><a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-October/006846.html">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-October/006846.html</a><br><br>Are you saying that you ran antechamber separately from chimera<br>and got the am1bcc charges for gtp ?<br><br>scott</div></blockquote></div></div><br><br></body></html>