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<TITLE>Re: [Chimera-users] Gasteiger charge</TITLE>
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<FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Thanks Eric for your reply. I will wait for the new build. <BR>
However, I have other NTP analogue to prepare for docking; so, I still need to find a way to correctly assign the Gasteiger charges for these ligands.<BR>
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I used AddH separately, the program does not add H to the phosphate group.<BR>
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Thanks for help,<BR>
Ibrahim<BR>
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On 10/13/11 6:11 PM, "Eric Pettersen" <<a href="pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>> wrote:<BR>
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</SPAN></FONT><BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>On Oct 13, 2011, at 1:29 PM, Ibrahim Moustafa wrote:<BR>
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</SPAN></FONT><BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'> Gasteiger charge <BR>
Dear Chimera developers:<BR>
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I want to assign Gasteiger charges for a ligand, as a preparative step for docking. The ligand is GTP, extracted from a protein complex structure.<BR>
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I wanted to add the Gasteiger partial charge, and explicitly chose to have a total charge of “-4” on the ligand molecule. However, the program assigned partial charges that sum to total charge of “-2” instead of “-4”.<BR>
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Any idea why the program assigned the Gasteiger partial charges incorrectly, ignoring the input total charge on the ligand.<BR>
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Amber's antechamber program (which Chimera uses for charge assignment) does not honor the '-nc' flag (net charge) for Gasteiger charges. It just uses what it believes the charge to be, which I guess in this case is -2 (weird choice!). You can see complaints about this if you google for "gasteiger" along with "nc".<BR>
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If you use the latest daily build (tomorrow's!) then you can use AM1-BCC charges for GTP. We've added "charge templates" for GTP/GDP/ADP/ATP since antechamber frequently fails with highly negatively-charged systems, so we used charges taken from the Amber parameter database <<a href="http://www.pharmacy.manchester.ac.uk/bryce/amber/">http://www.pharmacy.manchester.ac.uk/bryce/amber/</a>> for those commonplace residues. However, in constructing the template for GTP I missed HO3', so that's why you would need to get tomorrow's build.<BR>
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Finally, you should probably use AddH separately and see if Chimera adds a proton to the terminal phosphate of your GTP. If it does, delete it before adding charges. The template charges are for GTPs with no protonation on the terminal phosphate.<BR>
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--Eric<BR>
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</SPAN></FONT><FONT SIZE="6"><FONT FACE="Helvetica, Verdana, Arial"><SPAN STYLE='font-size:24pt'> </SPAN></FONT></FONT><FONT FACE="Helvetica, Verdana, Arial"><SPAN STYLE='font-size:12pt'>Eric Pettersen<BR>
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</SPAN><FONT SIZE="6"><SPAN STYLE='font-size:24pt'> </SPAN></FONT><SPAN STYLE='font-size:12pt'>UCSF Computer Graphics Lab<BR>
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</SPAN><FONT SIZE="6"><SPAN STYLE='font-size:24pt'> </SPAN></FONT><SPAN STYLE='font-size:12pt'><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a><BR>
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