<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:Courier New,courier,monaco,monospace,sans-serif;font-size:8pt"><font size="2"><span style="font-family: tahoma,new york,times,serif;">On </span></font><font style="font-family: tahoma,new york,times,serif;" face="Tahoma" size="2">Sat, February 6, 2010 at 11:08:30 AM, </font><font face="Tahoma" size="2">Antoine Delmotte <antoinedelmotte@hotmail.com><br>wrote:<br></font><font style="font-family: times new roman,new york,times,serif;" size="2">> Thank you very much for this, Bruce. It will help me, for sure. <br>> <br>> Could you just let me know where you found the parameters or how you
generated them?<br><br>Most of the parameters came from the entry for threonine in ffoplsaa.rtp<br>The remainder came from running the most recent beta test version of<br>topolbuild 1.3 with the command line<br><br><font size="1"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> /usr/local/bin/topolbuild -dir /usr/local/topolbuild -ff oplsaa -n tpo_pep -charge</span></font><br></font>
<div style="font-family: times new roman,new york,times,serif;"><font size="2"><br>which generates an OPLSaa topology with parameters found originally<br>in the Gromacs OPLSaa installation against a short peptide containing<br>phosphothreonine and sets the atom charges to the OPLSaa atom type<br>charges. I then edited the threonine entry from </font><font style="font-family: times new roman,new york,times,serif;" size="2">ffoplsaa.rtp according<br>to add in the phosphate atom types, and change those atom types that are<br>altered by the presence of the phosphate. Finally, I adjusted the charge<br>on the phosphorous from the charge given in ffoplsaanb.itp in order to<br>have the total charge come out as -2 for a fully ionized phosphate.<br>The exact ionization would depend on pH, of course, and I would have<br>to run the command for protonated TPO (TPH ? or TPH2 ? for the mono-<br>and di-protonated species?) to further correct atom types and
charges.<br><br></font><font size="2"><br></font></div><font style="font-family: times new roman,new york,times,serif;" size="2">-- <br>Bruce D. Ray, Ph.D.<br>Associate Scientist<br>IUPUI<br>Physics Dept.<br>402 N. Blackford St.<br>Indianapolis, IN 46202-3273</font><div><br></div>
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