<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:10pt"><span style="font-family: tahoma,new york,times,serif;">On </span><font style="font-family: tahoma,new york,times,serif;" face="Tahoma" size="2">Wednesday, August 12, 2009 at 8:47:33 PM, </font><font style="font-family: tahoma,new york,times,serif;" face="Tahoma" size="2">Nancy <nancy5villa@gmail.com> wrote:</font><br><br>> In an earlier message, it was stated that topolbuild generated
topologies with Gromos 53a6<br>> and OPLS-AA force fields. I am using
topolbuild (version 1.2.2), and the only files in the<br>> "dat/gromacs"
directory are for the force fields: 43a1, 43a2, 43b1, 45a3, 53a5, and
53a6. <br>> How is the OPLS-AA force field used?<br>
<br>First, I need to thank you in particular. First, while testing your molecules, I discovered a<br>case in the as yet unreleased topolbuild 1.3 in which my dihedral selection method failed<br>to select the dihedral choice with the maximum number of heavy atoms with OPLS-AA as<br>the force field. Second, also because of this, I discovered what one downloads as a "Sybyl<br>2" structure from one source of small molecule structures and how to edit it so that it meets<br>the syntax standards for a true mol2 file. Thank you very much for this assistance.<br><br>In the earlier message, I stated that topolbuild 1.2.1 ( and 1.2.2) generates topologies for<br>amber, gaff, glycam, 43a1, 43a2, 43b1, 45a3, 53a5, and
53a6. I stated that the <span style="text-decoration: underline;">as yet</span><br style="text-decoration: underline;"><span style="text-decoration: underline;">unreleased</span> topolbuild 1.3 will include OPLS-AA. The version of topolbuild you have,<br>is 1.2.2. Would you like to beta test topolbuild 1.3?<br><br><br>Sincerely,<br><div> </div>-- <br>Bruce D. Ray, Ph.D.<br>Associate Scientist<br>IUPUI<br>Physics Dept.<br>402 N. Blackford St.<br>Indianapolis, IN 46202-3273<div><br></div></div><br>
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