Hi, <br><br>while having a closer look at the topologies of aspartic- and glutamic-acid in OPLS-AA, I noticed that the charges of the carboxylic oxygen atoms are not consistent in the protonated forms of those residues:<br>
<br>from ffoplsaa.rtp of gromacs 4.0.7:<br><span style="font-family: courier new,monospace;">[ ASPH ]</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> [ atoms ]</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> N opls_238 -0.500 0 </span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> H opls_241 0.300 0 </span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> CA opls_224B 0.140 1 </span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> HA opls_140 0.060 1 </span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> CB opls_136 -0.120 2</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> HB1 opls_140 0.060 2</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> HB2 opls_140 0.060 2</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> CG opls_267 0.520 3</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> <b>OD1</b> opls_269 <b>-0.530</b> 3</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> <b>OD2</b> opls_268 <b>-0.440</b> 4</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> HD2 opls_270 0.450 4</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> C opls_235 0.500 5</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> O opls_236 -0.500 5</span><br>[ ... ]<br><span style="font-family: courier new,monospace;">[ GLUH ]</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> [ atoms ]</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> N opls_238 -0.500 1</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> H opls_241 0.300 1</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> CA opls_224B 0.140 1</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> HA opls_140 0.060 1</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> CB opls_136 -0.120 2</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> HB1 opls_140 0.060 2</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> HB2 opls_140 0.060 2</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> CG opls_136 -0.120 3</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> HG1 opls_140 0.060 3</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> HG2 opls_140 0.060 3</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> CD opls_267 0.520 4</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> <b>OE1</b> opls_269 <b>-0.440</b> 4</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> <b>OE2</b> opls_268 <b>-0.530</b> 5</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> HE2 opls_270 0.450 5</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> C opls_235 0.500 6</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> O opls_236 -0.500 6<br>
</span><br>in case of ASPH atom OD1 has a charge of -0.530 while it's equivalent in GLUH (OE1) has a charge of -0.440 and vice versa for OD2 and OE2.<br><br>While fast browsing over the OPLS-AA papers, I couldn't find a listing of the original charges to confirm which of the cases is the correct one. <br>
For all other forcefields for gromacs that have topologies for the protonated forms of aspartic- and glutamic-acid (gromos, ffencads and charmm27.ff (in GMX 4.5) the charges of OD1 and OD2 in ASPH match to the corresponding ones in GLUH.<br>
<br>I found this in the ffoplsaa.rtp of gromacs 4.0.7 and as far as I can see it's currently the same in the branches <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; font-size: medium;"><span class="Apple-style-span" style="font-family: monospace; font-size: small;"></span></span>release-4-0-patches and release-4-5-patches.<br>
<br>Cheers,<br>Oliver<br>-- <br>Oliver Stueker<br>NRC - National Institute for Nanotechnology /<br>University of Alberta, Canada<br>