Hi, 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:
from ffoplsaa.rtp of gromacs 4.0.7: [ ASPH ] [ atoms ] N opls_238 -0.500 0 H opls_241 0.300 0 CA opls_224B 0.140 1 HA opls_140 0.060 1 CB opls_136 -0.120 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 CG opls_267 0.520 3 *OD1* opls_269 *-0.530* 3 *OD2* opls_268 *-0.440* 4 HD2 opls_270 0.450 4 C opls_235 0.500 5 O opls_236 -0.500 5 [ ... ] [ GLUH ] [ atoms ] N opls_238 -0.500 1 H opls_241 0.300 1 CA opls_224B 0.140 1 HA opls_140 0.060 1 CB opls_136 -0.120 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 CG opls_136 -0.120 3 HG1 opls_140 0.060 3 HG2 opls_140 0.060 3 CD opls_267 0.520 4 *OE1* opls_269 *-0.440* 4 *OE2* opls_268 *-0.530* 5 HE2 opls_270 0.450 5 C opls_235 0.500 6 O opls_236 -0.500 6 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. 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. 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. 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 release-4-0-patches and release-4-5-patches. Cheers, Oliver -- Oliver Stueker NRC - National Institute for Nanotechnology / University of Alberta, Canada
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