Dear GMX usesr,<br><br>I have to do charge fitting for a small molecule like ethanol.<br>I have applied PRODRG to generate .gro and .itp for ethanol but it has wrong atomic charge.<br>To correct it I have to use gromos 43a1 force field parameters to assign charges on each atom (Is it right?) <br>
<br>I have red a paper ( Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies<br>Justin A. Lemkul, William J. Allen, and David R. Bevan*) about this issue. In this paper they assign these value to each atom:<br>
<br>H3C 0.000<br>CH2 0.150<br>O -0.548<br>H 0.398<br><br>My question is:<br>In a gromos 43a1 force field and in .rtp file for CH3 in ALA and TMP:<br><br>[ ALA ]<br> [ atoms ]<br> N N -0.28000 0<br>
H H 0.28000 0<br> <u> <b>CA CH1 0.00000 1<br> CB CH3 0.00000 1</b></u><br> C C 0.380 2<br> O O -0.380 2<br><br>[ TMP ]<br> [ atoms ]<br> N1 NR -0.36000 0<br>
C2 C 0.36000 0<br> NA2 NT -0.83000 1<br>.<br>.<br>.<br><u><b> CM13 CH3 0.18000 6</b></u><br> C15 C 0.18000 7<br> O15 OA -0.36000 7<br><b><u> CM15 CH3 0.18000 7</u></b><br>
C14 C 0.18000 8<br> O14 OA -0.36000 8<br><b><u> CM14 CH3 0.18000 8</u></b><br><br>and for atom O I have same problem:<br><br>[ ADE ]<br> [ atoms ]<br> P P 0.99000 0<br> O1P OM -0.63500 0<br>
O2P OM -0.63500 0<br> <b><u> O5* OA -0.36000 0</u></b><br> C5* CH2 0.00000 1.<br>.<br>.<br><br> <b><u> O2* OA -0.54800 8</u></b><br> H2* H 0.39800 8<br> C3* CH1 0.000 9<br>
<b><u> O3* OA -0.360 10</u></b><br><br>So I am confused which one of these charges must be considered as a correct charge when I dont have a reference like mentioned paper?<br><br>Thanks in advance.<br>P.Haghighi<br>