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