Dear Gromacs users,
I obtained the ITP file of glycerol molecule from the Dundee PRODRG server (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/). However, I heard that the charges are not accurate enough. So I estimated the charges of glycerol using Gaussian. The input file of Gaussian is gol.gjf, including all atoms of a glycerol molecule. The output of Gaussian is selected as follows: -------------------------- Gaussian Output ---------------------------------------------------------------------------- ----------- Mulliken atomic charges: 1 1 O -0.677102 2 H 0.422534 3 C -0.156687 4 H 0.224462 5 H 0.169912 6 C 0.007200 7 H 0.182644 8 O -0.586768 9 H 0.435753 10 C -0.171961 11 H 0.173527 12 H 0.190745 13 O -0.630544 14 H 0.416285 Sum of Mulliken charges= 0.00000 -------------------------------------------END of Gaussian Output ---------------------------------------------------------------- ------------------------------------------ ITP file ---------------------------------------------------------------------------- ------ [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 OA 1 GOL OAB 1 -0.095 15.9994 2 HO 1 GOL HAA 1 0.043 1.0080 3 CH2 1 GOL CAA 1 0.052 14.0270 4 CH1 1 GOL CAC 2 0.078 13.0190 5 OA 1 GOL OAD 2 -0.114 15.9994 6 HO 1 GOL HAB 2 0.036 1.0080 7 CH2 1 GOL CAE 3 0.053 14.0270 8 OA 1 GOL OAF 3 -0.095 15.9994 9 HO 1 GOL HAC 3 0.042 1.0080 -------------------------------------END of ITP file ---------------------------------------------------------------------------- -- Then it comes to edit the ITP file. But there are some problems puzzling me. Firstly, the ITP file just has 9 atoms ( see above) as the Dundee PRODRG server uses united-atom force field which neglects 5 unpolar hydrogen atoms while the result of Gaussian has 14 atoms. How should I edit the charges of ITP file? Or how could I edit the cgnr and charge fields of the ITP file with the Gaussian result? Is it reasonable and acceptable that a charge group has a decimal number of charges? Secondly, the charge group number of ITP file is 3 whereas the result of Gaussian has only one charge group(14 atoms as a whole group). Could the Gaussian package calculate the charges of a molecules by first dividing the atoms of the molecule into different charge groups? Any help/suggestions will be greatly appreciated! Thank you!! Chuan Liao
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