On Fri, Nov 13, 2020, Salman Zarrini wrote:
>
>*Charge*: Some decimal points of charge (0.002998) in total appear in the
>molecule making the structure charged and of course the decimal charge
>would scale up by adding more molecules in the system.
>The charge issue has nothing to do with converting to Gromacs format as the
>charge issue persists even if I convert them to LAMMPS input files.
You will need to manually adjust the charges to a sum of zero before
converting ot other programs.
>
>*Dihedral*: The dihedral are defined twice for some of the atoms as
>following:
>;ai aj ak al funct
>1 2 7 9 1 0.00000 4.91620 2
>1 2 7 9 1 0.00000 0.60250 3
>or
>3 1 2 7 1 180.00008 0.41840 2
>3 1 2 7 1 0.00000 1.60247 3
>or
>33 34 40 37 1 180.00008 0.41840 2
>33 34 40 37 1 0.00000 1.60247 3
>
>Nevertheless, I admit the dihedrals have different multiplicity which might
>get them to be counted as different dihedrals.
It is very common in Amber (and other) force fields for dihedrals to be
rerpresented with terms of different multiplicity.
....good luck....dac
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Received on Mon Nov 16 2020 - 05:30:02 PST
