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Isra3l / ligpargen

MIT License
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Net charge is not zero due to rounding #14

Closed BJWiley233 closed 2 years ago

BJWiley233 commented 2 years ago

Hi,

This error is actually discovered in either GROMACs or probably as well in APBS because for neutral molecules ligpargen will actually have slightly positive or negative charges in the gmx.itp and .pqr files due to rounding, i.e. total net charge for molecule is + or - (0.0001 to 0.0005). Is there a way we can correct this in ligpargen?

See: https://gromacs.bioexcel.eu/t/ligpargen-parameterized-ligand-for-opls-aa-m-introduces-a-non-integer-charger/428/5 https://gromacs.bioexcel.eu/t/total-charge-error-in-itp-files/486 https://gromacs.bioexcel.eu/t/ligpargen-toluene-itp-file/4023

Isra3l commented 2 years ago

Hey BJ,

You could change it manually just by removing/adding the charge difference to one atom of your molecule. As we are talking about tiny charge difference values it should not affect the simulation. When I will have time, I will fix it.

Thank you for your feedback, I appreciate it.

Israel

BJWiley233 commented 2 years ago

Yes @Isra3l, tiny differences so manually adjusting as we go 😄.