[gmx-users] OPLS forcefield amide charge
stella.nickerson at gmail.com
Fri Aug 28 01:13:04 CEST 2015
I am simulating a polymer using the OPLS forcefield. The polymer has a
sidechain with a secondary amide. Using the atom charges given in the
forcefield, the amide group (N, O, 2Cs, 2 Hs) has a net negative charge. I
don't understand why this is so, since to my knowledge amides are not
generally negatively charged. When repeated several times, the sidechain
gives my polymer a net negative charge, when in real life the polymer is
I'm not sure what to do. I don't want to just arbitrarily adjust the
charges in the forcefield, but I don't understand why the forcefield
charges work out this way unless the forcefield is flawed.
Can I just slightly adjust the charges in the amide group to come out
neutral. That seems... wrong.
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