[gmx-users] An extra charge

Alexander Alexander alexanderwien2k at gmail.com
Sat Jun 11 19:11:11 CEST 2016


Dear gromacs user,

I am expecting to get a uncharged GRO file of the Glutamic acid by invoking
below command, and selecting the protonated version of it, but I do not
know why I get unexpected total charge of "-0.110 e" at the end when I use
the OPLS-AA force field while the other FF's result to the expected
uncharged one?

~> gmx pdb2gmx -f glu.pdb -o glu.gro -water tip3p -ignh -ter -glu

OPLS-AA

Protonated (charge 0) (GLUH)

Total charge -0.110 e

Any comment, please?

Regards,
Alex


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