[gmx-users] coulombic color display all positive of the simulation model

MD refmac5 at gmail.com
Fri Mar 15 19:14:28 CET 2019

Hi Gromacs folks,
I ran a test run with an apo protein without any modifications and
simulated for 10 ns. However, the coulombic map of the pdb output from
gromacs is all positive (red colored by using the coloring method in
chimera). At first I thought it is chimera's error because there were added
Hydrogens. Then I did a test run by adding H back to a pdb structure from a
crystal and it displayed just fine.
Do you know what is causing the charges erros here?

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