[gmx-users] partial charge on protein

Mark Abraham Mark.Abraham at anu.edu.au
Tue Apr 7 09:18:08 CEST 2009

Homa Azizian wrote:
> Hi Justin and all
> when I do this command: pdb2gmx -ignh -f .pdb -o .pdb -water spce 
> with OPLS force field.
> it seems that the protein has the charge of -3, while the ligand has the 
> charge of 0.890 and finally it prints that the final charge is -2.11. I 
> neutralized this charge with 2 NA+ so -0.11 charge remain (sorry for my 
> mistake this is 0.11 not 0.08).

So you should go and look at this ligand's topology and see where the 
charge is going wrong. The partial charges should at least vaguely 
correlate with chemical intuition.


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