Dear amber users,
I want to do MM-GBSA calculations for protein-ligand complex according to
the following tutorial:
http://ambermd.org/tutorials/advanced/tutorial3/
My ligand is Doxorubicin and that is neutral. The total charge of protein
is -7.
Based on the tutorial, I am getting inpcrd and prmtop files for ligand,
protein, complex and solvated complex using tleap.
For ligand (lig), after using saveamberparm LIG lig.prmtop lig.inpcrd, both
of inpcrd and prmtop files were created without warning.
For protein (pr), after using saveamberparm pr pr.prmtop pr.inpcrd, both of
inpcrd and prmtop files were created with
WARNING: The unperturbed charge of the unit: -7.000000 is not zero.
For complex (comp), after using saveamberparm comp comp.prmtop comp.inpcrd,
both of inpcrd and prmtop files were created with
WARNING: The unperturbed charge of the unit: -6.999000 is not zero.
For solvated complex (comp_sol), after using addions comp_sol Na+ 0, 7 Na+
ions were added and after using saveamberparm comp_sol comp_sol.prmtop
comp_sol.inpcrd, both of inpcrd and prmtop files were created with WARNING:
The unperturbed charge of the unit: -0.999000 is not zero.
What is the reason for this difference in the charges?
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Received on Thu Sep 15 2016 - 12:00:02 PDT
