[Dock-fans] Amber Dock -protein charge

Rima Chaudhuri rima.chaudhuri at gmail.com
Wed Jan 21 09:23:50 PST 2009


I am re-scoring some ligands using Amber-dock 6.2. While generating
the complex and receptor input files(.inpcrd and .prmtop), the log
file reports a warning of the protein having  charge "WARNING: The
unperturbed charge of the unit: 10.999900 is not zero.".
I needed clarification on some issues. When running a MD simulation
using Amber, we always neutralize the whole system. Since, amber-dock
essentially minimizes and equilibrates, does the system here not have
to be neutral also? I understand even if the protein is neutralized
using antechamber, but while trying to dock say 1000 ligands with some
charged ones, the system will revert back to being not-neutral for the
complex. So, what is the suggestion for such cases?



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