[AMBER] MM-GBSA for protein-sugar complex

From: James Starlight <jmsstarlight.gmail.com>
Date: Tue, 12 Feb 2019 16:30:10 +0100

Dear Amber Users!

I am dealing with MM-GBSA of protein-sugar complex, where sugar was
parametrized using glycam params.
I wonder to ask whether it is possible usage of amber mask based on
the naming in PDB file in order to create separate topology for the

E.g if the sugar is composed from the following enteries: ROH, 5*(4XB), 0XB
could I use just -n :ROH:4XB:0XB expression to create topology of the
ligand by ante-MMPBSA?

#strit water and ions and create topologies
ante-MMPBSA.py -p ..... -s :WAT:Cl-:NA+ -n :ROH:4XB:0XB

Thank you in advance!


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Received on Tue Feb 12 2019 - 08:00:03 PST
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