Dear Amber community,
I have to build a system where I want that a set of atoms should not
"see" atoms from another set ie., they should be mutually excluded. I
know this is done in CHARMM by declaring explicitly, next to the
definition of each atom from one molecule, those atoms of another
molecule with which it should not interact. I need to carry out free
energy perturbation where I need to change one molecule into another.
So, I want to exclude atoms belonging too the initial molecule from
those in the final molecule.
Is there a way in amber where I can specify this? say by modifying the
prmtop files under "%FLAG NUMBER_EXCLUDED_ATOMS"
What is the format of doing this?
thanks a lot in advance,
Best regards,
Nitin
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Received on Wed Nov 08 2006 - 06:07:24 PST
