Dear amber users
My system is a complex containing protein + ligand. Based on MM-PBSA
tutorial, I have to create three gas phase prmtop and inpcrd file pairs as
well as one for the solvated complex:
Step 1) Protein.inpcrd / protein.prmtop
Step 2) ligand.inpcrd / ligand.prmtop
Step 3) complex.inpcrd / complex.prmtop
Step 4) complex_ solvated.inpcrd / complex_ solvated.prmtop
My protein has 2 negative charges.
Which step should I do addions in? Only step 4 or steps 1, 3 and 4.
Any help will highly appreciated.
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Received on Fri Dec 12 2014 - 03:30:02 PST
