2018 AMBER tutorial with 2nnq

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Prepare the files Convert 2nnq.lig.withH.charged.mol2 to pdb in chimera

Convert 2nnq.rec.withH.charged.mol2 to pdb in chimera

Copy into zzz.master

Move into 000.programs

Paramaterize the ligand

antechamber -i ../zzz.master/2nnq.lig.withH.charged.pdb -fi pdb -o 2nnq_lig.am1bcc.mol2 -fo mol2 -at gaff2 -c bcc -rn LIG -nc 1

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