Difference between revisions of "2018 AMBER tutorial with 2nnq"

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==Prepare the files==
==Prepare the files==

Revision as of 14:05, 19 March 2018


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

Check for missing force field parameters

parmchk2 -i 2nnq_lig.am1bcc.mol2 -f mol2 -o 2nnq_lig.am1bcc.frcmod