Difference between revisions of "2018 AMBER tutorial with 2nnq"
From Rizzo_Lab
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parmchk2 -i 2nnq_lig.am1bcc.mol2 -f mol2 -o 2nnq_lig.am1bcc.frcmod | parmchk2 -i 2nnq_lig.am1bcc.mol2 -f mol2 -o 2nnq_lig.am1bcc.frcmod | ||
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Revision as of 14:08, 19 March 2018
2nnq
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
Parameters
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
