Difference between revisions of "2018 AMBER tutorial with 2nnq"
From Rizzo_Lab
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| − | 2nnq | + | 2nnq with an explicit solvent model |
= Prepare the files = | = Prepare the files = | ||
Revision as of 14:14, 19 March 2018
2nnq with an explicit solvent model
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
TLeap
Move into 001.tleap_build
