Difference between revisions of "2018 AMBER tutorial with 2nnq"
From Rizzo_Lab
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Paramaterize the ligand | 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 | 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 | ||
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
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
