Difference between revisions of "2018 AMBER tutorial with 2nnq"
From Rizzo_Lab
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| − | Prepare the files | + | ==Prepare the files== |
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Convert 2nnq.lig.withH.charged.mol2 to pdb in chimera | Convert 2nnq.lig.withH.charged.mol2 to pdb in chimera | ||
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Copy into zzz.master | Copy into zzz.master | ||
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| + | ==Parameters | ||
Move into 000.programs | Move into 000.programs | ||
Revision as of 14:04, 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
