Sample Additional Ring Puckers
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1. create a directory and cd into it
mkdir ZINC000001664886 cd ZINC000001664886
2. copy the protonated smiles into the current directory
cp ../../normal_db2_gen/isomers/manual_gen/ZINC000001664886/ZINC000001664886.ism . awk '{print $1" "$2}' ZINC000361131264.ism > ZINC000361131264.smi
Or get the protonated smi from zinc:
http://zinc15.docking.org/protomers/342955170/
Copy to clipboard and past it into a file add the zinc name to file, so that it looks like this:
CC1CCC([NH3+])CC1 ZINC000001664886
3. for each isomer, give it a profix, like _1, _2.
vim ZINC000001664886.smi
4. run corina with enhanced pucked ring sampling
/nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=10,mc=10,wh ZINC000001664886.smi ZINC000001664886.mol2
5. splite the whole mol2 file into individual conformers
python ~tbalius/zzz.scripts/separate_mol2_more10000_mod.py ZINC000001664886.mol2 test
6. run build_ligand_mol2 for each mol2 conformer
foreach name (`ls ZINC000001664886*_test_*.mol2`) mkdir $name:t:r cd $name:t:r cp ../${name} . $DOCKBASE/ligand/generate/build_ligand_mol2.sh $name cd ../ end