Sample Additional Ring Puckers: Difference between revisions
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(Created page with " 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/isom...") |
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1. | 1. Create a directory and cd into it | ||
mkdir ZINC000001664886 | mkdir ZINC000001664886 | ||
cd ZINC000001664886 | cd ZINC000001664886 | ||
2. | 2. Get the protonated smi from zinc: | ||
http://zinc15.docking.org/protomers/342955170/ | http://zinc15.docking.org/protomers/342955170/ | ||
Line 14: | Line 10: | ||
CC1CCC([NH3+])CC1 ZINC000001664886 | CC1CCC([NH3+])CC1 ZINC000001664886 | ||
3. | Or copy the protonated smiles into the current directory if you already generated protomers: | ||
cp ../../normal_db2_gen/isomers/manual_gen/ZINC000001664886/ZINC000001664886.ism . | |||
awk '{print $1" "$2}' ZINC000001664886.ism > ZINC000001664886.smi | |||
3. For each isomer, give it a profix, like _1, _2. | |||
vim ZINC000001664886.smi | vim ZINC000001664886.smi | ||
4. run corina with enhanced pucked ring sampling | 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 | /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=10,mc=10,wh ZINC000001664886.smi ZINC000001664886.mol2 | ||
5. | 5. Split the whole mol2 file into individual conformers | ||
python ~tbalius/zzz.scripts/separate_mol2_more10000_mod.py ZINC000001664886.mol2 test | python ~tbalius/zzz.scripts/separate_mol2_more10000_mod.py ZINC000001664886.mol2 test | ||
6. | 6. Run build_ligand_mol2 for each mol2 conformer | ||
foreach name (`ls ZINC000001664886*_test_*.mol2`) | foreach name (`ls ZINC000001664886*_test_*.mol2`) | ||
mkdir $name:t:r | mkdir $name:t:r |
Revision as of 16:01, 21 June 2018
1. Create a directory and cd into it
mkdir ZINC000001664886 cd ZINC000001664886
2. 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
Or copy the protonated smiles into the current directory if you already generated protomers:
cp ../../normal_db2_gen/isomers/manual_gen/ZINC000001664886/ZINC000001664886.ism . awk '{print $1" "$2}' ZINC000001664886.ism > ZINC000001664886.smi
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. Split 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