Sample Additional Ring Puckers: Difference between revisions
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cd ZINC000001664886 | cd ZINC000001664886 | ||
(note that ZINC000100008245 and ZINC000100008245 are the same molecule and both favor both | (note that ZINC000100008245 and ZINC000100008245 are the same molecule and both favor both substituents in axial, not equitorial). | ||
2. Get the protonated smi from zinc: | 2. Get the protonated smi from zinc: |
Revision as of 17:19, 21 June 2018
1. Create a directory and cd into it.
mkdir ZINC000001664886 cd ZINC000001664886
(note that ZINC000100008245 and ZINC000100008245 are the same molecule and both favor both substituents in axial, not equitorial).
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 suffix, like _1, _2.
vim ZINC000001664886.smi
4. run corina with enhanced sampling of ring puckers
/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