View source for Sample Additional Ring Puckers


1. Create a directory and cd into it.
  mkdir ZINC000001664886 
  cd ZINC000001664886 

(note that ZINC000001664886 and ZINC000100008245  are the same molecule and both favor both substituents in axial. ZINC000100004326 has one substituents in equatorial).

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

  sed -i 's/1  ZINC/ZINC/g' ZINC000001664886.mol2  
This command will remove the number 1 which appears before the ZINC name to make it compatible with the python scripted
you can also manually edit the file to remove this number or even manually separate the files.  
  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