Sample Additional Ring Puckers

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Sometimes you need to sample more ligand conformations when docking. If you have a saturated ring, you may want to explore alternative ring puckering. Here is how you can generate more ring conformations.

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: 

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/ 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/ $name
    cd ../