Difference between revisions of "Sample Additional Ring Puckers"

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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. create a directory and cd into it
+
1. Create a directory and cd into it
 
   mkdir ZINC000001664886  
 
   mkdir ZINC000001664886  
 
   cd ZINC000001664886  
 
   cd ZINC000001664886  
  
2. copy the protonated smiles into the current directory
+
2. Get the protonated smi from zinc:  
  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/  
 
   http://zinc15.docking.org/protomers/342955170/  
  
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     CC1CCC([NH3+])CC1  ZINC000001664886
 
     CC1CCC([NH3+])CC1  ZINC000001664886
  
3. for each isomer, give it a profix, like _1, _2.
+
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. splite the whole mol2 file into individual conformers
+
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. run build_ligand_mol2 for each mol2 conformer
+
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 08:01, 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