View source for Rescoring with DOCK 3.7


We often want to get the score for a molecule without doing any docking.

DOCK3.7 now can do this internally.  In DOCK 3.6 this was done in an exteranl program scoreopt.  

== need files ==
To rescore you need 3 files:
    poses.mol2.gz
    amsol.txt.gz
    vdw.txt.gz

== how to generate need files ==

Currently, the format of the mol2 file is very rigid.  It must be in the same format as mol2s produced by DOCK 3.7.   

The following script will process a mol2 file produced by dock for rescoring. 
   1.run.rescore_prep.csh

Here is the script: 
  
 #rm poses.mol2.gz vdw.txt.gz amsol.txt.gz
 #
 #zcat test.mol2.gz >! poses.mol2
 
 set ligs_mol2 = $1
 
 
 #if $ligs_mol2:e == 'gz' then
 #   echo $ligs_mol2 $ligs_mol2:r $ligs_mol2:e 
 
 cp $ligs_mol2 poses.mol2
 
 #csh 2.rescore_get_parms_rerun_mod.csh poses.mol2 noamsol
 csh 2.rescore_get_parms_rerun_mod.csh poses.mol2 amsol
 gzip -f poses.mol2
 gzip -f vdw.txt
 gzip -f amsol.txt
 

Here is a script that will generate the amsol and vdw files from a mol2 file: 

   2.rescore_get_parms_rerun_mod.csh

Here is the script: 

 
 set mol2file = $1 
 set ifamsol  = $2
 
 set list = `awk '/  Name:/{print $3}' $mol2file`
 rm vdw.txt amsol.txt
 touch vdw.txt amsol.txt
 
 # (1) braekup mol2 file.  
 # 
   python /nfs/home/tbalius/zzz.scripts/separate_mol2_more10000.py $mol2file mol 
 # foreach molecule
   foreach mol2 (`ls mol*.mol2`)
     set name = $mol2:r
     echo $mol2
     rm -r $name 
     mkdir $name
     cd $name
     cp ../$mol2 .
 
 # (2) mape vdw parms on to the atomtypes
     python /nfs/home/tbalius/zzz.scripts/mol2toDOCK37type.py $mol2 vdw.txt
     #ls -lt | head
 
 # (3) run amsol
     if ($ifamsol == 'amsol') then 
        csh /nfs/home/tbalius/zzz.github/DOCK/ligand/amsol/calc_solvation.csh $mol2
        awk 'BEGIN{count=0}{if(count>0){printf"%s %s %s %s\n", $2, $4, $5, $3}; count=count+1}' output.solv >! output.solv2
     else if ($ifamsol == 'noamsol') then
        echo "amsol is not calculated."
     else 
        echo "ERROR. . . "
        exit
     endif  
     cd ../
     echo "########$name########" >> vdw.txt
     cat $name/vdw.txt >> vdw.txt 
 
     #paste $name/vdw.txt $name/output.solv2 | awk '{printf"%2s %3s %-6s %5s %5s %5s %5s\n", $1, $2, $3, $5, $6, $7, $8}' >> amsol.txt
     if ($ifamsol == 'amsol') then
        echo "########$name########" >> amsol.txt
        paste $name/vdw.txt $name/output.solv2 | awk '{printf"%2s %3s %5s %5s %5s %5s\n", $1, $2, $5, $6, $7, $8}' >> amsol.txt
     else
        cat vdw.txt | awk '{if(NF==1){print $0} else if(NF==4){printf ("%2d %3s %5.2f %5.2f %5.2f %5.2f\n", $1, $2, 0.0,0.0,0.0,0.0)}}' >! amsol.txt 
     endif 
 #
   end

It will generate the amsol file by reruning amsol using the docked poses. 

You could download the amsol file for the promoter of interest from zinc15.
for example:
  curl http://files.docking.org/protomers/08/06/14/455080614.solv > output.solv2
process it for dock: 
  echo "########$name########" >> amsol.txt
  paste vdw.txt output.solv2 | awk '{printf"%2s %3s %5s %5s %5s %5s\n", $1, $2, $5, $6, $7, $8}' >> amsol.txt   


It is also possible to get the amsol parameters from the db2 files:

   /mnt/nfs/work/tbalius/Water_Project_newgrid_mod_heme_charge/0008.rescore_get_parms_from_db_mod.csh

This is a bit messy and slow.  

Here is the script: 
 
 set mol2file = $1 ## dock3.7 output file
 #set ZINCID = $1
 #set db2file = $2
 set dbpath = $2
 
 #echo $ZINCID
 #echo $db2file
 
 set list = `awk '/  Name:/{print $3}' $mol2file`
 rm vdw.txt amsol.txt
 touch vdw.txt amsol.txt
 
 foreach ZINCID ($list)
 
   echo $ZINCID
   # get the number of atoms 
   awk 'BEGIN{flag=0}{if (flag == 1){print "atomnum="$1;flag=0} if ($1 == "'$ZINCID'"){flag = 1}}'  $mol2file # print the number of atoms # line after zinc id
   set atomnum = `awk 'BEGIN{flag=0}{if (flag == 1){print $1;flag=0} if ($1 == "'$ZINCID'"){flag = 1}}'  $mol2file` # print the number of atoms # line after zinc id
 
   set db2file = `grep -a20 $ZINCID  $mol2file | grep "Ligand Source File:" | awk '{print $5}' | sort | uniq `
   echo $db2file
   echo $dbpath/$db2file
   #zcat $db2file | awk 'BEGIN{count=0} /M    /{flag="False"};{if($2 =="'$ZINCID'" && $4 == "'$atomnum'" && flag=="False"){flag="True"; print "atomnum="$4 "::" $0; count=count+1};if (($1 == "A") && flag=="True"){print count":"$0}}' 
   #exit
   zcat $dbpath/$db2file | awk 'BEGIN{count=0} /M    /{flag="False"};{if($2 =="'$ZINCID'" && $4 == "'$atomnum'" && flag=="False"){flag="True"; count=count+1};if (($1 == "A") && flag=="True"){print count":"$0}}' > ! $ZINCID.parms.txt
   #zcat $db2file | awk 'BEGIN{count=0} /M    /{flag="False"};{if($2 =="'$ZINCID'" && flag=="False"){flag="True"; count=count+1; print "found '$ZINCID'"};if(($1 == "A") && (flag=="True") ){print count":"$0}}' 
    # this will only return the first ZINC ID incountered.
 
   echo "## $ZINCID parms" >> vdw.txt
   echo "## $ZINCID parms" >> amsol.txt
 
   # make vdw file
   grep "^1:" $ZINCID.parms.txt | sed 's/1://g' | awk '{printf "%2d %3s %-5s %2d\n", $2, $3, $4, $5}' >> vdw.txt
   #awk '{printf "%2d %3s %-5s %2d\n", $2, $3, $4, $5}' $ZINCID.parms.txt >> vdw.txt
   # amsol file
   grep "^1:" $ZINCID.parms.txt | sed 's/1://g' | awk '{printf "%2d %3s   %6.3f     %6.3f     %6.3f    %6.3f\n", $2, $3, $8, $9, $10, $11}' >> amsol.txt
   #awk '{printf "%2d %3s   %6.3f     %6.3f     %6.3f    %6.3f\n", $2, $3, $8, $9, $10, $11}' $ZINCID.parms.txt >> amsol.txt
 end #ZINCID

== INDOCK Parameters ==
Here is the parameters in the INDOCK file:

 DOCK 3.7 parameter
 #####################################################
 ### NOTE: split_database_index is reserved to specify a list of files
 search_type                   2
 mol2file                      poses.mol2.gz
 ligsolfile                    amsol.txt.gz
 ligvdwfile                    vdw.txt.gz
 #####################################################
 # NOTE: split_database_index is reserved to specify a list of files
 ligand_atom_file               split_database_index

note that the split_database_index file is not used it is just a place holder.