The calculation of RMSD between two chemical identical ligands sounds
trival, but a problem arise, if the order and the names of the atoms in
the two files are different. A matching between the two corresponding
atoms has to be done. Here, the problem of rotating groups like amidino
groups or benzyl rings and the missing bound information in PDB files
make it even more complicated. Most programs for calculating RMSD are
struggling either with non-peptidic molecules, file conversion or atom
matching. The utilitie program smart_rms (/sw/mcm/app/gold/gold_v3.0/utilities/smart_rms)
in combination with antechamber for file conversion seems to give
reasonable results. For calculating the RMSD between a bunch of docking
solutions and ligands of crystal structures the executables were
combined in the bash script gold_analysis.sh.
Procedure
prepare amber8 prepare
gold_3.0
converting PDB file (ligand1.pdb) with
crystal structure conformation of ligand into mol2 format (ligand1.mol2) antechamber
-i ligand1.pdb -fi pdb -o ligand1.mol2 -fo mol2
converting docking solution (ligand2.sdf) into mol2 format
(ligand2.mol2) antechamber
-i ligand2.sdf -fi mdl -o ligand2.mol2 -fo mol2
smart_rms -h
ligand1.mol2 ligand2.mol2
Program
gold_analysis.sh
-h options: -h
help -vers
version (EML version 08.06.2006) -d
$DIR directory (/home/henricsn/combine2go/data/urokinase/pdb/ligand/) -pdb1
$FILE pdb file of first molecule (eg. xray) -sdf1
$FILE sdf file of first molecule (eg. xray) -pdb2
$FILE pdb file of second molecule (eg. docking solution) -sdf2
$FILE sdf file of second molecule (eg. docking solution) -ranked
calculating rmsd for several docking solutions
$FILE _* template file name -all
calculating rmsd for all docking solutions in subfolders
$FILE _m* template file name -file
SD file name with multiple structures
Example
Save all the prepared ligands (see:
convert.sh) in the folder /home/henricsn/combine2go/data/trypsin/pdb/all_ligands/????.ligand.pdb The residue name must be
identical in the ligand.pdb file and in the SD file of the docking
solutions!
selecting all the docking solutions were a PDB code is given for
thrombin: echo
PDB_trypsin PDB_trypsin.list add_prop_sdf
-match PDB_trypsin -noskip -table PDB_trypsin.list
ranked_all_090606_3D.sdf ranked_all_090606_3D.PDB_trypsin.sdf
Start the script: gold_analysis.sh
-d /home/henricsn/combine2go/data/trypsin/pdb/all_ligands/ -file
ranked_all_090606_3D.PDB_trypsin.sdf