It is a popular problem in molecular physics in general, (and MD simulations in particular) that we want to overlay a energy-minimised structure with it’s starting structure. It can be further generalized to say that the problem is to overlay two atomic structures of sufficient similarity written in ‘.pdb’ format. This is due to the fact that energy minimization algorithms generally shift the Cartesian co-ordinate of the resultant structure; and as we might want to prepare the system as close to the experimental minima/crystallographic data with the ligand in a minimised state. Here I have written a short perl code to do the same. The general scheme is a brute-force RMSD alogorithm to match center of mass of selected atoms and choose the lowest RMSD value. A minimum of 5-7 atoms are required for the best matches. Also the resulting structure may have a smaller or larger number of atoms as long as the same atoms are matched properly. This is useful for example when you have to add hydrogen atoms to the experimental pdb structure and superimpose the resulting structure, or when yo delete a few side groups to a fit a smaller structure.

In this example given below we superimpose a larger ligand on a smaller ligand based on matching of 7 atoms as mentioned in the file “input.txt”. A ligand with 46 atoms is superimposed on the smaller 24 atom ligand

Step 1 : Select two PDB files of interest, with n common atoms.
Step 2 : Edit “input.txt” to point out the common atoms in both the system. RMSD is computed over the given atoms hence increasing the number increases the accuracy.
Step 3 : Edit the ‘rmsdtranslate.pl’ programme to accommodate the ‘FROM’ and ‘TO’ ligands.
Step 4 : Run perl rmsdtranslate.pl (In command line from current directory)
Step 5 : See result file ‘translate_NEWPDB.pdb’ and check with vmd or pymol.

Files :

1. crf46.pdb – Minimised molecule that has to be superimposed.
2. crf24.pdb – Initial molecule on which crf46 is superimposed.
3. input.txt – File connecting atom details common to both the system.
User should edit this file for there own system.
4. rmsdtranslate.pl – Perl code. user should edit input pdb file names accordingly.