Can anybody suggest tools for checking RMSD difference b/w docked ligand conformation and its native conformation in the co-crystallized form. For information, I have separated ligand from protein obtained from PDB(thus generating apoproteins) and redocked in Autodock Vina, thus generating .pdbqt files of docked ligand conformations (out.pdbqt). I have checked with PyMol and with it I can only visually compare the positional difference b/w native(x ray) and redocked (generated by software), but not able to get the quantitative RMSD value b/w them. Any suggestions?
ProFit might do what you want: http://www.bioinf.org.uk/software/profit/index.html
Profit does exactly what you are looking for, just don't use the server and download the software. It's for free: http://www.bioinf.org.uk/software/profit/index.html
On the other hand, the server should handle exactly what you need, provided you give the correct input. Just rename your structures to native.pdb and model.pdb and submit them. You can further specify zones of the alignment if you want to calculate more specifically the RMSD over a certain zone. For example, the following syntax tells profit to calculate RMSD only on the ligand, assuming chain A is the protein and chain B is the ligand:
zone A:A fit zone clear rzone B:B rms
This will give you two output values, the first for the first FIT command, which is the results of the RMSD only on chain A. The second output value is the value of the displacement over only the chain B, with the structures aligned on chain A.
You can also download and install the software to run locally: http://www.bioinf.org.uk/profit/
Finally, Pymol does give you a quantitative RMSD value. Click Escape after you've done the alignment and check the output for a line starting with RMS. Be careful though that for example, it does not like ligands with exotic names though! Profit should be your choice for this task.