Dear Concerned Forum-Member,
We have been studying ligand-receptor docking interactions using a chemotheraupeutic drug (ligand) and a DNA fragment (receptor). Starting from the pdb file for the receptor, and an sd file for the ligand, we made the docking in the starightforward (default) way, and then saved it as mol or mol2 file, then applied the Charmm force-field to the ligand-receptor complex. However the energy value for this complex is exactly same (to 5th decimal of kCal) with the energy value for the receptor alone, which means that the receptor and the said complex have been exactly the same, with the ligand remaining only as a sort of 'shadow' in the complex. So, dear vistor, how to get the ligand actually combined with the receptor and to get a non-zero interaction energy? Please advise! -- Rajib Lochan Sarma, India
We have been studying ligand-receptor docking interactions using a chemotheraupeutic drug (ligand) and a DNA fragment (receptor). Starting from the pdb file for the receptor, and an sd file for the ligand, we made the docking in the starightforward (default) way, and then saved it as mol or mol2 file, then applied the Charmm force-field to the ligand-receptor complex. However the energy value for this complex is exactly same (to 5th decimal of kCal) with the energy value for the receptor alone, which means that the receptor and the said complex have been exactly the same, with the ligand remaining only as a sort of 'shadow' in the complex. So, dear vistor, how to get the ligand actually combined with the receptor and to get a non-zero interaction energy? Please advise! -- Rajib Lochan Sarma, India
