When i try to dock ligands containing chlorine, bromine, Selenium etc. (elements containing lower case letters), the resulting atom gets converted from Cl to CL and the interactions change accordingly. When hydrogen bond interactions become essential, this causes a serious problem. Does anybody know probable solution to this error?
Autodock has nothing to do with the case sensitivity of atom nomenclature. It just uses the input (AD4_paramets.dat) which is required to recognize atoms in the pdbqt file of receptor or ligand. Look at the contents of attached file. I don't think the conversion from Cl to CL is an error. I suggest to use some other visualization programs to understand distance dependent interactions between ligand and surrounding residues.
- Badges
- Science topic
- Similar topics
- Mathematical Sciences
- Graphs