I have a ligand pdbqt file (with docking co-ordinate) which I converted to mol2 file to generate a .str file. However, in the .str file, the penalty scores were more than 50 (param penalty= 333.000 ; charge penalty= 417.066 ).
In order to cross-check, I uploaded another inhibitor structure extracted directly from a crystal structure PDB file. This time also the penalty scores were greater than 50 (param penalty= 155.000 ; charge penalty= 63.231). This was a bit puzzling to me. As the structure is experimentally driven, I expected the scores to be below 50 at the very least.
Should I proceed with the current molecule to generate topology or should I need to minimize the structure? Minimization, however, changes the conformation and therefore I cannot start with the docking co-ordinate of the ligand. Furthermore, I have done minimization in Avogadro ( uff force field) and redid the entire process but the penalty scores did not change. Also, how can I optimize the ligand to reduce the penalty score?
Hello ffTK and FFParam, and if anybody knows a software towards reparametrization thats Mac-compatible feel free to reply (ffTK and FFParam are not), thanks:)
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