There are two ways to assign atomic formal charges in MDL format. One is using the atom blocks (next to each atom) and another is using the CHG block at the end of atom blocks. Rdkit uses CHG block to record atomic formal charges, which is ignored in RxDock. I added a code that read CHG block properly. See line #198-218.
Can you point me where I can find more information regarding scoring function terms ends with ".0"? For example, there are two terms named rxdock.score.intra.diheral and rxdock.score.intra.dihedral.0. They have different scores and I am wondering how these two terms are different from one another.
Can you point me where I can find more information regarding scoring function terms ends with ".0"? For example, there are two terms named rxdock.score.intra.diheral and rxdock.score.intra.dihedral.0. They have different scores and I am wondering how these two terms are different from one another.
There was a few formatting issue when I tried to use scoring function with solvation. I have fixed it and attached the files below.
Hi, I have a big ligand and lots of rotatable bonds, however, many of these rotatable bonds are hydroxyl group that is involved in intra hydrogen bonds. I'd like to remove them from conformational sample. Is there a way to do that?
Hi, I have a big ligand and lots of rotatable bonds, however, many of these rotatable bonds are hydroxyl group that is involved in intra hydrogen bonds. I'd like to remove them from conformational sample. Is there a way to do that?