Hi there,

I am about to make a homology model of a protein with a bound substrate molecule. I would like to consider electrostatic interactions during the model refinement which means that I need a topology file for the substrate.

Is somebody aware of a program that can create a charmm top file for a small organic molecule starting from the pdb file? I know that Quanta can do this but don't have access to this program. I am looking for a non-commercial program.

Thanks in advance!

Best,

Oliver

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Oliver Hucke (PostDoc) Biomolecular Structure Center Dept. of Biochemistry University of Washington Health Sciences Building K-418C 1959 NE Pacific Ave Seattle, WA 98195 T:(206)685-7046 _______________________________________