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
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