From: jing liang (
Date: Mon Mar 09 2020 - 10:37:34 CDT


I am dealing with a small molecule for which I wrote a charmm topology
file. Then,
I uploaded the small molecule pdb file and the topology file I created.
After that,
I checked the structure and the option for topology was green. However,
the preparation phase I got the following message:

Error during structure preparation: Autopsf error ERROR: failed on end of
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over..

Do you know what is the issue? I have created the topology file for the
molecule only but I haven't added the proper values in the parameter file
I don't have them, for instance force constants, dihedrals, etc. I guess
values will be ignored if I do a QMMM simulation where the small molecule
is in
the QM region right?