Dear Colleagues,
I am running MD simulations of Zn containing protein-peptide complexes
using Cation-Dummy atom approach, with FF provided by Dr. Pang. The
initial 5 ns simulations look good and I am wondering what additional
inputs to be provided in order to run free energy calculations using
MMPBSA.py
I just followed the usual method hoping that the prmtop files should
provide all necessary FF parameters, but the system fails to recognize
Zn atom, as it gives the following error.
------------------------
bad atom type: Zn
------------------------
I could not find any useful input by browsing through the earlier messages discussed in this direction.
Any help would be sincerely appreciated !
Thanks,
Senthil Natesan, PhD
Dept. of Pharmaceutical Sciences,
Albany College of Pharmacy and Health Sciences,Colchester, Vermont 05403
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Received on Tue Jun 10 2014 - 08:30:03 PDT
