[AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py

From: Senthil Natesan <sen.natesan.yahoo.com>
Date: Tue, 10 Jun 2014 08:22:38 -0700 (PDT)

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

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 !


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
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