Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using

From: Senthil Natesan <>
Date: Tue, 10 Jun 2014 08:57:51 -0700 (PDT)

Thank you Jason.

I am running GB, PB and NMode analysis as well.

The input file is:

 startframe=50, endframe=99999, interval=100,
 igb=5, saltcon=0.150,
 nmstartframe=50, nmendframe=99999, nminterval=100,
 maxcyc=50000, drms=0.0001,

I submitted the job with the following input command: -O -i  -o mmpbsa.out -sp complex_solvated.prmtop -cp complex.prmtop -rp protein.prmtop -lp peptide.prmtop -y complex_solvated_prod1.mdcrd complex_solvated_prod2.mdcrd

The calculation ran successfully for the ligand (peptide), but failed for both complex and receptor as both contains Zn. The error message is

Error: No potential terms in sander output ! Check output files.

My understanding is that the input solvated and non-solvated prmtop files have the necessary FF parameters for Zinc. Isn't the case?

Please let me know how to provide the missing information.


Senthil Natesan

On Tuesday, June 10, 2014 11:41 AM, Jason Swails <> wrote:

On Tue, Jun 10, 2014 at 11:22 AM, Senthil Natesan <>


> 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.

Exact input files and output messages would help us provide targeted help.
(Was this GB?  PB?  sander?  mmpbsa_py_energy?)

This error message occurs because implicit solvent parameters (whether for
computing surface areas for nonpolar free energies or for computing the
location/shape of the dielectric boundary) are not typically determined for
metal ions.  So the solution is to find what part of the calculation
requires the definition of the Zn atom type and provide a value for the
radius (and recompile).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jun 10 2014 - 09:00:03 PDT
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