Re: [AMBER] Non-polar solvation free energy in AMBER11

From: Ray Luo, Ph.D. <>
Date: Thu, 11 Oct 2012 14:25:38 -0700

Dear Tong,

One thing to keep in mind is that inp=2, i.e. the approach separating
the nonpolar solvation energy into the dispersion and cavity terms,
only works for standard Amber atom types, i.e. those in upper cases,
not those with GAFF types ...

I'm not sure whether your error was due to this. If you want, please
email me, off the list, your detailed input, prmtop, and output files,
so we can take a look.

All the best,

On Wed, Oct 10, 2012 at 11:55 PM, Tong Zhu <> wrote:
> Dear everyone,
> Thank you very much for your time. I have a protein-ligand structure in
> which the ligand are coordinate with a zinc ion in the protein, and I
> want to calculated the binding free energy of this system. I have both
> AMBER12 and AMBER11.
> However, strangely, the in AMBER11 can work with this
> structure, but which in AMBER12 can not, Would you please give me some
> advice to find the reasons?
> The error information of amber 12 is :
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> ValueError: unsupported format character 'V' (0x56) at index 10
> Exiting. All files have been retained.
> I addition, If I use AMBER11 in my calculation, how can I use the
> (INP=2) option? I want the non-polar solvation free energy is modeled as
> two terms: the cavity term and the dispersion term.
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Received on Thu Oct 11 2012 - 14:30:03 PDT
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