Dear Kenneth,
Thank you for the answer, that problem has been solved. There is a new
problem which is the output file of my per-residue decomposition, I am not
sure which value is corresponding to which term. I have tried csv_format =
1, in the mmgbsa inputs but doesn’t seem to work out. I attached the output
file. will be great if you advise.
Regards,
Maryam
On Thu, Apr 9, 2015 at 11:40 AM, maryam azimzadehirani <
maryamai1988.gmail.com> wrote:
> Dear All,
> I am trying to run per-residue free energy decomposition for a ligand (46
> a.a) using Amber12. But I got this error which argues with my non solvated
> complex topology file:
>
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> sander found! Using /usr/local/packages/amber12/amber12/bin/sander
> mmpbsa_py_energy found! Using
> /usr/local/packages/amber12/amber12/bin/mmpbsa_py_energy
> cpptraj found! Using /usr/local/packages/amber12/amber12/bin/cpptraj
> Preparing trajectories for simulation...
> 10 frames were processed by cpptraj for use in calculation.
>
> Beginning PB calculations with
> /usr/local/packages/amber12/amber12/bin/sander
> calculating complex contribution...
> *CalcError: /usr/local/packages/amber12/amber12/bin/sander failed with
> prmtop structure_no_wat.parm7!*
>
> will you guide me how to fix this problem?
> I attached the input and the parm file.
> Best Regards,
> Maryam
>
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Received on Thu Apr 23 2015 - 00:30:02 PDT
