Hi Sebastian,
Can you look through the mdout file(s) to see if any errors were printed
because that might provide insight as why the calculation failed?
Cheers,
Dwight
On Mon, Sep 11, 2017 at 4:46 AM, Sebastian Franco Ulloa <
s.franco1412.uniandes.edu.co> wrote:
> Good morning,
>
>
> my name is Sebastian Franco-Ulloa, and I was wondering if you could help
> me with an error I am getting while trying to run a MMPBSA calculation. I
> extracted a frame (in pdb format) from an MD simulation of a
> protein-DNA-ligand-solvent system. From that frame I generated 4
> structures: the complete solvated system, the system without ions and
> water, the receptor (protein and DNA), and the ligand. Then I used tleap to
> create prmtop files for these four structures, and it worked fine. The
> problem arises when executing the MMPBSA.py script. Apparently, it properly
> reads the topology and structure files, but when it starts the GB
> calculation it exits with the following error:
>
>
> CalcError: /PATH/sander failed with prmtop com.prmtop!
>
>
> com.prmtop is the topology file of the system without water and ions.
>
>
> I appreciate very much all the help you could provide me with.
>
> Best,
>
> Sebastian Franco Ulloa
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--
T. Dwight McGee Jr.
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Wed Sep 13 2017 - 22:30:02 PDT
