Dear Dwight,
thank you for your response. Only one mdout file was written: __MMPBSA__complex__g.mdout.0
The error that is written in the end says:
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
FATAL: NATOM mismatch in coord and topology files
However, this seems a little strange to me because the topology was created with tleap from the pdb file I'm giving as input. I think you should know that the MD simulation was run in Gromacs, and then I took one frame (.gro) and converted it to .pdb to then use it with tleap and MMPBSA.py. The only thing I modified in the pdb files was that I added some lines with the keyword TER where the chains end (Gromacs always puts everything in one chain only). Could this be related to the error?
Again, thank you very much for the help,
Sebastian Franco-Ulloa
University of Los Andes
Bogotá, Colombia
________________________________
De: Dwight McGee <dwight.mcgee.gmail.com>
Enviado: jueves, 14 de septiembre de 2017 12:29:16 a. m.
Para: AMBER Mailing List
Asunto: Re: [AMBER] MMPBSA.py failing with topologies
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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 Thu Sep 14 2017 - 00:30:02 PDT
