On Tue, Apr 8, 2014 at 11:47 PM, Javier Alejandro Rendon Carrillo <
biotecnologo.rendon.gmail.com> wrote:
> Hi everyone,
>
> Im trying to run an mmpbsa calculations with the python script.
>
> I want to use the complex (protein-DNA) as complex obviously,
> protein as receptor, and DNA as ligand i have previously run out the
> simulations, the command line i been using is the next one
>
> *$MMPBSA.py.MPI -O -i mmpbsa.in <http://mmpbsa.in> -o
> FINAL_RESULT_MMPBSA.dat -sp complexwat.prmtop -cp complex.prmtop -rp
> protein.prmtop -lp adn.prmtop -y prod*.mdcrd > progress.log 2>&1*
>
>
> And the mmpbsa.in is the next file
>
> Input file for running PB and GB
>
> &general
>
> endframe=50, verbose=1,
>
> # entropy=1,
>
> /
>
> &gb
>
> igb=2, saltcon=0.100
>
> /
>
> &pb
>
> istrng=0.100,
>
> /
>
> I use complexwat.prmtop as the complex solvated and ions added , the
> complex.prmtop is the complex (protein-DNA), -rp is the protein and the
> ligand is the DNA -lp, and i get this error.
>
>
> *Reading command-line arguments and input files...*
>
> *Loading and checking parameter files for compatibility...*
>
> *PrmtopError: Complex natom != receptor natom + ligand natom*
>
> *Exiting. All files have been retained.*
>
> *application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0*
>
>
> 1. That means that the complex.prmtop file have not the same atom
> numbers as the sum between protein.prmtop atoms and and.prmtop atoms?
>
Correct.
> 2. The prod1.mdcr.gz and prod2.mdcr.gz, prod3.mdcr.gz and prod4.mdcr.gz
> must be uncompressed and join in one file?
>
No. You can use them as-is.
> 3. How i can solve the problem, extra atoms are due the ions water or
> other
>
You can use ParmEd to remove any extra atoms from either topology file if
you know what is causing the problem. Ultimately you need to make sure
that you make the topology files correctly in the first place.
> 4. Im trying run in parallel and in the MacOsx in both i have the same
> issue.
>
This is a problem with your topology files, so it doesn't matter how you
try to run it will raise this error.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 09 2014 - 03:30:02 PDT
