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?
2. The prod1.mdcr.gz and prod2.mdcr.gz, prod3.mdcr.gz and prod4.mdcr.gz
must be uncompressed and join in one file?
3. How i can solve the problem, extra atoms are due the ions water or
other
4. Im trying run in parallel and in the MacOsx in both i have the same
issue.
[image: Imágenes integradas 1]
--
LBG Javier Alejandro Rendón Carrillo
Laboratorio de Investigación y Desarrollo
Tel. (044) 81-80-52-05-76
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Received on Tue Apr 08 2014 - 22:00:02 PDT
