Script-for-QMMM-Simulation

Introduction:

Create a bridge between gromacs and cp2k for QMMM simulation is my main purpose all the time and this script QM.sh can realize QMMMM Simulation topology file creation from our initial protein Structure, which as follows are some tips when you run this QM script:

1.The topology file of the micromolecule

when you have already generate the .rtp file of the organic molecule, you'd better modify the file residuetypes.dat which is in your gromacs path /share/gromacs/top,and on the other hand, we also need to add our micromolecule's atomtypes which was produced by the ztop.py (reference link: http://bbs.keinsci.com/thread-22171-1-1.html) script to the atomtypes.atp in our own forcefields.

2.The RESP charge modification

Our script includes the RESP.h and you can call this script in anytime, so in order to achieve this target, you'd better set these environment variables just below:

    export PATH=$PATH:/home/szk/software/coordmagic
    export KMP_STACKSIZE=200M
    ulimit -s unlimited
    export Multiwfnpath=/home/szk/software/Multiwfn
    export PATH=$PATH:/home/szk/software/Multiwfn
    export PATH=$PATH:/usr/local/plumed/bin
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/plumed/lib
    export PATH=$PATH:/home/szk/software/cp2k/exe/local
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/szk/software/cp2k/lib/local/pdbg
    export PATH=$PATH:/usr/local/gromacs/bin
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/gromacs/lib
    export g16root=/home/szk/software
    export GAUSS_SCRDIR=/home/szk/software/g16/scratch
    source /home/szk/software/g16/bsd/g16.profile
    export AMBERHOME=/home/szk/Downloads/amber20_src
    export PATH=$PATH:$AMBERHOME/bin
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$AMBERHOME/lib
    source /home/szk/software/amber20/amber.sh

and your home path can be replaced by your own path, that's a easy operation :D reference link: (http://sobereva.com/multiwfn/)

3.Some existing problems

Still need to modify some little bugs when combining the pdb file of micromolecule and protein, because of the different atom type such as "O1", Secondly, some path settings are still needed to be improved later.

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