25 November 2016 3 8K Report

I want to run a MD of a protein in presence of a small molecule by using gomacs software also want to apply GROMOS 53A6 forcefield. But parametrization is a problem for me.  I have already tried PRODRG but it is not working currently and ATB is quite slow. So i am asking for help by which i can build a topology file. I am also asking after getting topology file should I process it by some other software or i can directly use this for MD simulation by gromacs

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