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
Anu Manhas
use antechamber that can be found in AMBER tools, SwissParam
http://ambermd.org/#AmberTools
http://swissparam.ch/
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Batsaikhan Mijiddorj
SwissParam generates charmm27 force field, it could not give GROMOS 53A6 forcefield. maybe ATB is better to use.
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