We want to simulate a protein-cabohydrate complex at various pH ranging from 6.8 to 7.4.
Can we do this on Gromacs?.
Do we have to simulate complex at different constant pH or the system will vary pH itself during simulation?
If simulating complex at various constant pH do we have to decide the protonation states of amino acids first then dock the carbohydrate?
Or can we decide the protonation states after docking?
Is there any alternative to Gromacs for this type of study?
I believe you can't perform simulation at different pH in GROMACS directly, you would have to change the protonation states by using gmx pdb2gmx in GROMACS.
If we perform it at different constant pH for various pH simulations do we have to protonate the protein first then dock the carbohydrate with it? Or can we just protonate the docked complex?
I never tried it on GROMACS, but the protonation state can also be changed using H++ server, which is a step in Ambertools MD simulation.
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