I have simulated the protein-ligand system by using the Gromacs force-field 43a1 after obtaining the docking results for semi-flexible and flexible docking.
My ligand is a steroid, and they only work related to this published have used amber package, which is not free.
Can I continue my analysis by using this Gromacs 43a1 force-field?
Usually in case of protein is better to use opls-AA FF that is optimized for aminoacid.
You can try using GROMOS 53a6 force field. Its quite good for protein-ligand system. You must include ligand position constraint to the system.
The AMBER force field can be used with GROMACS (and it is included in the standard distribution), so you do not need to use the AMBER package if all you need is the same force field. It is usually considered among the best force fields for protein molecular dynamics.
The GROMOS force fields are generally considered (from what I've heard from many, many users: I didn't compare them myself) to be not as good as AMBER, but they can be useful nonetheless.
What is critical however is the *parametrization* of your ligand. It has to be consistent with the force field you use and it has to be of good quality. Therefore your choice of force field will depend on how you can parametrize your ligand. Do you already have a known, good topology for the ligand? If yes, use the force field compatible with that topology. If not, look around to create an AMBER or GROMOS compatible ligand topology (I am unaware of tools able to create OPLS-friendly topologies but they may well exist).
You can use Amber force field with GROMACS.
For ligand parameters, you can use General Amber Force Field parameters. AmberTools is free, and you can use this package to generate both parameters and charges of ligand. Then, you can convert Amber format topology to Gromacs format topolgy. Acpype (https://code.google.com/p/acpype/) will be useful for this conversion.
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