the ligand force field parameters would be as good for unbound as bound, in
principle.
however implicit solvent might not be accurate for the complex, see some
recent work by Onufriev's group
https://www.ncbi.nlm.nih.gov/pubmed/29378399
On Fri, Jan 3, 2020 at 1:09 PM Madhur Aggarwal <
madhur.aggarwal.research.iiit.ac.in> wrote:
> Hi all,
>
> I want to run NEB on a protein+drug system, where my one end state is drug
> bound to the protein (state 1) and the other end state is drug unbound
> (away) from the protein (state 2).
>
> I am following Amber tutorial on Antechamber to generate drug parameters
> using gaff2 forcefield. This essentially means I am isolating my drug and
> generating it's .mol2 file, which is then being used to generate .frcmod
> and .lib files.
>
> I am using implicit solvent for my simulations, so the parameters I
> generated by using the method I described above should work fine for my
> state 2 (where the drug is isolated and away from the protein). But I am
> worried if it is correct to use these parameters for state 1 as well
> because the drug environment changes in state 1.
>
> I would like to know the thoughts of the amber community on this, what is
> recommended to be done? Is it fine if I go ahead with the same parameters
> for state 1 as well? If not, how can I generate correct drug parameters in
> a protein surrounded environment?
>
> Thanks,
> Madhur Aggarwal
> IIIT Hyderabad
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Received on Fri Jan 03 2020 - 10:30:02 PST
