I don't think that would work, the atoms that were previously bonded will
likely have very high steric repulsion if they are at the distance
corresponding to the bond.
can you explain what you are trying to compare to in terms of experimental
measurements?
On Mon, Apr 26, 2021 at 3:58 PM Hector A. Baldoni <hbaldoni.unsl.edu.ar>
wrote:
> Dear ambers experts,
>
> I want to run the mm-pb(gb)sa analys over a serie of inhibitors
> covalently bonded to the same Cys-Ezyme. It would be possible to delete
> all the bonded parameters associated to the covalent bond using parmed
> to account the Ez and INH dG energy contributions ?, which parmed
> commands I must to use ?
>
> Thank you for the help!!
> H.A.Baldoni
>
>
> --
> --------------------------------------
> Dr. Hector A. Baldoni
> Profesor Titular (FQByF-UNSL)
> Investigador Adjunto (IMASL-CONICET)
> Area de Quimica General e Inorganica
> Universidad Nacional de San Luis
> Chacabuco 917 (D5700BWS)
> San Luis - Argentina
> hbaldoni at unsl dot edu dot ar
> Tel.:+54-(0)266-4520300 ext. 6157
> --------------------------------------
>
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Received on Mon Apr 26 2021 - 13:30:02 PDT
