The charges and other parameters should not be related to the coordinates.
Please share the full details of how you build the system in tleap. Is the
ligand properly bound in the input pdb?
On Wed, Jul 12, 2023, 3:04 AM fateme haghighi via AMBER <amber.ambermd.org>
wrote:
> Dear all,
>
> I am using Ambertools to produce topology's files for MD simulation with
> gromacs.
> The problem I faced is that for Pfizer Covid inhibitor with nitrile bound
> and Main protease of SARS-Cov-2.
> The molecule lies into the binding pocket with docking, but when I use the
> gro file produced by Ambertools, it does not stick at the same binding
> pocket.
> When I use RESP charges, the molecule is far from the protein but with
> AM1BCC charges, it is near the binding pocket but yet not at the binding
> pocket. I have the same problem with another molecule: Isoharmnetin.
> Do you have any suggestion to resolve that problem?
>
> Thank you in advanced
>
>
>
>
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Received on Wed Jul 12 2023 - 04:00:02 PDT
