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 - 00:30:02 PDT
