Dear Prof David Case
I'm so thankful for reply.
Could you please an additional answer, if the ligand is covalently bonded with a cofactor such as FAD. Can i use ligand-FAD conjugate as a ligand coordinates input file in tleap. Next prepare complex between protein and ligand-FDA conjugate and proceed in similar way to simple md simulation process of non covalent bonded protein-ligand complex.
Best regards
Sincerely yours'
Professor, Ph.D, (Full) Dr. Awwad A. Radwan
(Current address: Pharmaceutical Technology center, Fac of Pharmacy, King Saud University, Al Ryiadh, Kingdom of Saudi Arabia, Office : +966-046-70562 Mob. 0505193925)
(Home country address: Dept of Org Pharm Chemistry, Faculty of Pharmacy, Assiut University, Assiut, Egypt. Home Tel +2088-292164 Office Tel +2088-411326 Fax +2088-332776 Mobile 0103-716131)
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Saturday, April 10, 2021 1:14 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Apply Lennar-Jones potential between small molecules
On Fri, Apr 09, 2021, A R wrote:
>
>I have an inhibitor ligand that interact covalently linked with the protein.
>The free ligand has propargyl fragment that is responsible for bonding to
>the protein through addition reaction on the triple bond.
>
>How I prepare starting coordinates and topology files using tleap and at
>same time consider this type of covalent bonding interaction between ligand
>and protein.
This is indeed an advanced type of problem. The approach I would take is to
create a modified residue that contains the proper covalent linkage.
Tutorial 5.3 is pretty close to what you want to do, so start with that.
But that is a fairly complex chromophore (for green fluorescent protein).
I'm hoping we can get someone to donate or create another amino acid
modification tutorial soon.
....dac
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Received on Sat Apr 10 2021 - 05:30:03 PDT
