Dear SIRs
Could you please answer?
I use amber20 under ubuntu 18.04.
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.
Are there any script or step by step tutorial that help learning this.
Great thanks
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: Thursday, March 18, 2021 2:51 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Apply Lennar-Jones potential between small molecules
On Thu, Mar 18, 2021, Carlos Simmerling wrote:
>do you have iwrap=1 in your simulation?
Following up on Carlos' question: There are *very* few places where iwrap=1
is the right thing to do.
I'm thinking that we should update the codes so that users who want this
option also have to put "yesIreallywanttouseiwrap=.true." in their input
files to get it to be turned on.
Some person wanting a "gold star" could look through the tutorials to see if
we ever recommend that option.
....dac
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Received on Fri Apr 09 2021 - 10:00:03 PDT
