Thanks Marcos
I was not clear in my message.
I do not want to dock the compound to the protein. I just want to place my compound at a random place near the protein and let him find its way to the binding site. Replicas simulation would provide me some confidence about what could be the putative binding pathway, binding mode.
Thanks
Best regards
-----Original Message-----
From: Marcos Serrou do Amaral [mailto:marcossamaral.gmail.com]
Sent: Tuesday, March 22, 2016 10:41 PM
To: AMBER Mailing List
Subject: Re: [AMBER] set up for a binding event MD
On Fri, Mar 18, 2016 at 2:02 PM, Arnoult, Eric [JRDUS] <EArnoult.its.jnj.com
> wrote:
> Have your tried using leap to place a ligand at different distances
> from its target? How to do it?
Dear Eric,
I don't know if it is possible to bind a ligand into a protein using leap.
But, recently, I needed to place a small peptide covalently bond to a large molecule. For that, I could figure out using Chimera program. It was a visual procedure and I only used one set of coordinates for "ligand".
HTH
---
Marcos
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Received on Fri Mar 25 2016 - 07:30:03 PDT
