There are just a few examples of such things being published in the
literature, for example the DE Shaw group. I suggest reading their methods
and seeing what was done. Expect it to take vast computational resources
unless you use biasing restraints. A good place to start is to look at
experimental binding rates for your target, and evaluate whether you can do
multiple replicas for that timescale.
On Mar 25, 2016 10:25 AM, "Arnoult, Eric [JRDUS]" <EArnoult.its.jnj.com>
wrote:
> 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 - 08:00:05 PDT
