I was looking more for the area measurements similar to the surf command.
If the ligand is considered as residue 1, the area it covers in the pocket
with respect to the amino acids.
On Thu, 28 Oct 2021 at 4:50 PM, Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> Athena,
>
> maybe the command 'nativecontacts' in cpptraj does what you want?
> Just have a look into the Amber manual.
>
> Best regards,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
> Am 28.10.2021 um 13:12 schrieb Athena N:
> > Hi,
> >
> > I have two different ligands binding to same pocket of protein spanned
> by 4
> > amino acids. The second ligand lose some contacts with the amino acids.
> One
> > ligand is a core molecule and the second has a bulkier side chain. I want
> > to know if it possible to get the area occupied by the ligand1 and ligand
> > 2. Kindly help.
> >
> >
> > Thank you in advance.
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>
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Received on Thu Oct 28 2021 - 08:00:02 PDT
