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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Received on Thu Oct 28 2021 - 04:30:02 PDT
