Re: [AMBER] Regarding area calculation of protein cavity

From: Dr. Anselm Horn <>
Date: Thu, 28 Oct 2021 13:19:47 +0200


maybe the command 'nativecontacts' in cpptraj does what you want?
Just have a look into the Amber manual.

Best regards,


Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)

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.
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Thu Oct 28 2021 - 04:30:02 PDT
Custom Search