[AMBER] H_bond

From: Thakur, Abhishek <axt651.miami.edu>
Date: Sun, 12 Feb 2017 16:22:13 +0000

Hi everyone,

I am bit confused, in my system I have a ligand bond to it.

I want to see that my ligand is forming Hydrogen bonds with which amino acids.

Can anyone suggest me how to do it? I am using cpptraj for this, I know how to see H-bond between all ligands,

Can any one help me in modifying my script?

trajin aMD_0_300ns.crd.gz
strip :WAT
strip :Cl-
hbond :1-339 out aMD_hb.out avgout aMD_hb.out

Should I just write my ligand number? instead of 1-339?

AMBER mailing list
Received on Sun Feb 12 2017 - 08:30:04 PST
Custom Search