If all you want is to see intermolecular hydrogen bonding just add the
'nointramol' keyword to omit intramolecular hydrogen bonds.
-Dan
On Sun, Feb 12, 2017 at 11:22 AM, Thakur, Abhishek <axt651.miami.edu> wrote:
> 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?
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Feb 13 2017 - 12:30:02 PST
