Re: [AMBER] error in hbond analysis

From: Jason Swails <>
Date: Fri, 6 Jun 2014 08:15:25 -0400

On Fri, Jun 6, 2014 at 2:51 AM, Arunima Shilpi <>

> Here for hbond analysis I used the following input file
> trajin md2.mdcrd
> donor :MET50.H

These masks are wrong. You can specify residue names OR residue numbers.
 But not both.

> donor :PHE453.H
> donor :GLY455.H
> donor :GLY457.H
> ​[snip]
> hbond distance 3.5 angle 120.0 includeself donor acceptor neighbor 2 series
> While running the command
> prtaj <>ptraj_hbond.out
> I got the following error
> PTRAJ: acceptor :ASP498.OD2
> WARNING in ptraj, acceptor: error in specification of res/atom selection

​This tells you that your acceptor mask did not match any atoms, indicating
there is a problem with your mask. The Amber manual has a description of
the mask syntax.

Also, it may be worth looking into the hbond command in cpptraj instead
(which typically eliminates the need to set a list of donors and
acceptors). This is described in the manual as well.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Jun 06 2014 - 05:30:02 PDT
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