Re: [AMBER] Hydrogen bond analysis problem

From: Daniel Roe <>
Date: Wed, 18 Sep 2013 09:16:51 -0600


On Wed, Sep 18, 2013 at 3:50 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09
<> wrote:
> acceptor mask :196.H :374.N1
> acceptor mask :210.HH12 :374.O1
> acceptor mask :210.HH11 :374.O2
> acceptor mask :98.H :374.O4

The 'acceptor mask' expects the heavy atom first, so you should have:

acceptor mask :374.N1 :196.H

etc. The ordering will affect how the angle is calculated.

> PTRAJ: donor mask :LEU198.O
> Mask [:LEU198.O] represents 0 atoms !!!NO ATOMS DETECTED!!!
> WARNING in ptraj, donor: No atoms selected (:LEU198.O), ignoring...

This is not a valid mask. You probably just want ':198.O'.

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Sep 18 2013 - 08:30:03 PDT
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