Re: AMBER: hbond analysis in ptaj/carnal

From: Thomas E. Cheatham, III <>
Date: Thu, 26 May 2005 11:05:00 -0600 (Mountain Daylight Time)

> I would like to use the O1P/O2P...H(wat) distance
> and O1P/O2P...H-O(wat) angle to restrict the
> search for H-bonds.
> =========
> 1. The distance cutoff in Amber is defined with
> the help of the heavy atoms distance, not
> with the H-bond distance.

I do not understand why you need the distance to the hydrogen (assuming
the angle cutoff works). Also note that the cutoff value in part will
determine the results (i.e. we really should not be using a cutoff here
but calculate a distribution).

> 2. The angle definition in Amber doesn't correspond
> to the standard H-bond angle definition.
> In ptraj/carnal, the angle is defined as H-DONOR-ACCEPTOR. However, the
> standard definition

In ptraj the cutoff angle refers to donor -- acceptorH -- acceptor (as I
now remember by going through the AMBER WWW google search of ptraj hbond
in the archives where I found my old e-mail on the subject). If you have
a linear h-bond, this angle will be 180. With a cutoff of 120, the angle
formed must be greater than this. However, for some reason the angle
stored is 180.0 - angle such that a linear h-bond would be zero and
therefore a value of ~30-40 deg is a reasonable h-bond.

> 1. Is there any way in Amber how to get
> a hydrogen bonding statistics using the
> the H-bond distance and the DONOR-H-ACCEPTOR
> angle as geometry criteria for hydrogen bonding?

Yes, ptraj.

> 2. If there is no way haw to treat the
> problems 1 and 2 at the same time, is it at least
> possible to overcome one of the two problems?

I still do not understand why you need the h distance. The code could be
altered to allow this.

> 3. I am not sure about the definitions od the
> DONOR and ACCEPTOR in ptraj and carnal.
> In ptraj, DONOR seemes to be defined as a lone pair
> donor, while in carnal DONOR seems to be
> defined as a donor of the hydrogen atom.
> It would mean that a DONOR in ptraj is
> actually an ACCEPTOR i carnal and vice versa,
> am I right?

Yes, ptraj is funny. When I wrote it, I assumed the donor/acceptor
referred to the lone pairs (kind of a Lewis definition) rather than a
hydrogen donor or acceptor. So yes, ptraj donors are single atom electron
pair donors; acceptors are two atoms...

For DNA, like you are looking at, I often use the appended script. Note
that this is extremely memory intensive (if you have a lot of frames) such
that you may be wise to break it up into separate runs for backbone/sugar,
minor and major grooves... If you want tight h-bond criteria,

  cutoff 3.2 angle 120.0

The prnlev commands (from 3 then to 0) show the detailed selection process
for each atom.

Try it out and see if you are getting what is expected.


trajin mdcrd

center :1-12 mass origin
image origin center
center :1-24 mass origin
image origin center
rms first mass out rms :1-24

prnlev 3

# backbone + sugar
donor mask .O1P
donor mask .O2P
donor mask .O3'
donor mask .O5'
donor mask .O4'

acceptor mask :12.O3' :12.H3T
acceptor mask :24.O3' :24.H3T
acceptor mask :1.O5' :1.H5T
acceptor mask :13.O5' :13.H5T

# minor groove
donor DG N3
donor DG5 N3
donor DG3 N3

donor DA N3
donor DA5 N3
donor DA3 N3

donor DC O2
donor DC5 O2
donor DC3 O2

donor DT O2
donor DT5 O2
donor DT3 O2

acceptor DG N2 H22
acceptor DG3 N2 H22
acceptor DG5 N2 H22

# major groove
donor DG O6
donor DG5 O6
donor DG3 O6

donor DG N7
donor DG5 N7
donor DG3 N7

donor DA N7
donor DA5 N7
donor DA3 N7

acceptor DA N6 H62
acceptor DA3 N6 H62
acceptor DA5 N6 H62

donor DT O4
donor DT5 O4
donor DT3 O4

acceptor DC N4 H42
acceptor DC3 N4 H42
acceptor DC5 N4 H42

prnlev 0

hbond series hbond out hbond_wat.out \
   solventdonor WAT O \
   solventacceptor WAT O H1 \
   solventacceptor WAT O H2 \
   time 1.0 angle -1.0 distance 3.5

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Received on Thu May 26 2005 - 18:53:00 PDT
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