AMBER Archive (2008)

Subject: SV: SV: AMBER: ptraj, hbond and non-bonded contacts

From: Samuel Genheden (a03samge) (
Date: Mon Mar 17 2008 - 07:00:52 CDT

Hello, Vlad
No, there's no typo. The accepor mask should have two atom masks and since I want to keep track of non-bonded contacts I have been recomended to specify the hevay atom twice. This should exclude the angle from the calculation and hence I'm specifying the :1827_at_CG2 twice.
/ Samuel


Från: genom Vlad Cojocaru
Skickat: må 2008-03-17 12:00
Ämne: Re: SV: AMBER: ptraj, hbond and non-bonded contacts

Hi Samuel,

I had the same problem and still didnt solve it. It seems to be a bug there or something about the syntax of the hbond command that is not written in the AMBER manual. So I dont think you are doing anything wrong. Lets see if anybody else has experienced this and managed to fix it.

Just to make sure ... the double printing of ":1827_at_CG2" in the acceptor mask is just your typing error, isnt it ?


Samuel Genheden (a03samge) wrote:

        Hello, again
        I've tested to specify the heavy atom twice but it does not seem to work for me. Here is my test input:
        trajin ../mdcrd 31 1270 1
        donor mask :403_at_CB
        acceptor mask :1827_at_CG2 :1827_at_CG2
        hbond distance 10.0 time 1.0 series test
        I know 10 Å is crazy for a threshold but this is just for debuging. So then I give this to ptraj and it process everything ok. It finds the masks and start accumulate the hbond data, but when it should dump all hydrogen bond information for occupancies > 0.00 this list is empty!
        I checked the distance between the two atoms by using the "distance" action and found that in average it was about 3.9 Å. So it should be well inside the threshold for the most of the time. Any suggestions? What am I doing wrong?
        Best regards,


        Från: genom Thomas Cheatham III
        Skickat: to 2008-03-13 18:49
        Ämne: Re: AMBER: ptraj, hbond and non-bonded contacts

> For the hydrogen contacts it is easy, I just use ptraj and the hbond facilities and it works fine.
> But how about the non-bonded contacts. Is it possible to use the hbond
> facility even for these contacts? As I see is the only problem how to
> define the acceptor atom. The acceptor command requires an hydrogen and
> the heavy atom which it is bonded to. Now I have carbons contacts that I
        The best solution is to specify the heavy atom twice; this ignores the
        angle so you simply get the contacts.
        acceptor ALA CB CB
        -- tec3
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Dr. Vlad Cojocaru

EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg

Tel: ++49-6221-533266 Fax: ++49-6221-533298


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