AMBER Archive (2008)

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

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Mon Mar 17 2008 - 06:00:41 CDT

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 ?

Vlad

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,
> Samuel
>
>
> ------------------------------------------------------------------------
> *Från:* owner-amber_at_scripps.edu genom Thomas Cheatham III
> *Skickat:* to 2008-03-13 18:49
> *Till:* amber_at_scripps.edu
> *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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-- 
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Dr. Vlad Cojocaru

EML Research gGmbH
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Tel: ++49-6221-533266
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

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