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

From: Vlad Cojocaru <>
Date: Mon, 17 Mar 2008 12:00:41 +0100

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.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.CB
> acceptor mask :1827.CG2 :1827.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:* genom Thomas Cheatham III
> *Skickat:* to 2008-03-13 18:49
> *Till:*
> *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
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Received on Fri Apr 18 2008 - 21:11:39 PDT
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