AMBER Archive (2008)

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

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Mon Mar 17 2008 - 11:51:54 CDT

> 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?

I just tested this and the problem is that the default angle criteria is
blocking matches from being found; disable the angles by specifying

  angle -1.0

hbond series test out hbond.dat distance 10.0 angle -1.0

-- tec3

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