(unknown charset) Re: SV: AMBER: ptraj, hbond and non-bonded contacts

From: (unknown charset) Thomas Cheatham III <tec3.utah.edu>
Date: Mon, 17 Mar 2008 10:51:54 -0600 (Mountain Standard Time)

> 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 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 . 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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Apr 18 2008 - 21:11:44 PDT
Custom Search