Hey,
Thanks, now it works fine!
/ Samuel
________________________________
Från: owner-amber.scripps.edu genom Thomas Cheatham III
Skickat: må 2008-03-17 17:51
Till: amber.scripps.edu
Ämne: Re: SV: AMBER: ptraj, hbond and non-bonded contacts
> 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?
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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Received on Fri Apr 18 2008 - 21:11:50 PDT
