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: owner-amber.scripps.edu genom Thomas Cheatham III
Skickat: to 2008-03-13 18:49
Till: amber.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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Received on Fri Apr 18 2008 - 21:11:39 PDT
