Hi,
On Tue, Feb 5, 2013 at 6:07 AM, DEBOSTUTI GHOSHDASTIDAR
<debostutighosh.gmail.com> wrote:
> When I followed that, however, I did not get any
> output, although I know there is interaction between the two atoms.
>
> Here's my input:
>
> donor mask :1.O1P
> acceptor lig N13 N13
Is your residue name really "lig"? I only ask because it's unusual to
have an all lower-case residue name and residue selection is
case-sensitive.
If you're certain that an N13 atom in "lig" comes within 3.5 Ang. of
:1.O1P (maybe from a prior distance calc?), I would suggest you re-run
ptraj on a small subset of frames with the print level set above 0
(i.e. "prnlev <N>") to make sure your atom selections are being read
properly and to give you some more info as to what ptraj is doing,
e.g.:
trajin mdcrd 1 10
prnlev 3
donor mask :1.O1P
acceptor lig N13 N13
hbond distance 3.5 time 2 series PO_lig out PO_lig.dat
Good luck,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Feb 05 2013 - 07:30:05 PST
