Hi,
You need to disable the angle calc in Hbond by setting 'angle -1'.
-Dan
On Wed, Feb 6, 2013 at 10:08 AM, DEBOSTUTI GHOSHDASTIDAR
<debostutighosh.gmail.com> wrote:
> Dear Amber users,
>
> My doubt remains...so Im posting this query again...
>
> I intend to obtain lifetime and occupancy data for electrostatic
> interaction between two atoms, using the hydrogen bond analysis
> facility of ptraj. However, both the atoms are not electron acceptors,
> i.e, neither have hydrogens attached to them. In one of the mail
> threads it was mentioned that in such a case, acceptor and acceptorH
> can be the same atom. 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
>
> hbond distance 3.5 time 2 series PO_lig out PO_lig.dat
>
> The output file shows no interaction although the donors and acceptors are
> recognised correctly. As suggested earlier, i checked ptraj output with
> prnlev 3 and it showed the acceptors are being read correctly. I also tried
> to find interaction using another set of acceptor atoms: O20 H21, and
> interactions were there . However when i used O20 O20, once again there
> were no interactions. I also increased the distance cutoff to 5 and even
> 10A. That too didnt work.
>
> Don't know where I am going wrong. Please help.
>
> Thanks
>
> --
> Debostuti
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--
-------------------------
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 Wed Feb 06 2013 - 10:00:03 PST
