Daniel...
Thanks a lot...it worked:)
On Wed, Feb 6, 2013 at 11:02 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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)
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Debostuti Ghosh Dastidar
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Received on Wed Feb 06 2013 - 22:00:03 PST
