Dear Dan,
I have tried this input file
trajin inactive_oligo_sol_300frames.mdcrd
center :1-661 mass origin
image origin center familiar
strip :WAT
strip :Na+
hbond H1 :661-666 :166-310 nointramol out Nhbond.agr avgout avg.dat
bridgeout Bridge.dat
but I am getting this error
Error: Atom 9937 was assigned a lower molecule # than previous atom. This
can
Error: happen if 1) bond information is incorrect or missing, or 2) if the
Error: atom numbering in molecules is not sequential. If topology did not
Error: originally contain bond info, 1) can potentially be fixed by
Error: increasing the bondsearch cutoff offset (currently 0.200). 2) can
be
Error: fixed by either using the 'fixatomorder' command, or using
Error: the 'setMolecules' command in parmed.py.
Error: Could not determine molecule information for inactive_EGFR.top.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for inactive_EGFR.top.
> trajin inactive_oligo_sol_300frames.mdcrd
Error: [hbond] Not all arguments handled: [ :166-310 ]
I am running cpptraj similar to ptraj: cpptraj topfile input.file
On Mon, Dec 15, 2014 at 12:23 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> If you use the cpptraj 'hbond' command with the 'nointramol' keyword
> it should do a reasonable job determining hydrogen bond donors and
> acceptors.
>
> -Dan
>
> On Sun, Dec 14, 2014 at 8:40 PM, maryam azimzadehirani
> <maryamai1988.gmail.com> wrote:
> > Dear Amber users,
> > Does anyone know how we specify the H-bonds donors and acceptors in
> ptraj,
> > while calculating the H-bonds between glycans(sugar residues) and
> Protein?
> > Regards,
> > Maryam
> > _______________________________________________
> > AMBER mailing list
> > 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 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
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Received on Sun Dec 14 2014 - 23:30:02 PST
