Hi,
On Mon, Dec 15, 2014 at 12:05 AM, maryam azimzadehirani
<maryamai1988.gmail.com> wrote:
> hbond H1 :661-666 :166-310 nointramol out Nhbond.agr avgout avg.dat bridgeout Bridge.dat
The 'hbond' command only requires one mask, so you can probably just
combine the two masks, e.g.
:661-666,166-310
make sure that you've read the manual entry for the cpptraj 'hbond'
command, it contains a more detailed explanation of what masks the
command uses and their associated keywords.
> 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.
As far as Amber error messages go, this one is about as informative as
they get. The atom ordering in your topology is non-sequential with
respect to molecules (for example, molecule 1 is atoms 1-10 and 20-30,
molecule 2 is atoms 11-19 etc.). You can use either of the suggested
fixes if you are doing analysis that requires molecule information,
e.g. 'closest'. The 'hbond' command does not rely on such info.
Hope this helps,
-Dan
PS - You could also try the 'autoimage' command instead of 'center'
and 'image'. An also be aware that 'strip' does change atom numbering,
which will affect your atom mask if you had e.g. any water or ions
in-between residues 310 and 661.
> 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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> 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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Received on Mon Dec 15 2014 - 01:00:02 PST
