Hi,
What version of cpptraj are you using (cpptraj --version)? You should have
version 13.22 - if not you need to update.
On Thu, Feb 27, 2014 at 10:33 AM, Alessandra Lacetera <
alessandra.lacetera.gmail.com> wrote:
>
> hbond HB out hb_LIG donormask :141-143 acceptormask :1-140 avgout avg.dat
> solventdonor O solventacceptor O H1 solventacceptor O H2 bridgeout
> bridge.dat
>
The solventdonor etc keywords in cpptraj expect mask expressions. As stated
in the manual, the 'hbond' command in cpptraj is one of the very few
commands that is *not* backwards compatible with ptraj - I suggest you
check the 'hbond' command in the cpptraj section of the AmberTools manual
for the full syntax. Also note that the definition of hydrogen bond "donor"
and "acceptor" in cpptraj follows the more conventional 'donors are bonded
to H, etc'. You probably want something like this with the 'nointramol'
keyword so that intra-molecular hydrogen bonds are ignored:
hbond HB out hb_LIG :1-143 nointramol solventdonor :WAT solventacceptor
:WAT.O avgout.avg.dat solvout solvavg.dat bridgeout bridge.dat
Let me know if you have any more questions,
-Dan
> where as donormask there's the ligand and as acceptormask the protein.
>
> I got this error:
>
> Warning: [hbond] Not all arguments handled: [ solventdonor O
> solventacceptor O H1 solventacceptor O H2 bridgeout bridge.dat ]
>
> and at the end:
> DATASETS:
> There is 1 data set: HB
> DATAFILE OUTPUT:
> hb_LIG: HB
> avg.dat: Acceptor,DonorH,Donor,Frames,Frac,AvgDist,AvgAng
>
> Why don't I have bridgeout?
>
> Thank you in advance
>
> Alessandra Lacetera
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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) 585-6208 (Fax)
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Received on Thu Feb 27 2014 - 10:00:04 PST
