Hi,
On Sat, Mar 22, 2014 at 2:13 PM, George Tzotzos <gtzotzos.me.com> wrote:
> I'm running the following input script
>
> trajin prod_0-20ns.nc
> hbond acceptormask :126&.N*,O* donormask :1-125&.N*,O* nointramol
> hbond out hb.dat dist 3.0 avgout avg.dat
> bridgeout bridgeout.dat solventdonor :WAT solventacceptor :WAT&.O
>
The 'bridgeout' etc keywords are part of the 'hbond' command, so they need
to be on the same line. You can make a line continuation by using the
backslash ('\') character like so:
hbond out hb.dat dist 3.0 avgout avg.dat \
bridgeout bridgeout.dat solventdonor :WAT solventacceptor :WAT&.O
-Dan
>
> whereby :126 is a ligand containing both N & O atoms
>
> The output produced by cpptraj is:
>
> Radius Set: H(N)-modified Bondi radii (mbondi2)
> INPUT: Reading Input from file cpptraj_hb.in
> [trajin prod_0-20ns.nc]
> [prod_0-20ns.nc] contains 2000 frames.
> [hbond acceptormask :126&.N*,O* donormask :1-125&.N*,O* nointramol ]
> HBOND: Donor mask is :1-125&.N*,O*, Acceptor mask is :126&.N*,O*
> Only looking for intermolecular hydrogen bonds.
> Distance cutoff = 3.000, Angle Cutoff = 135.000
> [hbond out hb.dat dist 3.0 avgout avg.dat]
> HBOND: Searching for Hbond donors/acceptors in region specified by *
> Distance cutoff = 3.000, Angle Cutoff = 135.000
> Dumping # Hbond v time results to hb.dat
> Dumping Hbond avgs to avg.dat
> [bridgeout bridgeout.dat solventdonor :WAT solventacceptor :WAT&.O]
> [bridgeout]: Command not found.
>
> Having looked at the AmberTools 13 manual, I fail to see what's wrong.....
> Any help in deciphering the problem is much appreciated
>
> Thanks in advance
>
> George
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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 Sat Mar 22 2014 - 15:00:03 PDT
