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
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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Received on Sat Mar 22 2014 - 13:30:03 PDT
