Hi,
I'm trying to use bridge option in the hbond analysis.
I've tried to change the script without having the result I'm searching for.
I'm interested in knowing if during the dynamic simulation I have water
molecules which create a bridge between the protein and ligand.
This is the last script I have tried:
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
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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Received on Thu Feb 27 2014 - 10:00:03 PST
