Hi dear Ambers!
Put simply.
I want analyse hbond between ligand and receptor, the command i am using:
parm ../wat_box.prmtop
trajin ../traj/md14.nc
hbond hbond_test out hbond.agr avgout hbond_avg_1.dat :250<@25 solventdonor :250<:10&:WAT solventacceptor :250<:10&:WAT.O solvout solvent.out bridgeout bridge.out series uuseries uu.dat donormask :1-250.O=,N= acceptormask :251-252.O=,N= nointramol
Please note, for a test, there is no image in command above, result goes that:
#Acceptor DonorH Donor Frames Frac AvgDist AvgAng
0MA_252.O2 GLN_76.HE22 GLN_76.NE2 2723 0.5446 2.8807 163.7136
0MA_252.O6 GLN_76.HE21 GLN_76.NE2 99 0.0198 2.8904 152.8243
0MA_252.O6 LYS_172.HZ3
LYS_172.NZ 3 0.0006 2.8335 146.1959
......
Next, add autoimage in command:
parm ../wat_box.prmtop
trajin ../traj/md14.nc
autoimage
hbond hbond_test out hbond.agr avgout hbond_avg_1.dat :250<@25 solventdonor :250<:10&:WAT solventacceptor :250<:10&:WAT.O solvout solvent.out bridgeout bridge.out series uuseries uu.dat donormask :1-250.O=,N= acceptormask :251-252.O=,N= nointramol
result is the same as first
#Acceptor DonorH Donor Frames Frac AvgDist AvgAng
0MA_252.O2 GLN_76.HE22 GLN_76.NE2 2723 0.5446 2.8807 163.7136
0MA_252.O6 GLN_76.HE21 GLN_76.NE2 99 0.0198 2.8904 152.8243
0MA_252.O6 LYS_172.HZ3
LYS_172.NZ 3 0.0006 2.8335 146.1959
......
Now, add image in hbond:
parm ../wat_box.prmtop
trajin ../traj/md14.nc
hbond hbond_test out hbond.agr avgout hbond_avg_1.dat :250<@25 solventdonor :250<:10&:WAT solventacceptor :250<:10&:WAT.O solvout solvent.out bridgeout bridge.out series uuseries uu.dat donormask :1-250.O=,N= acceptormask :251-252.O=,N= nointramol image
result:
#Acceptor DonorH Donor Frames Frac AvgDist AvgAng
0MA_252.O3 SER_205.HG SER_205.OG 1830 0.3660 2.7665 150.9378
0MA_252.O2 GLN_76.HE22 GLN_76.NE2 573 0.1146 2.8846 145.7732
0MA_252.O2 GLN_76.HE21 GLN_76.NE2 25 0.0050 2.8548 144.7897
0MA_252.O6 GLN_76.HE22 GLN_76.NE2 13 0.0026 2.8849 147.8818
The result is markedly different only because of the image.
so£¬what make me confused is the image. In my option, if trajectory need imaged, it is the same for using 'autoimage' in cpptraj and 'image' in hbond command. Can someone explain such problem.
BTW, cpptraj is the latest version with all update installed.
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Received on Wed Jan 06 2016 - 20:00:04 PST
