Using the following script
parm 3n7h_de4_solv.prmtop
trajin prod_100ns.nc
hbond H1 nointramol series out Nhbond.agr avgout avg.dat
\ bridgeout Bridge.dat solventdonor :WAT solventacceptor :WAT.O
go
write solutehb.agr H1[solutehb]
runanalysis lifetime H1[solutehb] out lifehb.agr window 10
produces the expected output e.g.
the avg. dat file (indicative few lines):
#Acceptor DonorH Donor Frames Frac AvgDist AvgAng
DE4_127.O1 SER_79.HG SER_79.OG 122 0.0122 2.7246 162.2751
DE4_127.O1 HIE_111.HE2 HIE_111.NE2 10 0.0010 2.8810 152.6329
DE3_126.OAN TRP_114.HE1 TRP_114.NE1 1 0.0001 2.8386 174.1757
#Solute-Solvent Hbonds:
#Acceptor DonorH Donor Count Frac AvgDist AvgAng
DE3_126.OAN SolventH SolventDnr 8643 0.8643 2.7484 163.2506
the bridge.dat file
#Bridging Solute Residues:
Bridge Res 95:CYX 114:TRP 126:DE3 , 3555 frames.
Bridge Res 114:TRP 126:DE3 , 2006 frames.
Bridge Res 95:CYX 126:DE3 , 1823 frames.
Changing the input line of the script by using a mask (residues 126 and 127 are ligands)
hbond H1 :126-127 nointramol series out Nhbond.agr avgout avg.dat
\ bridgeout Bridge.dat solventdonor :WAT solventacceptor :WAT.O
produces a similar but non-identical output for agv.dat
#Acceptor DonorH Donor Frames Frac AvgDist AvgAng
#Solute-Solvent Hbonds:
#Acceptor DonorH Donor Count Frac AvgDist AvgAng
DE3_126.OAN SolventH SolventDnr 8643 0.8643 2.7484 163.2506
DE4_127.O1 SolventH SolventDnr 214 0.0214 2.7486 158.8356
and no bridge H-bonds
#Bridging Solute Residues:
I’d be grateful for any explantation of this behavior
Regards
George
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Received on Mon Feb 23 2015 - 10:30:03 PST
