Dear Sir,
I would like to calculate the hydrogen bonding lifetimes from my bilayer
system.
I have done the hydrogen bonding calculation by executing command as below:
*hbond MyHB :1-128 dist 3.5 angle 120 \ avgout avghb.dat nointramol series
\ solventacceptor :WAT.O solventdonor :WAT \ solvout solvent_avg.dat
bridgeout bridge.datrunwritedata nhb.dat MyHB[UU] MyHB[UV]
MyHB[Bridge]writedata solutehb.dat MyHB[solutehb]writedata solventhb.dat
MyHB[solventhb]lifetime MyHB[solutehb] out
solute.lifetime.datlifetime MyHB[solventhb] out
solvent.lifetime.datrunanalysis*
>From above command (the two lines):
*lifetime MyHB[solutehb] out solute.lifetime.dat*
*lifetime MyHB[solventhb] out solvent.lifetime.dat*
generate two files with lifetime information. The
*solute.lifetime.dat* contain
info like:
#Set Nlifetimes MaxLT AvgLT TotFrames SetName
0 22 1 1.0000 22
BMR_3.O16-BMR_1.O22-H22
1 296 346 15.6959 4646
BMR_42.O22-BMR_1.O22-H22
2 992 12 1.4688 1457
BMR_42.O14-BMR_1.O22-H22
3 1 1 1.0000 1
BMR_42.O13-BMR_1.O22-H22
4 189 12 1.1429 216
BMR_57.O25-BMR_1.O22-H22
5 462 410 12.3074 5686
BMR_57.O16-BMR_1.O22-H22
I would like to know how I can go from here to calculate the
hb-lifetime between
solute and solute?
I have read the pages 556-557 from AMBER 14 manual, but I find it difficult
to see how one should start processing and getting the lifetime value.
I think simple example would help me much in this case.
Could you give me some example on how this can be obtained?
Your help is much appreciated.
Thank you.
Vijay
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Received on Tue Mar 10 2015 - 02:00:02 PDT
