[AMBER] Evaluating hydrogen boding lifetime

From: Vijay Achari <glycoamber.gmail.com>
Date: Tue, 10 Mar 2015 16:53:39 +0800

Dear Sir,

I would like to calculate the hydrogen bonding lifetimes from my bilayer

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

>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
         1 296 346 15.6959 4646
         2 992 12 1.4688 1457
         3 1 1 1.0000 1
         4 189 12 1.1429 216
         5 462 410 12.3074 5686

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.
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Received on Tue Mar 10 2015 - 02:00:02 PDT
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