Re: [AMBER] Calculation of Intramolecular hydrogen bonding using ptraj

From: Sudha Mani Karra <karra.md.gmail.com>
Date: Tue, 27 Jul 2010 11:51:55 -0500

Dear Thomas,

Turning off the angle works!! I have the output written and also I have
confirmed the distances using ptraj as well.
Can you please explain me regarding how I can interpret my result from as
shown below (first two line of the output are only shown).
What does the number in the parenthesis beside the distance,angle values
mean. Is it the deviation?
What does lifetime and maxoccupancy give me?

  atom# :res.atom atom# :res.atom atom# :res.atom %occupied
distance angle lifetime maxocc
| 115 :1.O10 | 104 :1.H20 92 :1.O8 | 96.06 2.818 ( 0.21)
34.14 (28.58) 45.5 ( 72.3) 390 |.@@@x@
.*@@*@@@@@@@@@@@*.x*@@@**@**@@@@@@@@@*@@@@@|

| 199 :1.O10 | 188 :1.H20 176 :1.O8 | 85.94 2.754 ( 0.19)
26.82 (26.37) 36.8 ( 70.6) 272 |.x@@@@@@@@@*@@*x@@**@@@o
.x*.@@o--*@@@@@@@@@@@@@|

Thanks for the help
-Su

On Tue, Jul 27, 2010 at 10:46 AM, Thomas Cheatham III <tec3.utah.edu> wrote:

>
> > I am actually trying to calculate the intramolecular hydrogen bonds that
> > exist in a residue in my simulation system. However, I am failing to get
> any
> > output written. I know that intramolecular hydrogen bonds exist in the
> > molecule. I have confirmed this by calculating the distances and angles
> > using VMD by loading my output file from the simulation.
>
> You can calculate the distances in ptraj too to confirm and/or make sure
> that the distances are less than 3.5 angstroms when you visualize. Also,
> turn off the angle (angle -1.0); normally I use angle 120.0 which is +/-
> 60 deg... angle 180 may be assuming it is exactly linear which would be
> rare indeed. --tec3
>
>
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Received on Tue Jul 27 2010 - 10:00:04 PDT
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