sir,
but what criteria would you prefer than defaults of cpptraj and vmd.?
On Mon, Sep 22, 2014 at 7:54 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Mon, Sep 22, 2014 at 12:37 AM, <leexa.intern.bii.a-star.edu.sg> wrote:
> > I was comparing my Hbond outputs using the Hbond command from both
> > ambertools12, and ambertools14.
> > There was discrepency for hydrogen bonding for some types of hydrogen
> > bonding between them.
> >
> > 1. H of water and O of protein was found to be the same
> > 2. H of bound to O/N of protein and O of water was found to have very
> high
> > fractions up to 2.5 compared to an expected maximum of ~1.
>
> The AmberTools 12 version of cpptraj didn't have the 'solventdonor'
> and 'solventacceptor' keywords implemented, so I'm not sure how you
> are even comparing them. Without knowing what input you gave to the
> AT12 version of cpptraj I can't really answer this.
>
> > Attached is the relevant files.
> > A view of the trajectory in VMD shows hydrogen bonding to only 1 water O
> by
> > the H most of the time, not 2.5 .
>
> The 'solventacceptor' and 'solventdonor' keywords track *any*
> solvent-solute hydrogen bond, which is why the fraction can be greater
> than 1. You don't say what criteria you're using in VMD, but note that
> the default values in VMD are more strict than the criteria you gave
> cpptraj, which may be why you see more hydrogen bonding in the latter.
> In VMD the defaults are distance 3.0 Ang., angle 20 (in VMD the angle
> is the deviation from 180). However, in your cpptraj run you specified
> distance 3.5, angle 120 (which is equivalent to angle 60 in VMD
> terms). What happens if you give distance 3.0, angle 160 to cpptraj?
>
> -Dan
>
> >
> >
> > Lee Xiong An
> >
> >
> >
> >
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> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
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Received on Mon Sep 22 2014 - 10:30:02 PDT
