VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 22 2005 - 14:03:03 CDT

Claire,
  I don't know if AMBER or ptraj perform coordinate wrapping, but is it
possible that this piece of structure that had its coordinates wrapped around
a periodic cell or something like that? Another possibility is that something
didn't match between the stripped mdcrd and the matching parm file you loaded
into VMD. Without having the actual files in hand, it's hard to guess what
the actual issue is.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 22, 2005 at 07:39:55PM +0200, Claire Zerafa wrote:
> Dear all,
>
> I am trying to visualise the trajectory of a protein in vmd at the end of
> an equilibration run. The protein was stripped of explicit solvent in
> amber8 using ptraj as follows:
>
> 1e3g_wat_calc_backbone_rms.in
> trajin /usr/people/claire/AMBER_FILES/1e3g_wat_md1.mdcrd
> trajin /usr/people/claire/AMBER_FILES/1e3g_wat_md2.mdcrd
> trajout /usr/people/claire/AMBER_FILES/1e3g_strip_wat.mdcrd
> rms first out /usr/people/claire/AMBER_FILES/1e3g_wat_calc_backbone.rms
> @CA time 0.2
> strip :WAT
>
> I then loaded the .prmtopfile and the 1e3g_strip_wat.mdcrd that was
> outputted from ptraj. I could visualise the protein trajectory well, but
> there seemed to be (I am doing this for the first time), a point outside
> the globular protein that formed what seemed to be a triangle of bonds that
> extended from outside the globular protein. My guess was that this could
> have been a remnant water, and that it was somehow left behind after
> stripping. I am not sure...I do not expect that there are any anomalies in
> the protein since graphs of energy, temperature, pressure, volume, density
> and rms are all as expected for the equilbration run I was using.
>
> Can you tell me whether this is something I should worry about please?
>
> Thanks
>
> cxx 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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