VMD-L Mailing List

From: Claire Zerafa (cporteli_at_waldonet.net.mt)
Date: Wed Jun 22 2005 - 12:39:55 CDT

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