VMD-L Mailing List

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Wed Jun 22 2005 - 16:57:47 CDT

Claire,

This is more of am amber question than vmd, so I will try to answer it.

First, I want to make sure you created a NEW prmtop file after stripping
the waters, Otherwise the atom count will be different.

Assuming you did this, I think your problem is that you did not say
nobox after your trrajout command in ptraj.

So, if you load the stripped mdcrd as 'crd' in vmd, then the box is not
expected, but it is present in your mdcrd coordinate.

If you read it in vmd as crdbox, then a box is expected but it disagrees
with what your prmtop says.

I would add nobox to your trajout command and try again.

Pls let me know if this helps (or not ;-))

Cheers

adrian

John Stone wrote:
> 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
>
> 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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