[gmx-users] How to compare two pdb files

Justin A. Lemkul jalemkul at vt.edu
Sat Jun 16 14:46:35 CEST 2012

On 6/16/12 8:38 AM, delara aghaie wrote:
> Dear Gromacs users
> I have downloaded two pdf files which are two mutants of anaplastic lymphoma kinase.
> 1))) Is there a tool to show me the differences of these two files, instead of
> just opening and comparing the files?

Well, there is a Unix tool called 'diff' but if the proteins are in different 
coordinate space, then every line is going to be different and the output will 
be largely useless.  If you want details of structural differences, likely there 
are papers associated with the structures that will discuss these.

> I mean something like gmxcheck which can be used to compare two .tpr files.
> =======================
> 2))) I used gmxcheck -s1 nvt.tpr -s2 npt.tpr
> this is part of what I see on the screen:
> v[66145] ( 1.06480e-01  9.85994e-01 -2.44960e+00) - ( 1.63632e+00 -2.50359e-01
> -1.80810e+00)
> v[66146] (-3.80410e-01  1.09785e+00  5.02946e-02) - (-1.09235e+00  5.81441e-01
> 6.14882e-01)
> v[66147] (-6.75499e-01 -2.94155e-01 -2.72414e-01) - (-1.56743e-01  3.27000e-01
> 5.79831e-01)
> v[66148] (-8.74980e-01 9.58384e-01  2.60418e-01) - ( 5.77259e-01  1.60197e+00
> -2.07888e-01)
> v[66149] (-2.48934e+00  2.33179e+00  5.83937e-01) - (-1.71840e-01  6.66768e-01
> -8.41716e-01)
> v[66150] (-3.37818e-01  1.18446e-01  2.11772e-01) - (-1.61150e-01  3.02961e-01
> 2.50209e-01)
> v[66151] ( 5.36540e-01 -4.19213e-01 -1.55670e-01) - (-2.47564e-01  6.73932e-03
> -2.75615e-02)
> what does it mean !!!???

The 'v' array is the velocity array.  Hence, the atoms with the given indices 
have different velocities, with (x,y,z) components listed.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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