[gmx-users] How to compare two pdb files

delara aghaie d_aghaie at yahoo.com
Sat Jun 16 14:54:29 CEST 2012

Dear Justin
I expected the gmxcheck program to print all the differences between nvt.tpr and npt.tpr.
It seems that this only writes the velocities of atoms in x,y and z direction.
Am I right?


 From: Justin A. Lemkul <jalemkul at vt.edu>
To: delara aghaie <d_aghaie at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, 16 June 2012, 17:16
Subject: Re: [gmx-users] How to compare two pdb files

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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