[gmx-users] How to compare two pdb files

delara aghaie d_aghaie at yahoo.com
Sat Jun 16 14:38:38 CEST 2012

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?
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 !!!???

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