[gmx-users] Re: g_rms and g_rmsdist on initial structure
jiangsl at phys.sinica.edu.tw
Fri Aug 24 16:33:48 CEST 2012
Thank you for your reply.
I checked the coordinates of all C-alpha atoms between two .pdb files.
They are exactly the same.
So I don't understand why g_rms(g_rmsdist) selecting group C-alpha give me
Erik Marklund wrote
> Since gromos-forcefields are not strictly all-atom forcefields, there
> might be a mismatch between atoms in the two structures.
> 24 aug 2012 kl. 15.35 skrev Hsin-Lin Chiang:
>> For example, I have a A.pdb as a initial structure file.
>> And I just used pdb2gmx on it to generate another B.pdb file with
>> GROMOS96 43a1 as its force filed.
>> Then I select C-alpha atoms to calculate RMSD.
>> echo 3 | g_rms -f B.pdb -s A.pdb
>> I suppose the RMSD value should be 0, but the value is high to about
>> Can someone explain for me?
>> Sincerely yours,
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> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: +46 18 471 6688 fax: +46 18 511 755
> erikm at .uu
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