[gmx-users] Re: g_rms and g_rmsdist on initial structure

[Hsinlin]

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
high values.

Sincerely yours,
Hsin-Lin

Erik Marklund wrote
> 
> Hi,
> 
> Since gromos-forcefields are not strictly all-atom forcefields, there
> might be a mismatch between atoms in the two structures.
> 
> Best,
> 
> Erik
> 
> 24 aug 2012 kl. 15.35 skrev Hsin-Lin Chiang:
> 
>> Hi,
>> 
>> 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
>> 0.5nm.
>> Can someone explain for me?
>> 
>> Sincerely yours,
>> Hsin-Lin
>> 
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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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