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

[Erik Marklund]

Because it uses the atom index, which is most likely NOT the same as your processed file will not contain certain hydrogens, which are present in A.pdb.

24 aug 2012 kl. 16.33 skrev 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
>> http://www2.icm.uu.se/molbio/elflab/index.html
>> 
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> 
> 
> 
> 
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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 xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html