[gmx-users] g_rms

[Tsjerk Wassenaar]

Hi Tatsiana,

No.

g_rms requires the input trajectory and the reference structure to
match. Actually, the trajectory (if .xtc format) does not even contain
information regarding the atoms; only coordinates. Tools depend wholly
on the reference structure for information on atom/residue names, etc.

Cheers,

Tsjerk

On Mon, Nov 10, 2008 at 5:36 PM, Tatsiana Kirys <nushki at mail.ru> wrote:
> Hi,
>
> i use g_rms to calculate rms,
>
> as reference structure (-s) i use myprotein.pdb file
> and trajectory (-f) is a trajectiry  after MD MDprotein.pdb.
>
> The thing is that myprotein.pdb  and  MDprotein.pdb have the same atoms BUT their order within a residue is DIFFERENT.
> example:
> myprotein.pdb:
> ATOM      1  N   ALA E   1      18.858 -22.883  26.306  1.00  0.00
> ATOM      2  CA  ALA E   1      19.106 -24.277  26.027  1.00  0.00
> ATOM      3  C   ALA E   1      20.206 -24.458  25.006  1.00  0.00
> ATOM      4  O   ALA E   1      20.156 -23.801  23.972  1.00  0.00
> ATOM      5  CB  ALA E   1      17.865 -24.819  25.301  1.00  0.00
>
> MDprotein.pdb:
> ATOM      1  N   ALA     1      18.861  24.179  26.290  1.00  0.00
> ATOM      2  CA  ALA     1      18.978  22.741  26.011  1.00  0.00
> ATOM      3  CB  ALA     1      17.670  22.190  25.440  1.00  0.00
> ATOM      4  C   ALA     1      20.069  22.592  24.949  1.00  0.00
> ATOM      5  O   ALA     1      20.120  23.450  24.070  1.00  0.00
>
> whether g_rms work correct in this case?
>
> g_rms -s myprotein.pdb -f MDprotein.pdb
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623