[gmx-users] RMSD

[Robert Johnson]

Hi Dhanajay,
Since you don't have a trajectory (yet) and are comparing different
structures, I think the easiest thing to do would be to compute this
with VMD (www.ks.uiuc.edu/Research/vmd). You would load your PDB files
in separately, go to the TK console and type:

set struct1 [atomselect <id1> "all"]
set struct2 [atomselect <id2> "all"]
...

Here, <id1> <id2> are the mol ID (given in the Main VMD window next to
each PDB file).
Then type:

measure rmsd $struct1 $struct2

Bob

On 4/24/07, Dhananjay <dhananjay.c.joshi at gmail.com> wrote:
> Hello all,
>
> I have 10 pdb files. I want to do simulation on each of them. But before
> that I want to check RMSD of each of them with others and want to know  an
> average RMSD over all 10 srtuctures. The  pdb files are o/p of
> protein-protein docking.
>
> In this case, can I make use of programme g_rms for the RMSD calculations ?
>
> Or any other suggestion/programme please
>
>
>
>
> --
> Dhananjay C Joshi
> Project Assistant
> LSB, C D F D
> ECIL Road, Nacharam
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