[gmx-users] RMSD

Robert Johnson bobjohnson1981 at gmail.com
Tue Apr 24 20:56:31 CEST 2007

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


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
> Hyderabad-500 076, INDIA
> Tel : +91-40-27151344
> Fax : +91-40-27155610
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