Re: RMSD calculation

From: Carlos Simmerling <>
Date: Tue 15 May 2001 19:13:47 -0400

If you have an SGI, you can easily use moil-view for this.
Just load the 15 residue crd and prmtop as molecule 1,
and the 9 residue fragment as molecule 2. When you open an rmsd
plot, you can select different atoms for each molecule
for the fit, as long as the number of atoms selected is the same.
Then run the dynamics and you will get your rmsd data which you
can save to a file.

Bill Ross wrote:

> I have the AMBER6 trajectory file for 15 residues peptide in water
> after MD run. There is correspondent parm file for this system.
> I wanted to calculate the RMSD for all structures collected in the
> trajectory file with a fragment of the peptide structure (9 residues)
> with different parm file. How to do it in CARNAL or any other
> analysis program compatible to AMBER6?
> I think the only way would be to map the structure with the 9
> residues to an artificial coordinate file matching the 15-residue
> prmtop. E.g. you could write a small program to pad the coordinates
> with 0's for the other 6 residues (and maybe waters), or using a pdb
> of the reference 9 residues, you could create the other 6 residues in
> leap (matching the sequence in the trajectory version):
>> x = sequence ( NALA ALA ALA ALA ALA ALA )
>> savepdb x init.pdb
> then join the 2 pdb files and
>> x = loadpdb joined.pdb
>> saveamberparm x ref.prm ref.crd
> Then strip the waters from your trajectory and use ref.prm to
> handle the trajectory using ref.crd as the coordinate ref for the
> 9 residues.
> Bill Ross

Carlos L. Simmerling, Ph.D.
Assistant Professor           Phone: (631) 632-1336
Department of Chemistry       Fax:   (631) 632-7960
SUNY at Stony Brook           Web:
Stony Brook, NY 11794-3400    E-mail:
Received on Tue May 15 2001 - 16:13:47 PDT
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