VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Apr 11 2006 - 13:57:58 CDT

Hi Anuradha,
is the error occuring as you load the files, or as you calculate the fit
and rmsd? It looks like you're trying to load the pdb and dcd into the
same molecule, which won't work since you have a different number of atoms.
Peter

Anuradha Mittal wrote:

> Hi,
> I am trying to find the RMSD of protein between each frame of a dcd
> file and a reference pdb file. The PDB and DCD files have different
> number of water molecules.
> While running the script pasted below, it is giving an error of
> "incorrect number of atoms".
>
> proc myrmsd { frame } {
> global ref sel all
> $all move [measure fit $sel $ref]
> puts "$frame: [measure rmsd $sel $ref]"
> }
>
> mol load psf prot.psf # for prot.dcd
> set all [atomselect top all]
> set ref [atomselect top "name CA" frame 0]
> set sel [atomselect top "name CA"]
> animate read pdb protein.pdb
> bigdcd myrmsd prot.dcd
>
> Is there any way of calulating rmsd from files with different number
> of atoms?
>
> Thanks
> Anu