VMD-L Mailing List

From: Anuradha Mittal (anuradha.mittal_at_gmail.com)
Date: Wed Apr 12 2006 - 09:24:45 CDT

Yeah, i was loading both the files into the same molecule. Its working fine
now.
Thanks for the help.
Anuradha

On 4/11/06, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
> 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
>
>