VMD-L Mailing List

From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Fri Jun 02 2006 - 11:35:53 CDT

Hi,

 From the GUI system you have to load them one by one I guess. If you
can lanch vmd from the command line you can:
if the pdbs are the same structure but different conformation you can
load them in the same molecule as frames with:
vmd -m -f *.pdb

if you want them in different molecules:
vmd -m *.pdb

If you want the rmsd using the frames approach use the RMSDTT plugin (in
vmd 1.8.4) instead of the RMSD Tool.

best,

luis

Robert Selwyne said the following on 06/02/06 09:47:
> Dear VMD Care taker
>
> Good Day!!!!!!!!!!!
>
> I have a set of 200 pdb files with me. I want to calculate the averaged
> rmsd for these 200 structures. I used the RMSD calculator, loaded my 200
> pdb structures one by one. But instead of loading the ID number ( 0-199)
> of the vmd-main screen, it is strangely loading 200 frames.
> Also please tell me is there any global command to load all these pdb
> files at once.
> I am not expert in scripts writing, so please explain the commands with
> the existing options that appears in the vmd-main screen.
>
> With Regards
> Robert
>
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