VMD-L Mailing List

From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Thu Jan 17 2008 - 10:26:44 CST

Hi Francesco,

make sure 'Trace' is not active in the atom selection box. For more
information about all the options take a look here:
http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/rmsdtt/#options

Best,
Luis

Francesco Pietra said the following on 01/17/2008 01:49 AM:
> I am carrying out MD of a protein-ligand (the latter non polymeric, large) in a
> POPC membrane. Things run satisfactorily, though I was unable to gather all
> information that should be possible.
>
> The ligand has O-hetero-rings, so that in visualizing rmsd with the RMDS traj
> Tool I would like to have the oxygen atom included. What I did in the window
> was to replace on top left box "protein" with "resname XYZ", where XYZ is the
> name of the ligand. I got the plot with the top indication (in red) "RMSD vs
> Frame "(resname XYZ) and name C CA N". This ligand has no aromatic carbons, nor
> nitrogen atoms. It has sp3 and sp2 carbons and ethereal oxygen. Where should I
> set these indications?
>
> I know I should educate myself throughly on VMD. Time is short.
>
> Thanks
> francesco pietra
>
>
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