VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Thu Jan 17 2008 - 11:11:35 CST

Hi Luis:
I forgot to ask in my previous mail: While for the protein I use ff99SB, for
the single residue ligand I use GAFF. That means that atom names are in small
case (otherwise corresponding to the upper case of ff99SB). I would like to
limit RMSD to certain atoms, especially the ethereal oxygen atom of the ligand.

Thanks
francesco

--- Luis Gracia <lug2002_at_med.cornell.edu> wrote:

> 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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> > http://www.yahoo.com/r/hs
> >
>

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