VMD-L Mailing List

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Sat Jun 05 2010 - 08:16:16 CDT

Hi Hassan,

If you are literally just typing 'UNK' in the selection window, then you are bound to get an error. There are certain keywords that you can use as single descriptors (e.g. 'protein', 'backbone', etc), but otherwise you need to use something like 'resname UNK' if the residue name for the small molecule is 'UNK'. It all depends on how VMD interprets the columns of the .gro file. You wouldn't be able to type '10' into the selection window and expect VMD to know if you want to see atom 10 or residue 10 or the first 10 atoms, etc.

As usual, I recommend reading the manual, specifically:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node87.html#ug:topic:selections

Josh

On Jun 4, 2010, at 11:49 PM, Hassan Shallal wrote:

> Dear Gromacs and VMD users.
>
> I am trying to visualize a simulation in which a small molecule is interactiong with a protein in a water box. The simulation has been produced using gromacs. I am using VMD for that purpose. I use the .gro and the .xtc files to load the trajectory to the VMD.
> What's the problem then?
> The problem is that I can't visualize anything in presence of water, so I need to have only the protein and the small moecule which is named UNK in the gro file, when I use selected atoms in the graphical representations in VMD to show the small molecule and I type UNK in the selected atoms, I get the following error message:
> the atom selection you typed couldn't be understood
> Does that mean that I will never be able to visualize the small molecule?
>
> Either the protein alone or the whole solvated system can be visualized, but I can't visualize both the protein along with the small molecule without the water...Could that be because in the .mdp file, I have haad protein and nonprotein descriptions? and that's why VMD can't isolate the UNK from the water? I don't know...
>
> Hey Justin, thanks alot for the prompt help with the other question I have had about snapshots...
>
> Any hint would be very appreciated...
>
> Thanks alot
>
> Hassan Shallal
> UOP