[gmx-users] visualizing small molecule in a trajectory file .trr and .gro using VMD

Mark Abraham mark.abraham at anu.edu.au
Sat Jun 5 06:27:46 CEST 2010

----- Original Message -----
From: Hassan Shallal <hshallal at PACIFIC.EDU>
Date: Saturday, June 5, 2010 13:52
Subject: [gmx-users] visualizing small molecule in a trajectory file .trr	and .gro using VMD
To: gmx-users at gromacs.org
Cc: vmd-l at mailhost.ks.uiuc.edu


> 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?   
Not without understanding how selections work in VMD, which must be in their documentation (hint, hint). Probably you want to select "resname UNK" - but be sure you've done the VMD tutorials because I'm sure they illustrate this idea.

 > 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...

VMD can do it, you just need to learn how to instruct it :-)

Mark |

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