Dear Researchers,
Hi,
I have performed an MD simulation with Gromacs 5.1.4. Now, I want to make a movie of simulation. After loading .xtc and .gro files into VMD 1.9.3beta1, I was able to create the protein and water molecules representations but I do not know how to make a rep of ligand. I will be grateful if anyone helps me solve this problem.
Sincerely
Alireza Mohebbi
If you write "all not water", you should be able to see the protein and the ligand - If you click on it details should be given regarding the resname if you can't find it via the coordinate file for some reason.
attached your gro file.
Any molecule has a set of resname or resid in the coordinate file. So just write resid (resname) and correct name.
If you write "all not water", you should be able to see the protein and the ligand - If you click on it details should be given regarding the resname if you can't find it via the coordinate file for some reason.
Thank you so much my dear friends. It worked. I have sat macro definition equal to “resname LIG” (as in the coordinate file) and another rep to "all not water"/ or with water . That was very interesting. I have attached the movie.
http://sendvid.com/i5bont88
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