Seen on VMD but not on Discovery Studio?

User discussions
1

GROMACS version: 2018. 3
GROMACS modification: No

I have a quick question about protein-ligand simulation.

I created a .gro file for my ligand, and tried to copy & paste its content into protein.gro.
When the combined file (.pdb) was opened on VMD, it shows both the protein and ligand, but when opened with Discovery Studio, the ligand doesn’t appear.

Will this cause any problem in later steps of MD simulation? or is it just Discovery Studio not recognizing some things?

Thank you.

2

Hi,
Can you see your ligand’s name on hierarchy (Ctrl+H)? If yes, your problem could be depend on representation of the ligand. If not then your ligand is not recognized by the Discovery Studio

3

It kind of appears on the hierarchy, but the ligand is under the AminoAcidChain, which is not right.
The ligand is not a protein. Probably something is not right with the ligand.pdb file?