How to change the 2D molecular structure into 3D?

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1

GROMACS version:
GROMACS modification: Yes/No
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How to change the 2D molecular structure into 3D?
I have tried MOE, but the result is not ideal.The MD result doesn’t work as we expected which we have referred to paper. Which software do you often use to produce 3D structure? Best be free.

2

get the 3d structure if the molecule existed, or draw a 3d structure- there are many tools like chemdraw, avogadro etc

3

If the molecule is available in https://pubchem.ncbi.nlm.nih.gov, you can often download 3D structures from there (in .sdf format, which you will need to convert to, e.g., .pdb, .mol2 or .gro format).