How to use LigPargen server for OPLS AA ligand topology generation?

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1

GROMACS version:
GROMACS modification: Yes/No
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I am uploading my extracted ligand.pdb file of protein ligand complex from GROMACS into LigPargen server. But it shows error and tells to upload smiles.So is it correct to upload smiles.

Further, when i used smiles it generates top and gro files which on further proceeding steps of equilibriation shows error of LINCS .

Therefore, please tell me how to use this server and how to overcome this LINCS error in NVT equilibriation step.

2

Hi,
Concerning your question on how to avoid error in NVT.
Did you energy minimize before simulating the system?
It may help to start the simulation from an energy minima.
Best regards
Alessandra