I have a problem with ligand-protein simulation in Gromacs. For research I need an MD simulation of the low molecular weight ligand and colchicine site of the tubulin dimer. Following Justin A. Lemkul's tutorial, I created a separate ligand topology file (using CGenFF) and a protein topology file. Probably because of the simulation of two protein alpha and beta chains, my protein topology file (topol .top) is different from the example topology file in Justin A. Lemkul's tutorial. Regardless of where in the topol. top where I write the parameters of the ligand topology, after creating the box and its solvation, the ligand is not rendered using PyMol. Also, the ligand topology data are absent in the solv.gro file after the complex solvation procedure. What am I doing wrong? Help me please
Hi,
one thing i noticed is the name of your ligand in the topol.top file. In the molecule type, it is written as 1UNK and the topology and parameters file for the ligand is mentioned as unk.top and unk.prm. Can you please check and make sure that the ligand’s name is same in the ligand topology and parameters file as well as in the molecule type in topol.top file and in complex.gro file. Because the name should be same everywhere so that it can be recognized. Please let me know if this checks out.
Keerthic Aswin, thank you very much for your help. Yes, the ligand name in the itp file was different than in the topol .top file. Unfortunately editing the itp file didn't help. Also, I didn't find the ligand name line in the prm file.
Hi,
you can try changing the ligand name in .gro file and topol.top to the same name in itp files. Please don’t change anything in the itp and prm files. Make corresponding changes in the gro file and topol file
complex.gro: for some reason, UNK atoms (lines 13311 to 13370) are not included in the total atom count (line 2: 13308). Change 13308 to 13370 and see what happens?
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