Error in solvation

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1

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While performing solvation step , gmx solvate adds 8134 water molecules. But when I saw my solv.gro file , it has added water molecules vaguely starting from the ligand coordinates. And when I run addition of ions step . The fatal error arises and reads that the water molecules in the topology.top file and the solv.gro don’t match . I thought that it might be due to the reason that my ligand residue has been named 1LIG and the software adds water directly from 2SOL hence the error . I tried renaming the ligand residue but to no avail. Please help me in this regard

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2

gmx solvate should not affect the original part of .gro file. Have you try to check what’s the missing 86 atoms in the .gro file generated in the previous step?

3

Thank you so much for your response. The problem got solved . Actually the name of the molecule in the molecule type section of topology file was mentioned as LIG 3 . So when I removed this 3 the problem got solved and there was no error observed . It seems this 3 was creating a confusion and an error