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
Dear Ranbir Singh Saluja,
When the message "The fatal error arises and reads that the water molecules in "the topology.top file and the solv.gro don't match" appears, what is the difference in the number of atoms between the two files?
Is the .itp ligand file properly included in the .top file?
If you need, please share the .gro files from the steps taken, along with the .top file, so that I can check.
With respect,
Hamed
Sir the problem was solved . Actually in the molecule type section of topology I had mentioned LIG 3 ----- 1 this created the error . As soon as I removed that 3 . The problem got solved and no error was observed .
- Badges
- Science topic
- Similar topics
- Computer Communications (Networks)
- Simulators