Hello,
I'm trying to proceed with NVT equilibration using command
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr
I get an error Invalid atom number 6920 in index file
These are the files that I already have
Will someone please advise on how I can resolve this?
Muhammad Zohaib Safdar
Check if your topology and coordinate files match: Make sure that the topology and coordinate files you are using correspond to the same system. Check the atom numbering in your index file: Check if the atom number mentioned in the error message corresponds to the correct atom number in the index file. If not, you may need to correct the atom numbering in the index file. Regenerate the index file: If the above steps do not work, you can regenerate the index file using the gmx make_ndx command. This command will create a new index file based on your system topology and coordinate files. Check for missing atoms: If the error persists after regenerating the index file, you may have missing atoms in your system. Check your topology and coordinate files for missing atoms and make sure that they are correctly defined in your system. Check for duplicate atoms: Sometimes, the same atom can be defined twice in the topology file, leading to errors in the simulation. Check for duplicate atom definitions in your topology file and remove any duplicates.
This error in GROMACS usually occurs when there is a mismatch between the number of atoms in the system and the atom numbering in the index file.
Here are some steps you can take to fix this error:
Here's an example of how to regenerate the index file:
gmx make_ndx -f system.gro -o system.ndx
Make sure to replace system.gro with your system coordinate file.
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