[gmx-users] Input file for energy minimization for solvated system: Error
Neena Susan Eappen
neena.susaneappen at mail.utoronto.ca
Sun Nov 11 21:04:51 CET 2018
Hello GROMACS users,
I was trying to create an input file for energy minimization of solvated system, using the following command:
grompp -v -f minim.mdp -c protein-solvated.gro -p protein.top -o protein-EM-solvated.tpr
Got the following error:
number of coordinates in coordinate file (1y6l-solvated.gro, 181577) does not match topology (1y6l.top, 182265).
I think the following error occurred because I skipped the following step:
Edit the topology file and decrease the number of solvent molecules. Also add a line specifying the number of NA ions and a line specifying the amount of CL.
1. How to open the topology file?
2. How do I determine number of NA and CL ions added? I just saw a massive list of these counterions being added, but not the total number.
3. My net charge on the protein was 6+, why do I need to add Na+ ions?
Any insight would be appreciated, Thank you,
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T
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