[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.

My question:

  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,

Neena Eappen
Graduate Student
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T

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