[gmx-users] Input file for energy minimization for solvated system: Error

Justin Lemkul jalemkul at vt.edu
Tue Nov 13 01:00:34 CET 2018

On 11/11/18 3:04 PM, Neena Susan Eappen wrote:
> 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?

A topology is a plain text file. Use a plain-text editor.

>    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.

genion tells you this.

>    3.  My net charge on the protein was 6+, why do I need to add Na+ ions?

We don't know what your genion command was, so we can't say.

Let solvate and genion do the work for you. Use the -p flag to have 
those programs update your topology for you, especially if you are not 
familiar with their contents or how to edit them. See e.g. 



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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