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

[Justin Lemkul]

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. 
http://www.mdtutorials.com/gmx/lysozyme/index.html

-Justin

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

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