[gmx-users] Error: Atomtype CH2 not found

[Justin Lemkul]

On 12/13/19 2:18 AM, Muthusankar wrote:
> Dear Gromacs users,
> I am simulating a protein-ligand complex and performing the grompp command
> before adding ions to the system. I got the error.
> *Fatal error: *(file: ligand.itp)
> Atomtype *CH2 not found*.
> *command used:*
> gmx grompp -f ions.mdp -c protein_box.gro -p protein.top -o ions.tpr
>
> Please guide me, How to rectify the problem.
>

This means you're trying to use an atom type that your force field 
doesn't recognize. Either you're mixing and matching force fields (never 
do this) or your ligand topology relies on new atom types that should be 
introduced into the force field, in which case the source of the ligand 
topology (server, etc.) should provide that information.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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