[gmx-users] Lysozyme tutorial-error with moleculetype

Justin A. Lemkul jalemkul at vt.edu
Mon May 21 19:46:41 CEST 2012

On 5/20/12 8:18 AM, delara aghaie wrote:
> Dear Gromacs Users
> I am doing Justin's Lysozyme tutorial. In EM step I got the error with molecule
> type. (I am using Gromacs, 4.0.5)
> It was about Cl and Na. I noticed that because I have selected OPLS forcefield,
> I should change the name of Cl and Na in my .top file to Na+ and Cl-.
> I did this and again when using grompp to create *.tpr file for energy
> minimization, it says that
> -----------------------------
> WARNING 1 [file topol.top, line 18272]:
> 8 non-matching atom names
> atom names from topol.top will be used
> atom names from 1AKI_solv_ions.gro will be ignored
> --------------------------------------
> Should I change the ions name in .gro file also to Cl-? is it only for atom name
> or also for atom number (coulumn 2 in .gro file)?

The names specified in the topology (and thus supplied to -pname and -nname) 
must match the [moleculetype] name(s) specified in ions.itp.  Previous versions 
of Gromacs (before 4.5) had a haphazard naming scheme that was standardized for 
4.5.  In the case of 4.0.5, you'll have to look up the proper names - genion 
will add them correctly if you do, otherwise you will also have to modify the 
residue and atom names in the coordinate file.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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