[gmx-users] Lysozyme tutorial-error with moleculetype

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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