[gmx-users] grompp error

Justin Lemkul jalemkul at vt.edu
Wed Jan 2 16:08:21 CET 2013

On 1/2/13 10:01 AM, Mijiddorj wrote:
> Hello all, I am new user of gromacs. I am doing Tutorial 1. When I run
> grompp, following problem occurred:Program grompp, VERSION 4.5.3Source code
> file: toppush.c, line: 1987Fatal error:No such moleculetype CL-For more
> information and tips for troubleshooting, please check the GROMACSwebsite at
> http://www.gromacs.org/Documentation/ErrorsHow can I solve this?Mijiddorj

You named your ions wrong.  Please read the help information from genion -h:

"The ion molecule type, residue and atom names in all force fields are the
capitalized element names without sign. This molecule name should be given
with -pname or -nname, and the [molecules] section of your topology updated
accordingly, either by hand or with -p. Do not use an atom name instead!"

Note that, if you are referring to my "Tutorial 1" on lysozyme, the naming issue 
is explained and the genion command should be copied verbatim, as I do not use 
any +/- signs in the -pname or -nname options.



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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