[gmx-users] Re: grompp error

Mijiddorj mijiddorj_batsaikhan at yahoo.com
Wed Jan 2 16:44:59 CET 2013

Dear Justin, Thank you for your helpful suggestion. 


 From: Justin Lemkul [via GROMACS] <ml-node+s5086n5004199h70 at n6.nabble.com>
To: Mijiddorj <mijiddorj_batsaikhan at yahoo.com> 
Sent: Wednesday, January 2, 2013 11:10 PM
Subject: Re: grompp error

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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