[gmx-users] Fatal error: No such moleculetype Cl

[Xavier Periole]

On Tue, 6 May 2008 13:17:29 +0530 (IST)
  namita at ncbs.res.in wrote:
> Dear Users
> 
> When I try adding charges (negative charges by adding Cl), using the command
> 
> /opt/gromacs/bin/grompp_mpi -np 32 -f em_cc.mdp -po det_em2.mdp -c
> 1A92_m1_neu.gro -p 1A92_m1.top -o 1A92_m1_em.tpr
> 
> it gives me the following error...
> 
> -------------------------------------------------------
> Program grompp_mpi, VERSION 3.3.1
> Source code file: toppush.c, line: 1293
> 
>Fatal error:
> No such moleculetype CL
> -------------------------------------------------------
> 
> 
> Could anyone tell me what would be the possible reason for this error?
Simply that the program does not know things you do not tell it!
you need to "#include ions.itp" in you topol.top file.

It looks like you are a beginner with gromacs ... I would advise you
to take the time to go through the tutorial and the wiki to get an
idea of what can be a solution for the problem(sssssss) you will
go through and try to solve them by yourself at least partially.
Using the list to get a quick answer to the step by step process of
setting up a simulation is not the best way to learn.
> 
> Thanks in advance
> 
> Namitha Mohandas
> National Center for Biological Sciences
> Tata Institute of Fundamental Research
> Bangalore
> India
> 
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------