[gmx-users] grompp error

[Justin A. Lemkul]

Q. Y. HUAN wrote:
>  Dear all.
> I wanted to run grompp in order to perform Em, but it showed me this fatal errer::
> 
> 
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> calling /usr/bin/cpp...
> processing topology...
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Cleaning up temporary file grompptz9Dth
> 
> -------------------------------------------------------
> Program grompp_d, VERSION 3.3.3
> Source code file: toputil.c, line: 61
> 
> Fatal error:
> Atomtype 'CH3' not found!
> -------------------------------------------------------
> 
> what is the error and where the source code file located?
> 

There are several possibilities for this error:

1. You haven't included the proper force field file (ff*.itp) in your topology.
2. You have otherwise mangled the format such that grompp simply cannot find the 
parameters it is looking for.
3. You are using atom types that do not exist within the force field you wish to 
use.

Without more information about your system, we can only guess.

-Justin
> thanks
> 
> 
> QIU YI HUAN
> A beginner of Gromacs user.
> 
> 
>       
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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