[gmx-users] gromacs (4.5) installation

[Justin A. Lemkul]

Moeed wrote:
> Dear experts,
> 
> I have installed newest version of gromacs (4.5) on our cluster. When I 
> issue the command below to test installation I get an error about atom 
> type CU+2. I am not using such atom type at all! Could you please help 
> me what wrong is. Thanks.
> 

No one can tell unless you describe what should be in the system, what is in the 
topology, what force field you're using, etc.

-Justin

> 
> grompp -f *.mdp -c *.gro -p *.top -o out >& output.grompp_md
> 
> 
> NOTE 1 [file md-NVT-revised.mdp]:
>   nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>   nstcomm to nstcalcenergy
> 
> 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
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.5
> Source code file: toppush.c, line: 1166
> 
> Fatal error:
> Atomtype CU2+ not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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