[gmx-users] gromacs (4.5) installation problem

[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.
> 
> My system contains only C and H atoms!. Force field: OPLSAA
> 
> 
> 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
> 
> 
> 
> 

This is probably a bug that has already been fixed, but is only available in the 
git repository.  The fix is to change the capitalization of both CU2+ and ZN2+ 
in oplsaa.ff/ions.itp.  They should be Cu2+ and Zn2+, respectively.  Otherwise, 
don't #include "ions.itp" in your topology if you don't need it.

-Justin

-- 
========================================

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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