[gmx-users] Fatal Error: The largest charge group contains 140 atoms. The maximum is 32

[Justin A. Lemkul]

Lalit wrote:
> Hi All,
> 
> At this time, I am very much interested in using gromacs utilities for 
> analysis with {.dcd, .psf} files. Especially, eg., for g_density.
> Primarily, I use NAMD/VMD for my work.
> 
> I am following this link from NAMD mailing list:
> 
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/14046.html
> 
> As suggest, by Axel, I was able to get the {.top} file.
> 
> However, when I used gromacs's "grompp" command:
> 
> $ grompp -f minim1.mdp -c BL1_only.pdb -p BL1_only.top -o BL1_only.tpr
> 
> I was returned with an error like this:
> 
> * * *
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
> Generated 231 of the 231 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 231 of the 231 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'molecule0'
> Excluding 3 bonded neighbours molecule type 'molecule1'
> 
> NOTE 1 [file BL1_only.top, line 1880]:
>   System has non-zero total charge: -5.999999e+01
> 
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.5.4
> Source code file: 
> /home/mandrake/rpm/BUILD/gromacs-4.5.4/src/kernel/grompp.c, line: 175
> 
> Fatal error:
> The largest charge group contains 140 atoms. The maximum is 32.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> 
> My system is a mixed bilayer with negative 60 charge on it.
> 
> I am searching gromacs mailing list and still looking for an answer.
> 
> Is there a way to use g_density with my set of files - {.psf, .pdb, .dcd} ?
> 

The problem is the .top - as the error states, you have far too many atoms in a 
charge group for grompp to actually let it pass.  For simply doing analysis and 
not an actual simulation, there is nothing wrong per se, but you will not be 
able to create the necessary .tpr file.  Charge groups should contain between 1 
and 4 atoms, based on functional groups.  The only way to make grompp work would 
be to re-number your charge groups.  See .rtp files for examples.

-Justin

> 
> Please suggest and help. 
> 
> Thanks a lot,
> --- Lalit
> 
> p.s.: All relevant files: BL1_only.pdb; BL1_only.psf; BL1_only.top & 
> minim1.mdp can be downloaded from:
> 
> http://lalitpkc.phy.uic.edu/~lalit/GROMACS_files 
> <http://lalitpkc.phy.uic.edu/%7Elalit/GROMACS_files>
> 
>  
> 
> 
> 
> 
> 

-- 
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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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