[gmx-users] Regarding error in ion neutralization step

[Mark Abraham]

On 5/11/2011 1:05 AM, kirubakaran palani wrote:
> Dear All
>
> Could any one help me to solve this error in gromacs 4.5.5 version. I 
> am running dynamics on apo protein and the protein shows negative 
> charge of -6 (after choosing OPLS-AA force filed) and when i was 
> neutralizing the -6 with +6 and generating the genion.tpr file there 
> it shows "No such moleculetype NA+" error. But the same protein was 
> running with out any error message in gromacs 4.0.7 version.

The naming convention has changed. See share/top/oplsa.ff/ions.itp

Mark

>
> The error message was given below.
>
> Kindly rectify the problem
> =======================================================================================
> [student at localhost gro]$ grompp -f em.mdp -p topol.top -c genion.gro 
> -o genem.tpr
>
>
> Ignoring obsolete mdp entry 'cpp'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
> 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
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: toppush.c, line: 1987
>
> Fatal error:
> No such moleculetype NA+
> For more information and tips for troubleshooting, please check the 
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> ========================================================================================
>
>
>
> Regards
>
> Kirubakaran P
>
>
>

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