[gmx-users] Adding ions

Kai Zhuang kai.zhuang at gmail.com
Wed May 25 22:32:01 CEST 2005

u need to edit ur top file manually afterward,
because for some reason genion is not designed to modify the top file for you.
so u open the top file, at the very end should be like

SOL     7092

that's the number before the change made with Cl
so you change the number to 7091

then u add an line something like
CL-        1

should work, at least that's the idea

On 5/25/05, Jordi Camps <jcamps at lsi.upc.edu> wrote:
> Here I come with more problems :-(
> I have a protein file with 126 residues. I generated the topology from the
> .gro file with pdb2gmx. Then I configured the box with editconf. Then I
> added the solvent with genbox. At least I wanted to neutralize the system
> with genion, but it gave me this error:
>         Fatal error: pbc_dx called before init_pbc
> This time I think that I followed all the standard steps. Do you know which
> could be the cause of this error?
> The command was:
>         $ genion -s 1agi.water.top -o 1agi.ion.gro -nn 6
> And the last lines before the error are:
>         Selected 12: 'SOL'
>         Number of (3-atomic) solvent molecules: 7092
>         Doing single force calculation...
>         Replacing solvent molecule 1626 (atom 6216) with Cl
>         Fatal error: pbc_dx called before init_pbc
> Thank you in advance,
> --
> Jordi Camps Puchades
> Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
> c/. Jordi Girona 1-3
> Modul C6-E201                     Tel. : 934 011 650
> E-08034 Barcelona                 Fax  : 934 017 014
> Catalunya (Spain)                 e-mail: jcamps at lsi.upc.edu
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Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
kai.zhuang at gmail.com

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