[gmx-users] Adding ions

[Jordi Camps]

Hello!

You are right. I must make this change, but first I need genion to run
smoothly. Right now, genion does not put any ion in my coordinate file.
I tried to active PBC and then genion worked, but I wanted to try to do this
simulation without PBC. Maybe is this a non-sense?

Thanks for your help :-)

-- 
Jordi Camps Puchades
Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
UPC-CIRI
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

-----Mensaje original-----
De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] En
nombre de Kai Zhuang
Enviado el: miércoles, 25 de mayo de 2005 22:32
Para: Discussion list for GROMACS users
Asunto: Re: [gmx-users] Adding ions


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
kai

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 
> UPC-CIRI 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
6478314789
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