[gmx-users] Adding ions

Jordi Camps jcamps at lsi.upc.edu
Wed May 25 20:54:30 CEST 2005

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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