[gmx-users] Re: pdb2gmx

Jon jon.ellis at utoronto.ca
Fri Jul 15 23:53:55 CEST 2005

Hi Javier
If you're trying to make an ordered series of your chain, you can use
genconf to stack your molecule, using the -nbox and -dist and -renumber
options. This is a useful method to create membranes. I think its been
covered in the list before.


Jon Ellis
Institute of Biomaterials and Biomedical Engineering/Dept of Chemistry
University of Toronto
jon.ellis at utoronto.ca

> First of all thank you very much for your really fast answers.
> Thanks to Robert Murawski, but I thought that genbox only works with
> small molecules (to solvate your system). Anyway I will try to use to
> replicate my initial system , only one chain and after could I use it
> to solvate the new system (with n chains)?
> Thank you for your help I really appreciate it
> Javier

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