[gmx-users] using editconf to duplicate membrane

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jul 7 09:22:11 CEST 2009

Hi Bing,

You do want to use genconf for that (the way you use it, editconf
scales the coordinates).

genconf -f xxx.pdb -nbox 2 2 1 -o zzz.pdb

The thing to make sure is that all molecules are whole before
processing them with genconf. The other possibility is to use editconf
to translate a few copies of your system and then stitch these fiels
together. But genconf is quicker and more convenient.



On Tue, Jul 7, 2009 at 7:26 AM, Bing Bing<jarbing09 at gmail.com> wrote:
> Dear all,
> I want to extend the membrane into 512 POPC with the starting structure of
> 128 POPC. I 've used :-
> editconf -f xxx.pdb -scale 2 2 1 -o zzz.pdb.
> I noticed that the pdb file that generated by editconf have only 1 set of
> 128 popc. Using vmd, the extended structure is in pieces, the no bond
> between each atom. When i checked the pdb file, i didn't find any atomic
> coordination for the extended set of POPC. Did i missed out anything here?
> or what I've done is wrong here?
> When i used genconf , the extended structure looks fine. But, i found some
> discussion regarding genconf whereby the structure will not be in one pieces
> if this command is used. Please advice.
> Thank in advance.
> Regards,
> bing
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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