[gmx-users] how to specify a location of a molecule in the system

[Erik Marklund]

Hi,

Perhaps you can do just like you did in pymol, but isntead of saving the 
file, mearly write down the coordinates of the newborn water and enter 
it into your gro-file.

Cheers,

Erik

Adva Suez skrev 2010-12-01 08.59:
> Hello all!
> I would like to insert a molecule to a membrane system and would like 
> to start from a specific position of the molecule (hydrocarbon or 
> lipid headgroups). I tried doing that in Pymol after converting the 
> merged gro into pdb (using editconf) but when I saved the file in 
> Pymol the order of the lipids atoms got mixed up and it does not match 
> the dppc.itp anymore. Then it caused problems in grompp.
> Do you have another way to set the position of the molecule in the 
> system? maybe without converting to PDB...??
>
>
> Thanks,
> Adva.
>
> -- 
> Adva Yeheskel
> Bioinformatics Unit
> Rm 001, Sherman bldg.,
>  G.S.W. Faculty of Life Sciences
>  Tel-Aviv University, ISRAEL 69978
>
>  Tel: 972-3-6406840; Fax: 972-3-6405098
>  E-mail: suezadva at tauex.tau.ac.il <mailto:suezadva at tauex.tau.ac.il>
>  Web-site:
> http://www.tau.ac.il/lifesci/bioinformatics.html 
> <http://www.tau.ac.il/lifesci/bioinformatics.html>
>


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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