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

[Justin A. Lemkul]

Adva Suez wrote:
> 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...??
> 

You can use editconf -translate/-rotate/-center to manipulate the position of 
the molecule.

-Justin

> 
> 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>
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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