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

[Adva Suez]

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
 Web-site:
http://www.tau.ac.il/lifesci/bioinformatics.html
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101201/7d7d43cb/attachment.html>