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: [email protected] <mailto:[email protected]>
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
[email protected] http://folding.bmc.uu.se/
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