[gmx-users] Insertion of polymer into the bilayer

[Mark Abraham]

varsha gautham wrote:
> Dear all,
> 
> I want to insert polymer in the aqueous phase of the bilayer.when i
> read through the mailing list i found that this can be done in three
> ways
> 
> 1.By using genbox command
> 
> genbox -cp polymer.pdb -cs bilayer.pdb -o merged.pdb
> 
> this results in the insertion of polymer molecules to the centre of
> the bilayer.what has to be done if i want to insert that just above
> the aqueous phase of the bilayer.

As I said three days ago, you can do this through "judicious use of 
editconf" having "read the man pages for genbox and editconf thoroughly" 
:-) See http://www.gromacs.org/pipermail/gmx-users/2009-February/039886.html

> 2.If this can be done with vmd using move-> then save cordinates, then
> tell me clearly how it can be done.
> 
> 3.If this  can be done with making a hole and inserting the polymer
> into this hole by means of  perl script.May i know where it is
> avilable?

Mark