[gmx-users] Insertion of polymer into the bilayer

[varsha gautham]

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.

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?

Thanks for giving your  valuble time to read this mail

-varsha