VMD-L Mailing List

From: Lalit (upmunyu_at_gmail.com)
Date: Mon May 18 2009 - 18:07:34 CDT

Hi,

I have a situation.

I got two separate pdb files. one - A lipid bilayer with water on both
sides, plus Z & minus Z direction, and say, named as BL1_WAT.pdb. Second - a
protein pdb file, say, named as prot_only.pdb.

Now, I want to put the protein manually 'at a particular place' within the
lipid bilayer. This I was able to do (using moveby command). Once, I placed
the protein wherever I wanted to, I saved the prot_only.pdb file as say,
prot_only_final.pdb file.

Here, so far, whenever, I visualized the protein's pdb file I was using:
Coloring Method: Structure & Drawing Method: NewCartoon AND it was looking
OK as it should be.

However, when I just added/concatenated/copied & pasted the two pdb files,
likewise, BL1_WAT.pdb and prot_only_final.pdb INTO a single pdb file, say,
BL_and_prot.pdb file and then made the selection: "protein" within Graphical
Representation (after loading the file: BL_and_prot.pdb) and wanted to 'see'
the protein using--> Coloring Method: Structure & Drawing Method:
NewCartoon, it wasn't possible?

So, the situation is that when I have two separate pdb files (one of then is
a common protein's pdb file) I was able to visualize the protein using:
Coloring Method: Structure & Drawing Method: NewCartoon BUT when I just add
this protein's pdb file with another system's (equilibrated lipid bilayer
with water & ions) pdb file, I wasn't able to make the selection (for
protein or corresponding residue IDs) as: Coloring Method: Structure &
Drawing Method: NewCartoon.

I know, initially, there are lots of clashes/overlapping between protein's
residues and water/lipid residues (and I expect to remove these steric
clashes during equibrium) but still I want to 'visualize' the protein (as
Coloring Method: Structure & Drawing Method: NewCartoon ) and I know its a
common practice!

Let, me also add that, when my protein was, say, 10 Angstrom away from one
of the sides of the bilayer I was able to 'visulize' the protein as Coloring
Method: Structure & Drawing Method: NewCartoon. However, as the protein
approaches the bilayer and as such I adjusted the protein the way I wanted
it to place (at the lipid/water interface) I wasn't able to 'visualize' the
protein as Coloring Method: Structure & Drawing Method: NewCartoon.

I am missing something here. Please help.

Many Thanks,
--- Lalit

Note: I don't want topology/parameters for the combined (protein & lipid
bilayer) system or don't need to use combine.tcl script(s) as I am getting
parameters/topology files from amber.