From: Lalit (
Date: Wed May 20 2009 - 13:36:56 CDT

Hello David,

Many thanks for the input.

Yes, I have removed the 'END' tag from the first PDB file (I am adding just
two PDB files).

I used cat command as well as text editor (gedit/RedHat Enterprise Linux WS
release 4) to check the PDB files. Everything (formatting, tags) are OK.
Even, I was able to run NAMD2. The runs were fine (I have all the desired
output files).

However, when I wanted to see the 'protein' (within/around the lipid

i) As Coloring Method: Structure & Drawing Method: NewCartoon I was NOT able
to visualize it.
ii) Also, with Drawing Method: Cartoon; NewRibbons, Ribbons, Tube,Trace; it
wasn't visuable (A faint/very small part/structure was showing on the
iii) Though it was showing the full protein's structure in Licorie, cpk,
vdw, points, Hbonds, Dynamicbonds, Bonds,Line; drawing methods. Which one do
not want!

I am using VMD 1.8.6 version. Both RedHat Enterprise 4 as well as Windows
version is showing exactly the same problem.

Please help.

Many Thanks,
--- Lalit

On Tue, May 19, 2009 at 11:00 AM, David Tanner <> wrote:

> A PDB file ends with the line 'END'. If you use the 'cat' command to
> concatenate 2 PDB files, you still need to remove the 'END' and other
> non-ATOM lines from the middle of the PDB file. Did you already remove these
> lines?
> Thank you,
> David E. Tanner
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> David E. Tanner
> Theoretical and Computational Biophysics Group
> 3159 Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews
> Urbana, IL 61801
> (217) 244 - 2905
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> On Mon, May 18, 2009 at 6:07 PM, Lalit <> wrote:
>> 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.