VMD-L Mailing List

From: David Tanner (dtanner_at_ks.uiuc.edu)
Date: Tue May 19 2009 - 11:00:30 CDT

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
dtanner_at_ks.uiuc.edu
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Mon, May 18, 2009 at 6:07 PM, Lalit <upmunyu_at_gmail.com> 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.
>
>