[gmx-users] best way to create a pdb file.

[K.A. Feenstra]

Senthil Kandasamy wrote:
> 
> What is the easiest way to accomplish the following?
> 
> I have a pdb file of a lipid bilayer. I need to insert a protein bundle
> into this bilayer. I have the pdb coordinates of the protein bundle
> also. Now, I edit the lipid pdb file to create a hole (that would
> approximately fit my bundle) at the center. Both the bundle and the
> lipids are centered using editconf. Upto this point, I have two pdb
> files. Now, what is the easiest way to create a single pdb file of this
> structure (That would essentially have the bundle inserted into the
> lipid layer)
> 
> I have to go through a lot of manual manipulations to be able to do that
> at this point. IS there an easier way to accomplish this?

Any simple text-editor (emacs, jot, notepad, even vi!) can do this.
Or even simpler 'cat protein.pdb bilayer.pdb > system.pdb' will do it...

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \_X-Mozilla-Status: 0009etting High, Knock Me Down"               |
|        | (Red Hot Chili Peppers)                                   |
|________|___________________________________________________________|