[gmx-users] merging simulation boxes

Mark Abraham Mark.Abraham at anu.edu.au
Fri Sep 18 01:37:57 CEST 2009

Paymon Pirzadeh wrote:
> I have a box of crystal (from another simulation) and a box of solvated
> protein. Now I want to put the protein close to my crystal.

Throw the water away, so you have two coordinate files, one of protein 
and one of crystal each in the same format. You can translate and rotate 
these with editconf if you want. Then you can literally concatenate them 
in a text editor, taking care to preserve formats correctly (e.g. .gro 
requires the number of atoms given in the first few lines is correct). 
Then box with editconf and solvate with genbox. Before you start, obtain 
.itp files for each type of molecule, which you can now use to build a 
.top file by hand (using pdb2gmx will probably fail or make headaches).

Alternatively, some "docking" software may offer some automation, or 
ways to generate a series of possible orientations.


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