[gmx-users] protein-dna interaction

Mark Abraham Mark.Abraham at anu.edu.au
Mon Aug 31 09:51:50 CEST 2009

leila karami wrote:
> Hi
> I want to study protein-dna interaction by gromacs. But I have 2 separate
> pdb file for protein and dna(there is no 1 pdb file containing both protein
> and dna). Can I do this correctly? Is this work current and usual? please
> guide me.

You will need to end up with one coordinate file containing both 
structures to be your MD starting structure. If you need to dock the 
protein and the DNA first, then you have a problem outside the scope of 
GROMACS, and should check the literature to see what people do in such 

If you just want to put them in the same general area and watch what 
happens, then you can just make sure the coordinates aren't overlapping 
and concatenate the files in a text editor, preserving the file format 
correctly. Good luck finding anything useful in the MD, in such cases!


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