Re: 2 proteins

From: L. Michel Espinoza-Fonseca (
Date: Tue Apr 17 2007 - 05:30:02 CDT

Hi Christine,

If I understood well, what you want is to perform protein-protein docking,
right? If that's the case, the situation is a little bit tricky, specially
if your proteins are relatively big.

If the only thing you want to get is a complex between two proteins, I
recommend you to try out some of the available protein-protein (rigid)
docking programs (ESCHER, for example). You could even use AutoDock, which
has been successfully used to get some interesting protein-protein
complexes. When you have a good model, then you can do some MD simulations
on your model; eventually, if you're interested in calculating the free
energy of binding, you could use some other method to achieve it (such as

Let us know if you need further information.


2007/4/17, Christine Horejs <>:
> Hi!
> I don't know, how to simulate the interaction between 2 proteins. I want
> to constrain one protein in its center of mass and pull the second protein
> to the first one to check the interactions between the 2 proteins!
> Does anybody know, how to set up such a simulation, mainly the
> configuration file? Do I need seperate pdb and psf files for the 2 proteins?
> I hope that anybody can help!
> Thank you very much and greetings from Vienna,
> Christine
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