[gmx-users] simulating dimer proteins

[Mark Abraham]

On 15/06/2012 3:56 PM, delara aghaie wrote:
> Dear Gromacs users
> I want to compare some properties of two Interferons via MD simulation.
> One comes with pdb ID : 1ITF. (It has 24 Models in single pdb file, 
> but each model with single chain.) I did pdb2gmx on this.
>
> The other is with pdb ID of : (1RFB). This has two chanis
> --------------------------------
> DBREF  1RFB A    1   119  UNP    P07353   IFNG_BOVIN      24    142
> DBREF  1RFB B    1   119  UNP    P07353   IFNG_BOVIN      24    142
> -------------------------------
>
> Now the question: Is it wise to select only chain A and do the 
> simulations on it in order to compare with the 1ITF, which has one chain?.
> I have read about simulating multiple chains in manual. But I think 
> the comparison between a protein with single chain and the other with 
> two chains may not be correct. (I want to compare gyration radiuses 
> and secondary structures)

The number of chains is not really the issue - you want to compare 
things that are comparable. If 1RFB contains a dimeric structure that 
does the same job as the monomeric 1ITF then they might be comparable.

>  I want to know if it is common to do MD on selected chain of a dimer?

It happens. Whether it makes scientific sense in your case is something 
you have to address.

Mark
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