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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