[gmx-users] simulating dimer proteins

delara aghaie d_aghaie at yahoo.com
Fri Jun 15 07:56:14 CEST 2012

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

Your help would be greatly appreciated

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