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 Regards D.M
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