<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt">Dear Gromacs users<br>I want to compare some properties of two Interferons via MD simulation.<br>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.<br><br>The other is with pdb ID of : (1RFB). This has two chanis<br>--------------------------------<br>DBREF 1RFB A 1 119 UNP P07353 IFNG_BOVIN 24 142<br>DBREF 1RFB B 1 119 UNP P07353 IFNG_BOVIN 24 142<br>-------------------------------<br><br>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?.<br>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)<br> I want to know if it is common to do MD on selected chain of a dimer?<br><br>Your help would be greatly appreciated<br><br>Regards<br>D.M<br></div></body></html>