Hi all!<br>The protein that I am trying to simulate has 3 chains. My aim is to apply harmonic constraints <br><br>to certain parts of the protein and (based on FRET derived distances) I am attempting to incorporate distance constraint between certain amino acids of different chains during EM and MD.<br>
<br><u>Harmonic Constraints</u><br><br>I figured, that for the harmonic constraining the input is in the file "posres_D.itp" and I specify<br><br>define = -DFLEXIBLE -DPOSRES in the em.mdp<br><br><u>Distance constraints </u><br>
<br>I would also like to have amino acids contrained, not by a fixed distance but within a range(say 45-75 angstroms). How do I go about doing this?<br>thanks<br>Jayant James<br><br>-- <br>Jayasundar Jayant James<br><br><a href="http://www.chick.com/reading/tracts/0096/0096_01.asp">www.chick.com/reading/tracts/0096/0096_01.asp</a>) <br>
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