Dear AMBER users,
> I have carried out cluster structure analysis of a 15-residue peptide> (under study) from the temperature based trajectory (obtained from REMD> simulation). It shows that population of native structure is always the> major one irrespective of the number of cluster("n") I put in the ptraj> input file:> >> >> >cluster out c-out representative pdb average pdb averagelinkage \> >clusters "n" mass rms "(:1-15) & .CA,C,N,O"> >> >> For example,> Two Cluster Distribution shows : 84.8% (native), 15.2%> Three Cluster Distribution shows : 71.8% (native), 13.0%, 15.2%> Four Cluster Distribution shows : 60.5% (native), 13.0%, 15.2%, 11.3%> Five Cluster Distribution shows : 55.5% (native), 13.0%, 5.0%, 15.2%,> 11.3% and so on..>> When I tried to find out rmsd values from the clusters, I have found that> for a particular conformation of the peptide having high value of rmsd is> included in native cluster and a conformation having a smaller value of> rmsd is included in non-native cluster, which led me to conclude tha
t rmsd> is not appropriate enough to explain the folded/unfolded behavior of this> peptide.> Hence the criteria (rmsd < 0.12 nm) that I assumed to put previously for> generation of melting curve is proved to be incorrect.> Will you please confirm me whether I can use the population of native structure> obtained directly from cluster structure analysis for generation of> melting curves or not.>> Thanking you for your valuable suggestions.>> With Regards..> Sincerely> Gargi
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Received on Sun Oct 06 2013 - 21:00:04 PDT
