Re: [AMBER] Generation of melting curves

From: Brian Radak <>
Date: Mon, 7 Oct 2013 09:39:08 -0400


It's been a long time since I've looked at protein folding, but I do recall
that rmsd is generally not as great of a distance metric for structural
similarity as one might desire. Other metrics such as radius of gyration
and solvent accessible surface area might be useful and I'm quite sure
cpptraj is capable of calculating these things (although I'm not sure they
can be used as a distance metric for clustering, I'm sure Dan or others can
comment on this).

For a good paper describing melting curves from replica exchange for a
variety of order parameters, I would recommend the following.

Pitera, J. W. and Swope, W. Understanding folding and design:
Replica-exchange simulations of "Trp-cag" miniproteins*. Proc. Natl. Acad.
Sci. USA* *2003**, 100*, 7587-7592.

It's fairly old and the authors use implicit solvent. There might be a
follow up with explicit solvent, but I don't have the citation.


On Sun, Oct 6, 2013 at 11:59 PM, Gargi Borgohai <>wrote:

> 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
> that 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
> _______________________________________________
> AMBER mailing list

================================ Current Address =======================
 Brian Radak                                             :     BioMaPS
Institute for Quantitative Biology
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Received on Mon Oct 07 2013 - 07:00:04 PDT
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