Here are the files with only CYX, HIE and HID names changed from the original cluster command output.
But I have taken the representative file and
So it seems like I get the representative structures from the MD trajectry with rather bad parameters like Ramachandran dihedrals etc. and only minimization corrects the a little, but I may expect that from the average structures, but the representative should be more native-like with better clashscores, better ramachandran parameters.
Sincerely yours,
Andrew
16.09.10, 02:18, "Thomas Cheatham III" <tec3.utah.edu>:
>
> > I am trying to get representative or average structure from molecular
> > dynamics trajectory. I want to use it or an ensembel of them for the
> > docking. I am using Molprobity as one of the assessment tools. I know
> > that it is not that straghtforward to use it for molecular models
> > assessment, but it is just some indicator for the comparison. The
> > strange thing that I get is that the quality of models which I get from
> > clustering both of representative structures and average is very bad
> > while PDB file generated from the rst file is much better. I can't
> > understand what is the basis for this. I can understand this for average
>
> We cannot understand either since we have no way to know what molProbity
> uses for assessment or whether the observed differences are "significant".
>
> If you are clustering the trajectories (and not the .rst files) then there
> is no reason that the "representative" should be equivalent to one of the
> .rst files. If you are clustering the .rst files directly, then the
> representative should match at least one of the .rst file structures; if
> it doesn't, this is an issue... (but lack of agreement could result from
> naming issues, see below).
>
> Looking at the overlap between the .rst and representative
> structures supplied, they are fairly close (1.6 A).
>
> There are differences in the naming, etc however... The restrt file has
> CYX residues (whereas the rep structure has CYS) at various places. The
> "rep" is in some Accelyrs PDB file format; this could be choking the
> molProbicity.
>
> The .rst file has CB hydrogens named "2HB" and "3HB" (which is not
> standard AMBER format (?) whereas the rep has "HB2" and "HB3". The .rst
> has "HIE", etc whereas the rep only has "HIS". Make sure when you are
> doing the molProb thing with PDB files were created by the same programs
> (i.e. same format, naming conventions, etc).
>
> --tec3
>
>
>
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Received on Thu Sep 16 2010 - 03:30:03 PDT
