Re: [AMBER] Aligning a dimer for PCA analysis

From: Dr. Anselm Horn <>
Date: Mon, 24 Jan 2022 10:33:09 +0100

Dimuthu Nirmani,

the problem you describe is a general issue in superimposing two
structures: Also a single molecule might have two conformationally
stable domains connected by a variable region.
And there are several ways to superimpose those structures, i.e. fit to
each domain or to the whole structure etc, yielding different overlays
and different RMSD values. Thus, your decision depends on the research
question, and there is no general answer.

For dynamic cross-correlation analyses in a system with two flexible
entities, fitting influences the results, of course: Fitting on one
entity would sort-of zero-out its movements; maybe can gain some
information for doing this for each entity separately, focussing on the
movements of the other entity.

Maybe this helps.

Best regards,


Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)

> Hi,
> I'm using CPPTRAJ to do a PCA analysis on a dimer. However, monomers are non-covalently attached therefore moving and rotating a lot from one another. I'm having trouble aligning both monomers at the same time because of this. If I align the entire protein due to movements of monomers some parts of the monomers are not aligning well and that gives me an incorrect output. is there a way to align these structures? I have also copied my commands below (which also includes correlation matrix and distance matrix commands)
> parm nowater_glyco.psf
> trajin nowater1.dcd
> autoimage anchor :588-1174
> createcrd deglyco-average-traj
> run
> parm ionizedph77.pdb [structX]
> reference ionizedph77.pdb parm [structX]
> crdaction deglyco-average-traj rmsd reference [structX] :1-1174.CA,C,O,N
> run
> crdaction deglyco-average-traj matrix covar \
> name covar :1-1174.CA
> runanalysis diagmatrix covar out evecs.dat \
> vecs 10 name myEvecs \
> nmwiz nmwizvecs 5 nmwizfile glyco2A.nmd nmwizmask :1-1174.CA
> run
> crdaction deglyco-average-traj matrix correl :1-1174.CA :1-1174.CA out glyco2correlmatA.dat
> run
> crdaction deglyco-average-traj matrix dist :1-1174.CA :1-1174.CA out glyco2distmatA.dat
> Thank you !
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Received on Mon Jan 24 2022 - 02:00:02 PST
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