Re: [AMBER] Aligning a dimer for PCA analysis

From: Daniel Roe <>
Date: Fri, 21 Jan 2022 14:23:25 -0500


One thing you may want to try is doing 'unwrap' on the trajectory
(instead of re-imaging); this should remove any imaging artifacts. I
would test it first by doing unwrap and then visualizing the
trajectory before proceeding with any PCA.


On Fri, Jan 21, 2022 at 11:21 AM Kodituwakku,Dimuthu Nirmani
<> wrote:
> 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 Fri Jan 21 2022 - 11:30:02 PST
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