[AMBER] Aligning a dimer for PCA analysis

From: Kodituwakku,Dimuthu Nirmani <dkodituwakku.ufl.edu>
Date: Fri, 21 Jan 2022 16:19:36 +0000


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
parm ionizedph77.pdb [structX]
reference ionizedph77.pdb parm [structX]
crdaction deglyco-average-traj rmsd reference [structX] :1-1174.CA,C,O,N
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
crdaction deglyco-average-traj matrix correl :1-1174.CA :1-1174.CA out glyco2correlmatA.dat
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 - 08:30:02 PST
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