[AMBER] cpptraj: structures not aligned anymore after 'run' keyword

From: Guillaume Roellinger <roellinger.bio.mx>
Date: Wed, 14 Jan 2015 13:06:23 +0000

Dear all,

During a PCA with cpptraj, for some reasons after the keyword 'run', the structures from the MD trajectory are not aligned anymore even if I aligned them with the keyword 'rms' before the 'run'. In case of PCA, this leads to a wrong result for the projection: unaligned snapshots are projected onto the PCs from evecs.dat.

I solved the problem by adding 'rms RMSD2 reference out RMSD2.dat .CA' just after the 'run' and before 'readdata' but I wonder: Is this the normal behavior of cpptraj to get back to the unaligned frames after the 'run' keyword?

(I am using AmberTools14, cpptraj V14.22 and calling cpptraj using '$AMBERHOME/bin/cpptraj -i PCA.in ' )

Thanks for your help,




parm myParm.prmtop

trajin myMDtraj.mdcrd parmindex 0
parm averageStructureCA.prmtop
reference averageStructureCA.pdb parmindex 1
rms RMSD reference out RMSD.dat .CA
matrix covar name cvmat out cvmat.dat .CA
diagmatrix cvmat out evecs.dat vecs 50 name mymodes

readdata evecs.dat
projection modes evecs.dat out project.dat beg 1 end 50 .CA
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Received on Wed Jan 14 2015 - 05:30:06 PST
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