Dear all,
I need to make 3 Calpha atom based cross-correlation matrix after aligning
reference pdb frame with 15 MD frames (from same PDB). The cross
correlation values require to come from RMSD between reference frame and
each MD frame i.e. from reference amino acid (i) Calpha and respective MD
frame ith amino acid Calpha and (i+1)th amino acid Calpha. It may be the
dot product between calculated two single Calpha-Calpha correlation values
(Please correct me if I am wrong!).
Is it possible in amber?
Thanks in advance,
Best regards,
Arpita
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Received on Tue Aug 15 2017 - 23:00:03 PDT
