Normally I use the following input file for ptraj to generate the correlation matrix for all the C-alpha at oms:
trajin mdcrd
rms first .CA
matrix correl name correlation @CA out correl-matrix
Now I would like to generate a correlation matrix that contains all the C-alpha atoms as well as the atoms in the substrate (e.g., in the pdb file the name of the substrate is "SUB", the atom number of the substrate runs from 3000 to 3020). I want to know if there is a way of incorporating the information about atom type as well as atom number (or residue name) in the
input file. I can specify the protein atoms by type (CA) and the substrate atoms by their atom numbers, and the problem is that how to combine both in the input file to produce a matrix that's for both?
Thank you for your help
SUN XI
University of Tennessee, Knoxville
Knoville, TN 37996
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Received on Thu Sep 22 2011 - 22:30:02 PDT
