[AMBER] cpptraj - atomicfluct

From: George Tzotzos <gtzotzos.me.com>
Date: Mon, 15 Sep 2014 15:57:57 -0300

Im trying to calculate B-factors for the backbone CA atoms of selected residues (18-125)

My input script (atomicfluct.in) is:

trajin prod_20ns.nc
rms first mass out rmsd_first.dat :18-125.CA
atomicfluct out bfactor.apf .CA byatom bfactor

Both ptraj and cpptraj produce an output (bfactor.apf) that fails to select the residues in the mask. Instead it produces B-factors for all residues (1-125).

In addition, the bfactor.apf output in ptraj shows residue numbers whereas in cpptraj atom numbers.

Id appreciate any suggestions how to modify the script to select only the residues in the mask and additionally to have cpptraj generating an output with residue numbers rather than atom numbers

Thanks in advance for any suggestions



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Received on Mon Sep 15 2014 - 12:00:02 PDT
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