AMBER Archive (2006)

Subject: AMBER: how to calculate the RMSD and B-factor for all atoms of residue

From: haixiao jin (jinhx952_at_gmail.com)
Date: Mon Mar 06 2006 - 02:13:04 CST

dear Amber users,
     at the most time, we just need to obtain the RMSD and B-factor of CA
atom or backbone atoms.
     however, to get the conformation change of a special loop in MD
simulation, the RMSD and B-factor of all atoms in this loop is useful. but i
do not know how to make the input file for ptraj analysis.
    is there anyone who made the input file for analysis the RMSD and
B-factor for all atoms? i need you help, thank you!

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