[AMBER] Problem related to the trajectory analysis

From: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>
Date: Thu, 4 Oct 2012 02:20:10 +0800 (SGT)

Dear all
I want to analyze the rmsd of the backbone of a protein structure. The protein is dimer and residue 1-396 and 398-793 are the amino acids. The 397 and 794 no residue are the substrates for two chain. I have the trajectory file. I use the following to compute the rmsd in the script file
rms first out BB.out :1-396.CA,N,C :398-793.CA,N,C time 0.1
Is it correct? Is it compute the rmsd of backbone for two chains?
With best regards
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Received on Wed Oct 03 2012 - 11:30:04 PDT
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