AMBER Archive (2008)

Subject: AMBER: RMSD calculation using AMBER7

From: Biman Jana (bjana_at_sscu.iisc.ernet.in)
Date: Sat Jan 19 2008 - 07:16:46 CST

Dear Users,
          I am doing a temperature dependent study of aqueous dupleax DNA.
I have a 38 base pairs (76 residue) DNA. I want to calculate the RMSD of
the DNA at each temperature. I am a new user and know very less about
calculating RMSD using ptraj or carnal. Can anybody please tell me what
will be the standard ptraj.in file for this. Any suggestions will be
highly appreciated.

Biman Jana 

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