AMBER Archive (2003)

Subject: AMBER: how to calculate vibration frequency?

From: A. Hungie (hungie01_at_hotmail.com)
Date: Wed Dec 03 2003 - 08:46:26 CST

Dear all,

I am using Amber 6 package. I have 20 ps MD trajectory file stored every 2
fs of DNA configurations (performed by SANDER).
I would like to calculate the vibration frequency of nucleobases along the
trajectory. What module of AMBER6 can be used? Can ptraj does this? By the
way, it is not a big deal to re-simulate, if necessary.
Thank you very much in advance.

Regards,
Hungie

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