AMBER Archive (2007)

Subject: AMBER: How to use AMBER Parameter Database ?

From: Qiang Zhong (zqiang320_at_webmail.hzau.edu.cn)
Date: Wed Aug 22 2007 - 03:53:04 CDT

Dear Amber users:
          I have a protein complex which is consist of ADP ,Ca2+ and THP. I find
parameter file of these non-standard residue in http://pharmacy.man.ac.uk/amber/.
But I have some problem , THP is simple, I just need use command:loadOff
amber_thp.lib.
It is ok, but ADP and Ca2+ is not like THP, They are .prep format. I don't know
how to use it.
Could some body tell me
how to do? Thank you very much!

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