AMBER Archive (2007)

Subject: AMBER: How to use AMBER Parameter Database ?

From: Qiang Zhong (zqiang320_at_webmail.hzau.edu.cn)
Date: Tue Aug 21 2007 - 07:36:46 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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