AMBER Archive (2006)

Subject: AMBER: simulate proteins with non-standard residues

From: Hui Lei (h.lei_at_qmul.ac.uk)
Date: Wed May 24 2006 - 12:10:08 CDT

Dear AMBER users,

I am a new user of AMBER, and I am trying to simulate proteins with non-standard
residues, such as laccase with four copper ions. I read the tutorial about
Plastocyanin (1PLC) which contains one copper ions, but still I am not so sure
how to load these residues into AMBER, shall I create a new library for each of
these four copper ions and then define the bonded atoms etc. parameters? BTW, I
am now using the tleap not xleap as somehow the cluster I am running AMBER on
does not support xleap.

I really appreciate your advice. Thanks a lot!

Best regards,
Hui
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