AMBER Archive (2006)

Subject: RE: AMBER: parameters for Nickel and iron

From: Junmei Wang (
Date: Tue Sep 26 2006 - 16:38:08 CDT

Hi, Rachel,
I am sorry for not replying this email promptly. In my opinion, you may
create a model molecule that has four CYS coordinating with Ni cation,
then run gaussian optimization and generate resp charges, then generate
two kinds of residues: Ni cation and CYS,which has different charges
from those of the standard CYS residue. You might need to manually add
bonds between Ni and S of CYS in Leap. You also need to derive many
force field parameters by yourself (be cautious, it is possible that
more than two kind of bond angles (S-Ni-S), 90 or 180 degrees involved
depending on the configuration of the model molecule).
I am not sure if you could just ignore the covalent bonds and Ni becomes
a localized cation, if it is OK, you do not need to generate a new
residue for CYS at all.
Good luck

However, Junmei, after I read the information you gave about using
antechamber I still don't quite understand how to use it. For example, I
have Ni ions bound to four CYS residues (e.g. CYS11, CYS35, CYS100,
CYS218), do I just need to cut these residues from the original PDB file
and follow the procedures? Do I need to have Gaussian software or it can
be done only using antechamber? And also the way it tells is quite
different from what the amber workshop tutorial 5 does it, can you
please tell me more about it? I tried to cut those residues out from the
PDB and followed the tutorial 5, it gave me error message 'can't open
ANTECHAMBER_AM1BCC.AC', why is that? Thanks a lot, I am such a newbie in
this, and thank you very much in advance.

        Best regards,

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