Re: AMBER: parameters for Nickel and iron

From: Rachel <>
Date: Wed, 27 Sep 2006 14:53:45 +0100

Hi, Junmei,

Thanks for your time to reply my question, I am now currently using Gaussian
to calculate the charges, and in the mean time I am trying to derive the
other parameters, can I ask are there any guidelines of deriving force field
parameters( I have read the parameter development chapter in the AMBER
manual)? or are there any similar examples I can follow?

Thanks again!
Best wishes,

On 9/26/06, Junmei Wang <> wrote:
> 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
> Junmei
> 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,
> Rachel

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Oct 01 2006 - 06:07:04 PDT
Custom Search