Re: [AMBER] Building parameter files for a zinc finger

From: FyD <>
Date: Sat, 11 Jan 2014 14:01:13 +0100

Dear Yip Yew Mun,

> I'm currently planning to simulate a zinc finger where 4 cysteine
> residues are coordinated to a zinc ion. I changed the CYS to CYM. I
> also created a non-standard residue for the zinc ion. I wish to ask
> if I need to explicitly use the command "bond" to bond the SG atom
> of my CYM residues to the zinc ion.?

If you decide to use R.E.D. Server Dev. provide a PDB input for the
active site (no need to define the bonds if the geometry given as
input is reasonable); R.E.D. Python will generate the FF for you and
list missing FF parameters if any.

4 cys(-) + Zn2+ -> total charge : -2

Zn 30 (12) [Ar].3d10.4s2 || || || || || ||
Zn++ [Ar].3d10 || || || || ||
     -> spin multiplicity 1

Provide a Project.config file with only

Provide a file with only
MOD_GAUSSIAN_JOB = "complex"

tar zcvf Archive.tgz Mol_red1.pdb Project.config

& upload this archive file at
(after registration: see to get a
private account)

then we will discuss about the data generated:

regards, Francois

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Received on Sat Jan 11 2014 - 05:30:02 PST
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