Re: [AMBER] Generating parameter and topology files for a protein with multiple Zinc ions

From: Bill Ross <>
Date: Wed, 24 Aug 2016 21:19:37 -0700

It seems to me these instructions should generalize to multiple ions,
which you need to place manually yourself and bond explicitly I believe,
before loading the pdb you create elsewhere with all atoms:

Or you could place the ions in xleap and bond them there.


On 8/23/16 6:00 PM, Aditya Padhi wrote:
> Dear AMBER users,
> I am working with a Protein having DNA and multiple Zinc fingers. The Zing
> fingers are coordinated and stabilized by multiple Zinc ions i.e. around 6
> in number.
> When I am generating the parameters for Zinc ions using ZAFF for MD
> simulations in AMBER having multiple Zinc ions, it doesn't generate the
> .inpcrd file and after some tweaks, when I do it again, it saves the
> .prmtop and .inpcrd files but it keeps only 1 Zinc ion that too in the
> water box way far from the protein.
> I wanted to know if the ZAFF only works for a protein system having 1 Zinc
> ion or is there any way to include multiple Zinc ions and successfully save
> the parameter and coordinate files for all of them?
> Your help would be highly grateful.
> With best regards
> Aditya
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Received on Wed Aug 24 2016 - 21:30:02 PDT
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