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

From: Aditya Padhi <adi.uoh.gmail.com>
Date: Wed, 24 Aug 2016 10:00:15 +0900

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
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Received on Tue Aug 23 2016 - 18:30:03 PDT
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