Re: [AMBER] tleap ask for bond to zinc ion

From: David A Case <>
Date: Mon, 24 Aug 2015 08:34:04 -0400

On Sun, Aug 23, 2015, Jorgen Simonsen wrote:
> I am trying to run a short simulation of an enzyme containing a zinc site -
> I am using leaprc.ff14SB
> when I build the complex I get the following error which I guess is that it
> tries to add a bond between the zinc ion and a sulfur atom

You left out key information: what are exact commands you used to "build the
complex"? Somehow, you probably loaded a file with connectivity information
in it, that asked LEaP to create the Zn-S bond.

Amber's advanced tutorial 20 goes over the procedure for simulating zinc ions
both with and without adding bonds to neighboring atoms. You might look there
for clues. It sounds like you with to use the "nonboded model" described


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Received on Mon Aug 24 2015 - 06:00:05 PDT
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