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

From: Marcelo Andrade Chagas <>
Date: Mon, 24 Aug 2015 14:33:00 -0300

Dear ...

what is the coordination number of the ion Zn?

This means that your frcmod file are missing information
is for chemical and angle connection.

These parameters are constant force between the atoms, minimum distance and
minimum angle

I'm having a similar problem here. I am studying a triesterase
with an active site where it has two ions penta-coordinated Zn.

One has to parameterize these values ​​that are missing and / or use values
High force constant to make the simulation.

Search AMBER directories frcmod.ionslrcm_cm_tip3p this directory
for to see its structure.

Also, you probably will have to make the connections between the atoms
if the program is not doing it.

Xleap used in the following command and view its active site. If you are
not connecting
between these atoms you have to delete the hydrogen atom added by
xleap (using erase) and connect dragging from one atom to another (using

ie, you will have to complete the frcmod file and edit the file structure
in xleap.

edit file name

Best regards

Marcelo Andrade Chagas, MSc
(PhD student)
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
Departamento de Química da Universidade Federal de Minas Gerais - UFMG

2015-08-23 12:49 GMT-03:00 Jorgen Simonsen <>:

> Hi all,
> I am trying to run a short simulation of an enzyme containing a zinc site -
> I am using leaprc.ff14SB
> with the following parameters for the ions present in the complex:
> loadoff ions08.lib
> loadamberparams frcmod.ionsjc_tip3p
> loadamberparams frcmod.ionslrcm_cm_tip3p
> 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 that is
> coordinating it but I am not sure why it adds a covalent bond and also how
> to solve it
> Building bond parameters.
> Could not find bond parameter for: Zn2+ - S
> Building angle parameters.
> Could not find angle parameter: Zn2+ - S - CT
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 1270 improper torsions applied
> Building H-Bond parameters.
> Thanks in advance
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Mon Aug 24 2015 - 11:00:02 PDT
Custom Search