[AMBER] tleap ask for bond to zinc ion

From: Jorgen Simonsen <jorgen589.gmail.com>
Date: Sun, 23 Aug 2015 08:49:01 -0700

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
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Received on Sun Aug 23 2015 - 09:00:03 PDT
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