RE: AMBER: Zinc parameters

From: Ross Walker <>
Date: Thu, 27 Jul 2006 10:26:29 -0700

Dear Nitin,

> loadamberparm frcmod.zna
> it gives an error "syntax error"

This was a typo in the original message it should be loadamberparams.
> after this, when i load my protein with zinc, it still can not
> identify the zinc atom.

The frcmod file only describes the non-bond parameters and mass of the zinc.
It does not include the charge or atomic element of the zinc. You need to
follow the text in the original message you reference more closely. You need
to create a unit in Leap called ZNA and make the atom type ZN. Save it as a
lib file with saveoff. Then you need to change the zinc residue name in your
protein to be ZNA. Load leap, load the frcmod file, load the lib file then
load your protein.

Note, if you explicitly want to bond residues to the zinc then you will need
to also provide bond, angle and dihedral parameters in the frcmod file.
All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Sun Jul 30 2006 - 06:07:10 PDT
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