Re: [AMBER] Zinc parameterization

From: Pengfei Li <>
Date: Thu, 31 Jul 2014 17:34:40 -0400

Hi Nadia,

This is the information that tleap could not recognize the ZN metal ion residue group in the pdb file.

This is because in ZAFF.prep, the ZN ion group in Cys4-Zn metal site was named
as ZN1. You can change the residue name in pdb file from ZN to ZN1 then try
to generate the topology and coordinate files again.

Hope it helps,

On Jul 31, 2014, at 12:55 PM, Nadia Li <> wrote:

> Dear Amber users,
> My protein has two Cys4-Zn, so I used MCPB to generate ZAFF.frcmod and
> ZAFF.prepi (see below). Then I loaded these two files into leap, and then
> load my protein. But the ZN is still not recognized and I got "Unknown
> residue: ZN number: 74 type: Terminal/beginning
> ..relaxing end constraints to try for a dbase match-no luck". Did I miss
> anything? Anyone can help me with this? Thank you very much.
> *MCPB -i mcpb.bcl -l mcpb.log*
> *mcpb.bcl*
> *loadParam AMBERHOME/dat/mtkpp/parm94.xmlloadParam
> AMBERHOME/dat/mtkpp/parm_gaff.xml loadParam
> AMBERHOME/dat/mtkpp/metals/metalParm.xml*
> *loadParam AMBERHOME/dat/mtkpp/ZAFF/ZAFF_parm.xmlwriteFrcmodFile
> ZAFF.frcmod ZAFF*
> *loadLib AMBERHOME/dat/mtkpp/ZAFF/ZAFF.xmlwritePrepFile ZAFF.prepi Zn-CCCC*
> *quit*
> Regards,
> Nadia
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Received on Thu Jul 31 2014 - 15:00:02 PDT
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