Hi Pengfei,
Thank you very much for your useful information. It worked well after
changing ZN to ZN1.
But meanwhile, I found there is a S-S bond mistakenly formed among two
Cysteines. I manually deleted it in leap, but I am wondering whether there
is other ways to avoid forming wrong S-S. Any idea on that?
Thanks,
Nadia
On Thu, Jul 31, 2014 at 2:34 PM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> 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,
> Pengfei
>
> On Jul 31, 2014, at 12:55 PM, Nadia Li <amber.nadiali.gmail.com> 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*
> > *set AMBERHOME $AMBERHOME*
> >
> >
> > *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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Thu Jul 31 2014 - 16:00:02 PDT
