In my protein, it is every four cysteine with one Zinc ion, and these two
units of Cys4-zn are not linked together. The disulfide formed in one unit
between two Cysteines.
Actually, I also have this problem with other proteins that two adjacent
cys form S-S, and then in leap it will report missing parameter for the
s-s.
Hope I made the question clear. Please let me know if you have any
suggestions. Thank you!
Nadia
On Thu, Jul 31, 2014 at 6:28 PM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Nadia,
>
> No problem. Do the two Cys groups all bind to the Zinc ion?
>
> All the best,
> Pengfei
>
> On Jul 31, 2014, at 6:37 PM, Nadia Li <amber.nadiali.gmail.com> wrote:
>
> > 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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> >>
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>
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Received on Fri Aug 01 2014 - 11:00:02 PDT
