Hi Pengfei,
Thanks a lot for your prompt reply. In my case, I changed Cys in the pdb
file to CY1 in accordance with the ZAFF. The S-S was in the PDB file before
processed by leap. I removed the line of S-S from pdb, but when loaded into
leap, the S-S was still seen and detected by leap.
Thanks,
Nadia
On Fri, Aug 1, 2014 at 2:54 PM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Nadia,
>
> In AMBER FF the Cys group which has S-S linkage with another Cys
> group has a residue name as CYX, which is different from CYS and CYM,
> Another two Cys groups in AMBER FF. I guess the problem is about the
> residue name in pdb file but not sure.
>
> Jason, can leap automatically assign the S-S bond to Cys residues which
> has a CYS residue name in pdb file but has two S atoms are close to each
> other?
>
> All the best,
> Pengfei
>
> On Aug 1, 2014, at 1:34 PM, Nadia Li <amber.nadiali.gmail.com> wrote:
>
> > 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
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> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>>
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Received on Fri Aug 01 2014 - 15:30:02 PDT
