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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Received on Thu Jul 31 2014 - 19:00:02 PDT
