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
>>>>> _______________________________________________
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>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
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Received on Fri Aug 01 2014 - 15:00:04 PDT
