Pengfei is right, two nitrogen atoms in histidine might be able to coordinate to zinc ion thus you have to pre-determine the histidine type. In addition to visually inspection, you can also use web based tools such as MolProbity to clean the structure and have it determine the histidine type for you - most times it will get the correct rotamer but I would still recommend visual check after that.
Yue
On Jul 10, 2014, at 2:46 PM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
> Hello Christy,
>
> Right. ZN-CCCH has two different combinations. The two combinations are not interchangeable.
>
> For one situation the H means HID, which means the Histidine with hydrogen on the delta nitrogen, it uses
> the epsilon position nitrogen to coordinate with Zn ion.
> For the other situation the H means HIE, which means Histidine with hydrogen on the epsilon nitrogen, it uses
> the delta position nitrogen to coordinate with Zn ion.
>
> The HID was named as HD1 while the HIE was named as HE1 in the ZAFF.
>
> You can check your system to see which atom on Histidine coordinated to Zn ion and then
> determine which combination you should choose.
>
> Hope it helps.
>
> All the best,
> Pengfei
>
>
> On Jul 10, 2014, at 2:39 PM, Christy Lee <chrstl810.gmail.com> wrote:
>
>> Hello Pengfei,
>>
>> I noticed ZN-CCCH has two different combinations.
>> Is there a specific scenario or situation that pertain to each of the
>> ZN-CCCH combinations? Or are they interchangeable?
>>
>> Christy
>> On Jul 8, 2014 8:14 AM, "Pengfei Li" <ambermailpengfei.gmail.com> wrote:
>>
>>> Hi Christy,
>>>
>>> On Jul 7, 2014, at 5:54 PM, Christy Lee <chrstl810.gmail.com> wrote:
>>>
>>>> Hi Pengfei,
>>>>
>>>> I just checked the charges and you were right, thank you!
>>>>
>>>> For the future reference, are there any documentations on the residue
>>> type
>>>> combinations (like CY2, HE1, ZN2 for example) to use in the case of
>>>> ZN-CCCH, ZN-CCCC, ZN-CCHH?
>>>>
>>>
>>> Here I made a summary for the residue type combinations for each metal
>>> cluster in ZAFF:
>>> (You can also check the ZAFF.xml file for the details. )
>>>
>>> Zn-CCCC CY1 ZN1
>>> Zn-CCCH CY2 HE1 ZN2
>>> Zn-CCCH CY3 HD1 ZN3
>>> Zn-CCHH CY4 HD2 ZN4
>>> Zn-CHHH CY5 HD3 ZN5
>>> Zn-HHDD AP1 HE4 ZN8
>>> Zn-HHHD AP2 HD8 HD9 HE5 ZN9
>>> Zn-HHHH HDD Z10
>>> Zn-HHHO HD4 HD5 HE2 WT1 ZN6
>>> Zn-HHHO HD6 HD7 HE3 OH1 ZN7
>>> Zn-HHOO HDA WT2 Z11
>>> Zn-HOOO HE6 WT3 Z12
>>>
>>> Here the residue with HD as beginning is HID and with HE as beginning is
>>> HIE, with WT as beginning is water
>>> and with OH as beginning is hydroxyl group.
>>>
>>>> I was just wondering because in ZAFF.xml, it lists two different
>>>> combinations for the case of ZN-CCCH.
>>>>
>>>
>>> Right, the two different combinations for ZN-CCCH, one has H as HIE, and
>>> the other has H as HID.
>>> In ZAFF.xml file, you can find the first ZN-CCCH group has C as CY2 and H
>>> as HE1
>>> The second ZN-CCCH has C as CY3 and H as HD1.
>>>
>>>> Much gratitude,
>>>> Christy
>>>
>>> No problem. Hope it helps.
>>>
>>> All the best,
>>> Pengfei
>>>
>>>
>>>> On Jul 7, 2014 2:05 PM, "Pengfei Li" <ambermailpengfei.gmail.com> wrote:
>>>>
>>>>> Hi Christy,
>>>>>
>>>>> I also referred to that three residues: CY2, HE1 and ZN2.
>>>>>
>>>>> The data I have obtained are:
>>>>> For the CY2, the total charge is -0.53642
>>>>> For the HE1, the total charge is 0.17266
>>>>> For the ZN2, the charge is 0.43655
>>>>> So the total charge would be -0.53642*3 + 0.17266 + 0.43655 = -1.00005
>>>>>
>>>>> Can you check your data again? Thanks!
>>>>>
>>>>> All the best,
>>>>> Pengfei
>>>>>
>>>>> On Jul 7, 2014, at 1:18 PM, Christy Lee <chrstl810.gmail.com> wrote:
>>>>>
>>>>>> Hi Pengfei,
>>>>>>
>>>>>> I used CY2, HE1 and ZN2 from the directory you gave and still got the
>>> non
>>>>>> integer, -.7684.
>>>>>> Which cysteine, histidine and zinc were you referring to?
>>>>>>
>>>>>> Thank you,
>>>>>> Christy
>>>>>> On Jul 6, 2014 9:39 AM, "Pengfei Li" <ambermailpengfei.gmail.com>
>>> wrote:
>>>>>>
>>>>>>> Hi Christy,
>>>>>>>
>>>>>>> You can load the set of library under the directory
>>>>>>>
>>>>>>> $AMBERHOME/dat/mtkpp/ZAFF/201108/
>>>>>>>
>>>>>>> That one will gives you a Zn-CCCH metal site with -1 charge on it.
>>>>>>>
>>>>>>> Hope it helps,
>>>>>>>
>>>>>>> All the best,
>>>>>>> Pengfei
>>>>>>>
>>>>>>> On Jul 3, 2014, at 7:11 PM, Christy Lee <chrstl810.gmail.com> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>> ZAFF.prep
>>>>>>>> <
>>>>>>>
>>>>>
>>> https://docs.google.com/file/d/0B9GWOTD3JI6DaHFaR0VtUWN5VzNNWXNfdEk4WnNmY1VSWHlV/edit?usp=drive_web
>>>>>>>>
>>>>>>>>
>>>>>>>> ZAFF.frcmod
>>>>>>>> <
>>>>>>>
>>>>>
>>> https://docs.google.com/file/d/0B9GWOTD3JI6DX3FlTDhuY3RKbDF4OVlFQVZDTVdCMGxaYnZz/edit?usp=drive_web
>>>>>>>>
>>>>>>>>
>>>>>>>> mcpb.bcl
>>>>>>>> <
>>>>>>>
>>>>>
>>> https://docs.google.com/file/d/0B9GWOTD3JI6DVmh4R3ZaM0dYWnJkU2ZNX3NrendzcnhIcEU4/edit?usp=drive_web
>>>>>>>>
>>>>>>>>
>>>>>>>> MCPB.log
>>>>>>>> <
>>>>>>>
>>>>>
>>> https://docs.google.com/file/d/0B9GWOTD3JI6DNEV6cDYwV3RmZ2hNcEk4WTJsamF3S3R3bnRn/edit?usp=drive_web
>>>>>>>>
>>>>>>>> Hi Pengfei,
>>>>>>>>
>>>>>>>> I used this command:
>>>>>>>> MCPB -i mcpb.bcl -l MCPB.log
>>>>>>>> and I have attached these files here.
>>>>>>>> I have also attached frcmod and prep file; hoping that it would help.
>>>>>>>>
>>>>>>>> Thank you,
>>>>>>>> Christy
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Jul 2, 2014 at 2:12 PM, Pengfei Li <
>>> ambermailpengfei.gmail.com
>>>>>>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Hi Christy,
>>>>>>>>>
>>>>>>>>> How did you do the charge fitting? Can you send me the input file
>>> for
>>>>>>> the
>>>>>>>>> charge
>>>>>>>>> fitting step you did by using MCPB?
>>>>>>>>>
>>>>>>>>> All the best,
>>>>>>>>> Pengfei
>>>>>>>>>
>>>>>>>>> On Jul 2, 2014, at 5:07 PM, Christy Lee <chrstl810.gmail.com>
>>> wrote:
>>>>>>>>>
>>>>>>>>>> Hello
>>>>>>>>>>
>>>>>>>>>> We used MCPB for the ZAFF parameter.
>>>>>>>>>> I can see from
>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>
>>> $AMBERHOME/AmberTools/examples/mtkpp/MCPB/CCCH-2GIV/data/2GIV_large_mk.log
>>>>>>>>>> file that histidine was treated as neutral.
>>>>>>>>>> However, the resulting charge of the local system comes out to be a
>>>>> non
>>>>>>>>>> integer.
>>>>>>>>>> It has the charge of -.7684
>>>>>>>>>>
>>>>>>>>>> Thank you,
>>>>>>>>>> Christy
>>>>>>>>>>
>>>>>>>>>> Hello Christy,
>>>>>>>>>>
>>>>>>>>>> Where did you get the ZAFF parameters?
>>>>>>>>>>
>>>>>>>>>> I checked the
>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>
>>> $AMBERHOME/AmberTools/examples/mtkpp/MCPB/CCCH-2GIV/data/2GIV_large_mk.log
>>>>>>>>>> file,
>>>>>>>>>> , which is the RESP charge output gaussian file of the CCCH system.
>>>>> and
>>>>>>>>>> found the total charge of the system is -1,
>>>>>>>>>> which shows it treats the Histidine as neutral.
>>>>>>>>>>
>>>>>>>>>> All the best,
>>>>>>>>>> Pengfei
>>>>>>>>>>
>>>>>>>>>> On Jul 1, 2014, at 5:00 PM, Christy Lee <chrstl810.gmail.com>
>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hello AMBER users,
>>>>>>>>>>>
>>>>>>>>>>> We used ZAFF parameters for ZN interacting with three cysteines
>>> and
>>>>>>> one
>>>>>>>>>>> histidine.
>>>>>>>>>>> The expected charge of the local system is neutral:
>>>>>>>>>> (Zn+2)(C-)(C-)(C-)(H+).
>>>>>>>>>>> However, we have histidine with a neutral charge.
>>>>>>>>>>> What could be the problem?
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Thank you,
>>>>>>>>>>> Christy
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Received on Thu Jul 10 2014 - 15:30:02 PDT
