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 Tue Jul 08 2014 - 08:30:02 PDT
