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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>>>>>
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>>>>
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Received on Mon Jul 07 2014 - 14:30:02 PDT
