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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Received on Sun Jul 06 2014 - 10:00:02 PDT
