Hi Liyang,
It is kind of strange. Can you send me the MCPB.py input file and the files were quoted in it (in a separate email, if you preferred)?
Kind regards,
Pengfei
> On Jan 25, 2017, at 12:54 PM, Liyang Zhu <liyangzhu.lbl.gov> wrote:
>
> Hi Pengfei,
>
> The U ion was treated as independent residue all the time. I mean the
> residue number, such as following. The former time, I use a residue
> number of "1", which can not generate files at the first step of
> MCPB.py. When change to "3" or other number but not "1", it is ok.
> However, I test that some element such as FE, ZN with a residue number
> "1", it is still ok. The PDB file is strictly following the format of
> version 3.
>
> ATOM 1 U U 3 0.000 0.001 -0.001 1.00 0.00
> U
> ATOM 2 O2 MYL 2 -0.001 1.753 0.001 1.00 0.00 O
> ATOM 3 O3 MYL 2 0.000 -1.752 -0.003 1.00 0.00 O
>
>
> Yours,
> Liyang
>
> 2017-01-25 7:54 GMT-08:00 Pengfei Li <ambermailpengfei.gmail.com>:
>> Hi Liyang,
>>
>> Good to know that. Did you mean that in the former time you treated the U ion inside a residue in the PDB file but now it is treated independently as an separate residue in the PDB file?
>>
>> Kind regards,
>> Pengfei
>>
>>> On Jan 22, 2017, at 6:01 PM, Liyang Zhu <liyangzhu.lbl.gov> wrote:
>>>
>>> Dear Pengfei,
>>>
>>> It works, thank you for your help! The original problem was because
>>> the residue number of U was set as 1, then it would report a error:
>>> UnboundLocalError: local variable 'nresname' referenced before assignment
>>>
>>> By changing the residue number of U to other number other than 1,
>>> there is no problem now.
>>>
>>> Many thanks
>>> Liyang
>>>
>>>
>>> 2017-01-21 20:11 GMT-08:00 Pengfei Li <ambermailpengfei.gmail.com>:
>>>> Hi Liyang,
>>>>
>>>> The current version of MCPB.py support U ion. It is needed to specify both the atom name and residue name as “U” in the original PDB file for the MCPB.py modeling.
>>>>
>>>> Kind regards,
>>>> Pengfei
>>>>
>>>>> On Jan 21, 2017, at 9:57 PM, Liyang Zhu <liyangzhu.lbl.gov> wrote:
>>>>>
>>>>> Dear David,
>>>>>
>>>>> Thank you for your reply! I tried to use MCPB.py to generate the force
>>>>> field. However, there is a problem at first step. Because the atom type and
>>>>> residual name of metal element uranium is manually assigned as U, but
>>>>> MCPB.py can not recognize U. Other metal element with two letters, such as
>>>>> FE, ZN, PU, has no such problem.
>>>>>
>>>>> So I am wondering some metal ions such as K, V, Y, U, if the atom type is
>>>>> K, V, Y, U, while residual name can be made up with 3 capitalized letter.
>>>>>
>>>>> Thank you very much
>>>>> Liyang
>>>>>
>>>>>
>>>>>
>>>>> 2017-01-21 19:24 GMT-08:00 David Case <david.case.rutgers.edu>:
>>>>>
>>>>>> On Wed, Jan 18, 2017, Liyang Zhu wrote:
>>>>>>>
>>>>>>> Recently I read a article, in which it said that "the UO2(NO3)2 salts
>>>>>> were
>>>>>>> constrained to remain bound and neutral."
>>>>>>>
>>>>>>> I am wondering how to constrain UO22+ and NO3- ions as a whole.
>>>>>>
>>>>>> You should read the paper carefully, and maybe ask the authors what they
>>>>>> did.
>>>>>> I'm guessing(!) that they defined a neutral UO2(NO3)2 molecule, with bonds
>>>>>> between the U atom and its four closest neighbors.
>>>>>>
>>>>>> You could look at the MCPB program for help in generating parameters, or
>>>>>> do a
>>>>>> internet search on something like "UO2(NO3)2 force field". I tend to use
>>>>>> Google (www.google.com) as a search engine, and it shows several promising
>>>>>> hits for the above search string. But you are certainly free to use
>>>>>> whichever
>>>>>> search engine you are most comfortable with.
>>>>>>
>>>>>> ...good luck....dac
>>>>>>
>>>>>>
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Received on Wed Jan 25 2017 - 14:00:02 PST
