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 Sun Jan 22 2017 - 16:30:02 PST
