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 Sat Jan 21 2017 - 20:30:02 PST
