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 - 08:00:04 PST
