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 - 11:00:04 PST
