This problem is because there is bug in the code for dealing with the ion with atom name and residue name just with one letter. Users can use the developer version of MCPB.py -
https://github.com/Amber-MD/pymsmt/tree/release2 <
https://github.com/Amber-MD/pymsmt/tree/release2> to solve this kind of problem.
> On Jan 25, 2017, at 3:56 PM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
> 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 Feb 01 2017 - 08:00:02 PST
