[gmx-users] Regarding use of g_x2top utility in Gromacs

[David van der Spoel]

On 26/11/17 17:08, Rakesh Pant wrote:
> Dear Alex,
> 
> But g-x2top doesn't work till we define all atom types in .n2t file.
> 
Please do not use this at all. Use acpype or something.

> Thanks
> 
> 
> On 26-Nov-2017 9:34 PM, "Alexandr Nasedkin" <nasedkin at chalmers.se> wrote:
> 
> Hi,
> 
> You will need to have both ffbonded.itp and ffnonbonded.itp .
> 
> atomname2type.n2t is needed for g_x2top to make it work correctly.
> 
> Good luck.
> 
> 
> -Alex
> 
> 
> 
> On 26/11/2017 10:52, Rakesh Pant wrote:
> 
>> Dear,  Alex
>> Does it mean, we do not need to define all the atomtypes in the .nt2 file.
>> It is enough to define all types in bonded and non-bonded itp.
>>
>> Thanks,
>> Rakesh
>>
>>
>>
>> <https://mailtrack.io/> Sent with Mailtrack
>> <https://mailtrack.io/install?source=signature&lang=en&refer
>> ral=rakesh.pant at students.iiserpune.ac.in&idSignature=22>
>>
>> On Sun, Nov 26, 2017 at 3:27 PM, Alexandr Nasedkin <nasedkin at chalmers.se>
>> wrote:
>>
>> Edit the content of you ffnonbonded.itp file approximately this way:
>>>
>>> [ atomtypes ]
>>> ;name    at.num    mass        charge    ptype    sigma epsilon
>>> C    14    12.00    1.08    A    0.44000        0.63      ;
>>> OCE    8    15.999400    -0.70    A    0.35400        0.159705  ; C-O-C
>>> Bridging Oxygen;
>>> OCH    8    15.999400    -0.51    A    0.35400        0.159705  ; C-O-H
>>> Oxygen;
>>>
>>> HCO    1     1.008000    0.32    A    0.04490        0.235725  ; H-O-C
>>> Hydrogen;
>>> ....
>>>
>>> You would need to search literature for respective ff parameters: all the
>>> above parameters are taken from another topology to give a template.
>>>
>>>
>>> -Alex
>>>
>>>
>>> On 26/11/2017 10:37, Rakesh Pant wrote:
>>>
>>> Dear Alex,
>>>>     If I use O atoms to define the respective functional groups, then how
>>>> to
>>>> include the C atoms present in the molecule.
>>>>
>>>> Thanks,
>>>> Rakesh
>>>>
>>>>
>>>>
>>>> <https://mailtrack.io/> Sent with Mailtrack
>>>> <https://mailtrack.io/install?source=signature&lang=en&refer
>>>> ral=rakesh.pant at students.iiserpune.ac.in&idSignature=22>
>>>>
>>>> On Sun, Nov 26, 2017 at 3:08 PM, Alexandr Nasedkin <nasedkin at chalmers.se
>>>>>
>>>> wrote:
>>>>
>>>> Hi,
>>>>
>>>>> As I understood the problem, you need to distinguish between surface and
>>>>> buried carbons?
>>>>>
>>>>> You could define two atomtypes that differ in name and use it to process
>>>>> with x2top.
>>>>>
>>>>> Below is an example of *.n2t lines. You would need to change the charges
>>>>> and bondlengthes.
>>>>>
>>>>> ...
>>>>>
>>>>> O    OCH    -1.05    15.9994    2    C    0.154 H 0.1    ; oxygen, -OH
>>>>> group
>>>>> O    OCE    -1.05    15.9994    2    C    0.154 C 0.154    ; bridge
>>>>> oxygen
>>>>>
>>>>> ...
>>>>>
>>>>> Then you need *.n2t file in your ff.
>>>>>
>>>>> Good luck!
>>>>>
>>>>>
>>>>> -Alex
>>>>>
>>>>>
>>>>> On 25/11/2017 22:06, Justin Lemkul wrote:
>>>>>
>>>>>
>>>>> On 11/25/17 3:31 PM, Rakesh Pant wrote:
>>>>>>
>>>>>> But then I how will include the C atom (which is also one of the
>>>>>>
>>>>>>> atomtypes)?
>>>>>>>
>>>>>>> No idea, but I know people on this list have dealt with graphene oxide
>>>>>>>
>>>>>> before, so hopefully someone else chimes in.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>
>>>>>> --
>>>>>>
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>>>>>
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>>


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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