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

[Rakesh Pant]

But then I how will include the C atom (which is also one of the atomtypes)?

Thanks,




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On Sun, Nov 26, 2017 at 1:56 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/25/17 3:21 PM, Rakesh Pant wrote:
>
>> Dear Justin,
>>
>> I am trying to use it for graphene oxide (layer), then what would be a
>> better way if not g_x2top.
>>
>
> Epoxide O and phenolic O have different connectivity (two C vs. one C and
> one H), so write the .n2t entries first based on O rather than C.
>
> -Justin
>
> Thanks,
>>
>>
>>
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>> ral=rakesh.pant at students.iiserpune.ac.in&idSignature=22>
>>
>>
>> On Sun, Nov 26, 2017 at 1:48 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> On 11/25/17 3:12 PM, Rakesh Pant wrote:
>>>
>>> Dear All,
>>>>
>>>> How does the utility g_x2top works?
>>>> If we have similar connectivity in a molecule, then how will it read
>>>> different atom types. Suppose a C atom is connected to 4 bonds (3 carbon
>>>> atoms and 1 O atom, say in epoxy group) and similarly another C atom is
>>>> also connected to 4 atoms (3 C atoms and 1 O atom, but the different
>>>> functional group, e.g phenolic group). Both are present in the same
>>>> molecule, then how should we define both in the .n2t file so that
>>>> g_x2top
>>>> reads both the atomtypes.
>>>>
>>>> The only difference in that case might be bond lengths, though they may
>>> not be different enough to be distinguished (they would have to differ by
>>> at least 10% to be outside of the default tolerance). x2top is not a
>>> particularly smart program, and whatever it matches first will be what it
>>> writes to the topology. If you have some very complex molecule, this may
>>> not be a useful tool.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
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>>>
>>> jalemkul at vt.edu | (540) 231-3129
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>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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-- 
Rakesh Pant/राकेश पंत
Research Fellow/अनुसंधान फेलो
Indian Institute of Science Education and Research (IISER)
भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान
Pune-411008, India/ पुणे - ४११००८, भारत
Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm