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

[Justin Lemkul]

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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>
> 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.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
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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

==================================================