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

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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