[gmx-users] six member ring won't stay flat

[Justin Lemkul]

On 1/17/18 6:11 PM, Mark Abraham wrote:
> Hi,
>
> If you poke your finger into something, it isn't going to stay flat. :-)

And to add on to this, in the CHARMM parametrization protocol, the first 
step is always an in vacuo geometry optimization (QM vs. MM comparison) 
to make sure the topology is sensible. If that doesn't check out, there 
are problems that can be easily spotted before subjecting the new 
residue to any other complicating factors like water and other parts of 
the protein.

-Justin

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

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