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

[MD]

On Thu, Jan 18, 2018 at 7:43 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>

​​Thank you Justin. What would you look at to make a judgement to see if
the topology is sensible after the vacuo geometry optimization? Or as long
as there were no errors or bad notes along the run it should be good?
Thank you,
Ming

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