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

[MD]

Coolbeans! Thank you Justin :)
Ming

On Jan 18, 2018 7:54 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 1/18/18 7:51 AM, MD wrote:
>
>> 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?
>>
>
> You look at the structure to see if it is sensible (and here, sensible is
> defined as properly reproducing QM-optimized geometries and/or known
> high-resolution experimental geometries - start with QM and compare against
> empirical evidence later).
>
> The absence of errors or notes when executing grompp tells you precisely
> nothing about the integrity of the physical model; it only tells you if
> you've forgotten to do something. I can populate every parameter field with
> absolute garbage and grompp will happily carry on preparing my doomed
> simulation :)
>
> -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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.