[gmx-users] six member ring won't stay flat
refmac5 at gmail.com
Thu Jan 18 14:18:26 CET 2018
Coolbeans! Thank you Justin :)
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:
>>>> 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)
>>> 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.
>>> 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 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
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