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

[MD]

I have a question related to charmm. Does charmm have a name/structure
chart for all the parametrized molecules? I want to borrow some parameters
info from those molecules but often I can't quickly figure out what they
are.
Ming

On Jan 18, 2018 8:18 AM, "MD" <refmac5 at gmail.com> wrote:

> 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
>>
>> ==================================================
>>
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>