[gmx-users] six member ring won't stay flat
refmac5 at gmail.com
Thu Jan 18 14:46:04 CET 2018
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
On Jan 18, 2018 8:18 AM, "MD" <refmac5 at gmail.com> wrote:
> 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
>>>> 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
>>>> 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
>>> 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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