[gmx-users] Turn on/off residues in gromacs

[Justin Lemkul]

On 10/22/18 7:29 AM, Quyen Vu Van wrote:
> Dear all,
> sorry for my unclear question,
> I attached here the quick draw picture of what I am saying, please take a
> look: https://www.dropbox.com/s/eycsm3qsywhgxjv/model.pdf?dl=0

What you are trying to do is both technically challenging and physically 
questionable. The free energy options allow you to modulate the 
interactions of a [moleculetype] with the remainder of the system; you 
can't easily decompose individual residues of a protein, which is part 
of a single [moleculetype]. You could manually define A- and B- states 
in the topology and there are various tools to do that.

The bigger problem is, even if you accomplish what you seek in terms of 
the technical setup, it's physically unrealistic. As Mark noted, you 
have an unsatisfied valence at the C-terminus of each residue at each 
interval of time. This is not physically real, as amino acids are simply 
transferred between tRNA and onto the growing polypeptide chain. Simply 
"growing" residues onto the chain will not come close to mimicking 
protein synthesis in any meaningful way.

-Justin

> Thank you and best regards,
> Quyen
>
> On Sat, Oct 20, 2018 at 6:27 AM Quyen Vu Van <vuqv.phys at gmail.com> wrote:
>
>> Dear Mark,
>> I mean that e.g my protein has 10 residues in pdb file but at t=0, Gromacs
>> will only calculate the interactions of all atoms in residue 1
>> t= 1ns (for example) Gromacs will calculate the interactions of all atoms
>> in residues 1 and 2, and so on till t= XXX ns, interactions of all atoms of
>> full protein is take into account.
>> Best regards,
>> Quyen
>>
>>
>> On Fri, Oct 19, 2018, 18:42 Mark Abraham <mark.j.abraham at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> What do you mean by turning a residue off? What would terminate the
>>> chemical bond to the residue that it was bound to?
>>>
>>> Mark
>>>
>>> On Fri, Oct 19, 2018, 14:40 Quyen Vu Van <vuqv.phys at gmail.com> wrote:
>>>
>>>> Dear Gromacs community,
>>>> How can I turn off/on residues in the protein, I want to mimic the
>>> process
>>>> of protein synthesis.
>>>> Thank you and best regards,
>>>> Quyen
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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