[gmx-users] Simulation a labeled protein

[Faezeh Nami]

For MD simulation of metalloproteins, people generally change the charge of
atoms attached to the metal center based on quantum mechanics studies.
 If an .itf file shouldn’t be modified, how these changes can be made?

Faezeh
On Fri, Jul 22, 2011 at 1:15 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Faezeh Nami wrote:
>
>> Dear Itamar
>>
>> Thank you for the reply.
>>
>> If I modify Cys parameters in the *rtp file in order to add the Cys-label
>> parameters, it will be applied to other Cys in the protein as well. Isn't
>> it?
>>
>>
> Set the name of your modified residue to something unique (in both the
> input coordinate file and the .rtp entry).
>
>
> In case of modification of *itp file, should I modify all nr or qtot after
>> the Cys? What about bonds?
>>
>
> What .itp file do you want to modify?  Making changes to the pdb2gmx output
> is a bad idea.  You'll have to change any and all subsequent atom numbers,
> and that extends to all of the bonded parameters as well, and you will have
> to add lots in.  This procedure is very error-prone.  I would suggest
> building (and thoroughly checking) an .rtp entry for your modified residue.
>
> -Justin
>
> Best,
>> Faezeh
>>
>>
>> On Thu, Jul 21, 2011 at 5:51 AM, Itamar Kass <itamar.kass at monash.edu<mailto:
>> itamar.kass at monash.edu**>> wrote:
>>
>>    Hi Faezeh,
>>
>>    You can modify the FF and add the Cys-label parameters to the *rtp
>>    and *hdb files, such that pdb2gmx will be able to use them. Another
>>    why is use the original pdb as a starting point and modify the
>>    output *gto, *itp and *top files.
>>
>>    Just remember that in anycase, it is better to copy the files into
>>    your local directory so an change you made will not effect other
>>    simulations.
>>
>>    Cheers,
>>    Itamar
>>
>>
>>    PS I can recommend on this site which can help you in the process
>>    http://compbio.biosci.uq.edu.**au/atb/<http://compbio.biosci.uq.edu.au/atb/>
>>
>>
>>    On 21/07/11 7:43 PM, Faezeh Nami wrote:
>>
>>>    Dear all
>>>
>>>    I am trying to simulate a protein which a label  (a small organic
>>>    molecule) is covalently attached to a cysteine. Worth to say there
>>>    is no label in the original pdb file of protein and it was
>>>    attached to the Cys. using a software.
>>>    Should I insert the label parameters into the conf.gro file or I
>>>    need to modify a force field? If there is someone who has
>>>    experiences in such systems, please have some advice.
>>>    Thanks in advance,
>>>    Faezeh
>>>
>>>
>>>
>>>
>>    --
>>
>>    "In theory, there is no difference between theory and practice. But, in
>> practice, there is." - Jan L.A. van de Snepscheut
>>
>>    ==============================**=============
>>    | Itamar Kass, Ph.D.
>>    | Postdoctoral Research Fellow
>>    |
>>    | Department of Biochemistry and Molecular Biology
>>    | Building 77 Clayton Campus
>>    | Wellington Road
>>    | Monash University,
>>    | Victoria 3800
>>    | Australia
>>    |
>>    | Tel: +61 3 9902 9376 <tel:%2B61%203%209902%209376>
>>    | Fax: +61 3 9902 9500 <tel:%2B61%203%209902%209500>
>>    | E-mail: Itamar.Kass at monash.edu <mailto:Itamar.Kass at monash.edu**>
>>
>>    ==============================**==============
>>
>>
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> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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