[gmx-users] Simulation a labeled protein
Justin A. Lemkul
jalemkul at vt.edu
Fri Jul 22 15:15:12 CEST 2011
Faezeh Nami wrote:
> 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?
>
QM studies will also tell you that fixed charges on metal ions bound to proteins
are insufficiently accurate. If you feel that you have some justification for
what you're doing, by all means, proceed and change the charges, but you still
haven't said what .itp file you're trying to modify and in what way. My
suggestion was to leave any protein topology that pdb2gmx produces alone if it
involves adding or removing atoms or changing bonded parameters. Itamar
suggested modifying by hand the output .gro, .itp, and .top files in order to
introduce a new residue. I disagree with this recommendation as it is very
error prone and inefficient.
-Justin
> Faezeh
>
> On Fri, Jul 22, 2011 at 1:15 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
> <mailto: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>
> <tel:%2B61%203%209902%209376>
> | Fax: +61 3 9902 9500 <tel:%2B61%203%209902%209500>
> <tel:%2B61%203%209902%209500>
> | E-mail: Itamar.Kass at monash.edu
> <mailto:Itamar.Kass at monash.edu> <mailto: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 <http://vt.edu/> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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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
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