[gmx-users] Problem - How to center a protein in a CG simulation

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Nov 10 18:11:44 CET 2014 

Hey :)

The protein is a dimer. Are you sure there is a real problem?

Cheers,

Tsjerk

On Mon, Nov 10, 2014 at 6:07 PM, Carlos Navarro Retamal <cnavarro at utalca.cl>
wrote:

> Dear Tsjerk,
> I forgot to mention it, but indeed i used -pbc mol, as follows:
>
>
> > trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc mol -o
> LastFrame.gro
> >
> >
> >
>
> And using this file (LastFrame.gro) i run initram, getting my protein
> split on different side of the box.
> What could it be?
> Best Regards,
> Carlos
> --
> Carlos Navarro Retamal
> Bioinformatic engineer
> Ph.D(c) in Applied Science, Universidad de Talca, Chile
> Center of Bioinformatics and Molecular Simulations (CBSM)
> Universidad de Talca
> 2 Norte 685, Casilla 721, Talca - Chile
> Teléfono: 56-71-201 798,
> Fax: 56-71-201 561
> Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
>
>
> On Monday, November 10, 2014 at 1:35 PM, Tsjerk Wassenaar wrote:
>
> > Hi Carlos,
> >
> > You used -pbc nojump on the last frame with the .tpr as reference, which
> > means it removes the jumps with respect to the tpr, and that will give
> > rubbish. You should use -pbc mol and try again.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Mon, Nov 10, 2014 at 5:25 PM, Carlos Navarro Retamal <
> cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)>
> > wrote:
> >
> > > Dear Erick,
> > > First of all thanks a lot for your reply.
> > > Your are correct. I know that there’s not a ‘middle’ part in the system
> > > (based on the PBC), i was just trying to say that i need a structure
> where
> > > the protein will be surrounded by the POPC membrane in order to have
> > > ‘valid’ structure to start the AA MD simulations.
> > >
> > > I run the following commands:
> > >
> > > > trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc
> nojump
> > > -o LastFrame.gro
> > > >
> > >
> > >
> > >
> > > followed by:
> > >
> > > > trjconv -f LastFrame.gro -s dynamic-NO-Elastic.tpr -fit rot+trans -o
> > > conf.gro
> > > >
> > >
> > >
> > > without luck ( the proteins is not fix either with these commands).
> > > what should i do?
> > >
> > >
> > > Dear Tsjerk,
> > > Thanks for your kind reply.
> > > I did what you suggested, without luck:
> > > > ./initram.sh (http://initram.sh) -f LastFrame.gro -o
> aa_gromos54a7.gro -to gromos54a7 -p
> > >
> > > topol.top
> > > (in the input file the protein is intact)
> > > CG-model:
> > > http://cl.ly/3V3E1O2R0L31
> > > AA-model
> > > http://cl.ly/0U2r2n0F290i
> > >
> > >
> > > Thanks to both of you for all your help,
> > > Best Regards,
> > > Carlos
> > >
> > > --
> > > Carlos Navarro Retamal
> > > Bioinformatic engineer
> > > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > > Center of Bioinformatics and Molecular Simulations (CBSM)
> > > Universidad de Talca
> > > 2 Norte 685, Casilla 721, Talca - Chile
> > > Teléfono: 56-71-201 798,
> > > Fax: 56-71-201 561
> > > Email: carlos.navarro87 at gmail.com (mailto:carlos.navarro87 at gmail.com)
> or cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)
> > >
> > >
> > > On Monday, November 10, 2014 at 12:16 PM, Erik Marklund wrote:
> > >
> > > > Dear Carlos,
> > > >
> > > > I guess it's just not obvious to most of us why this is a problem at
> > > all. If the protein diffuses (as proteins do) you can just
> translate/rotate
> > > it back to where it was. Strictly speaking , there is no 'middle' in a
> > > periodic system. Or are we missing something?
> > > >
> > > > In any case, adding restraints can affect the dynamics and you can
> often
> > > use trjconv -nojump followed by trjconv -fit to get your protein sit
> > > steadily in the middle of your box, assuming the protein was where you
> > > wanted it to be in the first place.
> > > >
> > > > Kind regards,
> > > > Erik
> > > >
> > > >
> > > > Erik Marklund, PhD
> > > > Postdoctoral Research Fellow, Fulford JRF
> > > >
> > > > Department of Chemistry
> > > > Physical & Theoretical Chemistry Laboratory
> > > > University of Oxford
> > > > South Parks Road
> > > > Oxford
> > > > OX1 3QZ
> > > >
> > > > On 10 Nov 2014, at 15:01, Carlos Navarro Retamal <cnavarro at utalca.cl
> (mailto:cnavarro at utalca.cl)
> > > <mailto:cnavarro at utalca.cl>> wrote:
> > > >
> > > > nobody?
> > > > if there is not a way to do this at this moment (after the
> simulation)
> > > >
> > >
> > > is there a way to apply a restraint to maintain fix the protein in the
> > > middle of the POPC bilayer (other than elastic network) during the MD
> > > simulation in order to avoid this problem?
> > > > Best regards,
> > > > Carlos
> > > >
> > > > --
> > > > Carlos Navarro Retamal
> > > > Bioinformatic engineer
> > > > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > > > Center of Bioinformatics and Molecular Simulations (CBSM)
> > > > Universidad de Talca
> > > > 2 Norte 685, Casilla 721, Talca - Chile
> > > > Teléfono: 56-71-201 798,
> > > > Fax: 56-71-201 561
> > > > Email: carlos.navarro87 at gmail.com<mailto:carlos.navarro87 at gmail.com>
> or
> > > >
> > >
> > > cnavarro at utalca.cl<mailto:cnavarro at utalca.cl>
> > > >
> > > >
> > > > On Monday, November 10, 2014 at 2:11 AM, Carlos Navarro Retamal
> wrote:
> > > >
> > > > Dear gromacs users,
> > > > I’m trying to replicate the following paper:
> > > >
> > >
> > >
> http://www.nature.com/ncomms/2014/140708/ncomms5377/full/ncomms5377.html
> > > >
> > > > On that way i:
> > > > - Create a CG (two different ones, with and without elastic-network
> > > >
> > >
> > > restraints) representation of my K2P protein by using martinize.py
> > > > - I embedded it in a POPC bilayer membrane using insane.py
> > > > After some energy minimization and equilibration i run a 500ns MD of
> > > >
> > >
> > > production.
> > > > The problem was that during both simulation the protein starts to
> move
> > >
> > > across the box to a different box.
> > > > By using tryconv as follows:
> > > > trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc mol
> -o
> > > >
> > >
> > > LastFrame.gro
> > > >
> > > >
> > > > i was able to ‘fix’ the protein (fix the pbc issue of the protein),
> but
> > > its remains out of the box.
> > > > I even used -center keyword without luck.
> > > > And since i need a structure where the protein remains in the middle
> of
> > > >
> > >
> > > the POPC membrane in order to perform the ‘backward’ step to obtain an
> AA
> > > representation of my system and perform a new MD simulation i’m kind of
> > > stuck.
> > > > I don’t know what to do :/
> > > > Hope someone can help me.
> > > > Have a nice week,
> > > > Carlos
> > > >
> > > >
> > > > --
> > > > Carlos Navarro Retamal
> > > > Bioinformatic engineer
> > > > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > > > Center of Bioinformatics and Molecular Simulations (CBSM)
> > > > Universidad de Talca
> > > > 2 Norte 685, Casilla 721, Talca - Chile
> > > > Teléfono: 56-71-201 798,
> > > > Fax: 56-71-201 561
> > > > Email: carlos.navarro87 at gmail.com<mailto:carlos.navarro87 at gmail.com>
> > > >
> > >
> > > (mailto:carlos.navarro87 at gmail.com) or cnavarro at utalca.cl (mailto:
> cnavarro at utalca.cl)<mailto:
> > > cnavarro at utalca.cl> (mailto:cnavarro at utalca.cl)
> > > >
> > > > --
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> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > Gromacs Users mailing list
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-- 
Tsjerk A. Wassenaar, Ph.D.

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