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

Mon Nov 10 17:25:19 CET 2014

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 -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 or 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>> 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)
>  
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