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

[Carlos Navarro Retamal]

Dear Justin,
It worked! :D
Thanks a lot.
I first preprocess  the whole trajectory,  
> trjconv -f dynamic-NO-Elastic.xtc -s equilibration.tpr -pbc mol  

And after that i center the protein  

> trjconv -f trajout.xtc -s equilibration.tpr -pbc mol -center -skip 50 -o test.xtc
In order to extract the last frame i used the following command:

> trjconv -f test.xtc -sep -o LastFrame.gro

The only ‘issue’ was that the frames i saved with -sep content the description of each atom as follows:

>  
>     1LYS     BB    1   5.4   6.9   8.4
>     1LYS    SC1    2   5.3   7.2   8.5
>     1LYS    SC2    3   5.0   7.3   8.6
>     2ARG     BB    4   5.1   6.8   8.5
>     2ARG    SC1    5   5.1   6.6   8.7
>     2ARG    SC2    6   5.0   6.5   9.0
>  



so i got an error with initram. To avoid this i performed a minimisation of this lastFrame.gro file in order to obtain the correct description of each atom. After that, FINALLY, the backward process worked :D

Thanks to all of you :D

ps- During the CG simulation using Elastic-Network i saw big movements of the K2P protein, and when i compared it with respect to the inicial AA model i saw how a part of the CAP of the K2P channel is completely rotate to another side of the protein.
 I used 500 kj/mol^-1/nm^-2 as the tutorial suggest.  
Should i increase the elastic force constant to 1000 (or even more), or instead try ElNeDyn?  
I didn’t want to use this approximation, since the tutorial emphasise that using it will be huge change on the martini ff.
Best regards to all of you,
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 8:45 PM, Justin Lemkul wrote:

>  
>  
> On 11/10/14 10:01 AM, Carlos Navarro Retamal 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?
> >  
>  
>  
> I don't know why the -center option isn't working. That's precisely what it  
> does. Other things to try:
>  
> 1. Often I find that PBC routines do not work well when dealing with a single  
> coordinate file. Processing the trajectory, then extracting the frame(s) of  
> interest works all the time.
>  
> 2. Try the -fit transxy option of trjconv. It's designed for interfacial and  
> membrane systems.
>  
> -Justin
>  
> --  
> ==================================================
>  
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>  
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>  
> jalemkul at outerbanks.umaryland.edu (mailto:jalemkul at outerbanks.umaryland.edu) | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>  
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