[gmx-users] PBC - Protein - ligand

[Justin A. Lemkul]

Steven Neumann wrote:
> Dear Gmx Users,
>  
> I know that this problem has been discussed may times but I cannot find 
> the solution to get rid of pbc in my system: protein and ligand. I 
> followed the workflow:
>  
> 
> 1.      First make your molecules whole if you want them whole
> 
> trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc
> 
> 2.      Cluster your molecules/particles if you want them clustered
> 
> 3.      Extract the first frame from the trajectory as reference for 
> removing jumps if you want to remove jumps.
> 
> trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb
> 
> 4.      Remove jumps if you want to have them removed using the first frame
> 
> trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc
> 
> 5.      Center your system using some criterion. Doing so shifts the 
> system, so don't use |trjconv -|pbc| nojump| after this step.
> 
> trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc
> 
> 6.      Put everything in some box.
> 
> trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc
> 
> 7.      Fit if desired and don't use any PBC related option afterwards.
> 
> trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o 
> mdfinal.xtc
> 
>  
> 
> I used SYSTEM everywhere as output orinput. However, my ligand is still 
> jumping like a fly around the stable protein. Do you have any suggestions?
> 
>  

Center on either the protein, the ligand, or some custom index group of residues 
surrounding the ligand.  Centering on the whole system usually doesn't do 
anything useful.

-Justin

> 
> Steven
> 

-- 
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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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