[gmx-users] Re: PBC - Protein - ligand

[Justin A. Lemkul]

Steven Neumann wrote:
> Hi Tsjerk,
> 
> Thank you. Unfortunately my ligand is not with protein. I put my ligand 
> around my protein (in water) running separate simulations to see where 
> can it bind. It is close to protein but not within. Any other suggestion?
> I used also pbc -res so I observe my ligand close to protein but 
> sometimes still changing its position rapidly... No clue for now how to 
> solve it...
> 

I have no idea why the proposed protocol isn't working, but I know that one 
should be able to do something very simple, along the lines of the following, 
for this to work:

1. trjconv -s md.tpr -f md.xtc -o pbc_fix.xtc -pbc mol
2. trjconv -s md.tpr -f pbc_fix.xtc -o center.xtc -center (center on the protein)
3. trjconv -s md.tpr -f center.xtc -o fit.xtc -fit rot+trans (choose protein for 
fitting)

-Justin

> Steven
> 
> On Monday, November 7, 2011, Tsjerk Wassenaar <tsjerkw at gmail.com 
> <mailto:tsjerkw at gmail.com>> wrote:
>  > Hi Steven,
>  >
>  > Step 2: Cluster your molecules.
>  > This is where you have to forge a reference frame that you can use to
>  > remove jumps from your trajectory. If the ligand is not with the
>  > protein at the start, you'll have to shift it so that it is. Maybe
>  > -pbc cluster is your friend there. I do assume that the ligand is
>  > really with the protein and not in the solvent...
>  >
>  > Cheers,
>  >
>  > Tsjerk
>  >
>  > On Mon, Nov 7, 2011 at 5:17 PM, Steven Neumann <s.neumann08 at gmail.com 
> <mailto:s.neumann08 at gmail.com>> wrote:
>  >>
>  >>
>  >> On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>  >>>
>  >>>
>  >>> 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
>  >>>
>  >>
>  >> Thank you guys but...
>  >>
>  >> I am trying and it does not work... my ligand is jumping like an idiot
>  >> outside the box changing its position even two dimensions of box in one
>  >> frame. I removed -ur compact from the first line and I tried 
> centering on
>  >> ligand or protein (centering group: LIG or Protein, output: SYSTEM). No
>  >> results...
>  >> My ligand at the begining of the simualtion is not within the protein.
>  >> Please, help :(((( I tried this workflow with many ligands and same 
> protein
>  >> - it worked! Now it does not...
>  >> Here is my workflow:
>  >>
>  >>
>  >> 1.      First make your molecules whole if you want them whole.
>  >>
>  >> trjconv -f md.trr -s md.tpr -pbc whole -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
>  >> (system)
>  >>
>  >> 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 (tried centering on 
> LIG or
>  >> PROTEIN)
>  >>
>  >> trjconv -f mdwholeNOjump.xtc -n Ligand.ndx -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
>  > --
>  > Tsjerk A. Wassenaar, Ph.D.
>  >
>  > post-doctoral researcher
>  > Molecular Dynamics Group
>  > * Groningen Institute for Biomolecular Research and Biotechnology
>  > * Zernike Institute for Advanced Materials
>  > University of Groningen
>  > The Netherlands
>  > --
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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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