[gmx-users] Re: PBC - Protein - ligand
Steven Neumann
s.neumann08 at gmail.com
Tue Nov 8 09:53:04 CET 2011
On Mon, Nov 7, 2011 at 9:47 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
>
Thank you Justin. From this workflow my ligand is binding the protein most
of the frames but sometimes it rapidly jumps to different part of the box
and come back again. Then remains with protein and situation is repeated:
in one frame it changes its position and come back to protein remaining.
:((((((((( no clue...
> 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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>> gmx-users at gromacs.org>
>>
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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