[gmx-users] Re: PBC - Protein - ligand
Steven Neumann
s.neumann08 at gmail.com
Tue Nov 8 10:30:02 CET 2011
Thank you Justin, Mark and Tsjerk.
I used the following workflow
trjconv -s md.tpr -f md.xtc -o pbc_fix.xtc -pbc mol
trjconv -s md.tpr -f pbc_fix.xtc -n index.ndx -pbc cluster -o
pbcfixcluster.xtc (Protein+ligand group)
trjconv -s md.tpr -f pbcfixcluster.xtc -o center.xtc -center (center on the
protein)
trjconv -s md.tpr -f center.xtc -o Cluster1.xtc -fit rot+trans (choose
protein for
fitting)
Trajectory looks very good from the time when ligand stacked to the
protein (90% of trajectory) but at the begining of the trajectory (when it
is away from protein) it still jumps. I think that is the best solution I
have found. If you know how to fix begining please let me know.
Steven
On Tue, Nov 8, 2011 at 8:53 AM, Steven Neumann <s.neumann08 at gmail.com>wrote:
>
>
> 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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