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.neuman...@gmail.com>wrote: > > > On Mon, Nov 7, 2011 at 9:47 PM, Justin A. Lemkul <jalem...@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 <tsje...@gmail.com<mailto: >>> tsje...@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.neuman...@gmail.com<mailto: >>> s.neuman...@gmail.com>**> wrote: >>> >>> >> >>> >> >>> >> On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul >>> <jalem...@vt.edu<mailto: >>> jalem...@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 >>> > -- >>> > gmx-users mailing list gmx-users@gromacs.org <mailto: >>> gmx-users@gromacs.org> >>> >>> > >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >>> posting! >>> > Please don't post (un)subscribe requests to the list. Use the >>> > www interface or send it to gmx-users-requ...@gromacs.org <mailto: >>> gmx-users-request@**gromacs.org <gmx-users-requ...@gromacs.org>>. >>> >>> > Can't post? Read >>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> >> -- >> ==============================**========== >> >> 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> >> >> ==============================**========== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >
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