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...
Steven On Monday, November 7, 2011, Tsjerk Wassenaar <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> wrote: >> >> >> On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul <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 > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at 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 >
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