Hi Tsjerk,<br><br>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?<br>
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...<br><br>Steven<br><br>On Monday, November 7, 2011, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:<br>
> Hi Steven,<br>><br>> Step 2: Cluster your molecules.<br>> This is where you have to forge a reference frame that you can use to<br>> remove jumps from your trajectory. If the ligand is not with the<br>> protein at the start, you'll have to shift it so that it is. Maybe<br>
> -pbc cluster is your friend there. I do assume that the ligand is<br>> really with the protein and not in the solvent...<br>><br>> Cheers,<br>><br>> Tsjerk<br>><br>> On Mon, Nov 7, 2011 at 5:17 PM, Steven Neumann <<a href="mailto:s.neumann08@gmail.com">s.neumann08@gmail.com</a>> wrote:<br>
>><br>>><br>>> On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>>>><br>>>><br>>>> Steven Neumann wrote:<br>
>>>><br>>>>> Dear Gmx Users,<br>>>>> I know that this problem has been discussed may times but I cannot find<br>>>>> the solution to get rid of pbc in my system: protein and ligand. I followed<br>
>>>> the workflow:<br>>>>><br>>>>> 1. First make your molecules whole if you want them whole<br>>>>><br>>>>> trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc<br>
>>>><br>>>>> 2. Cluster your molecules/particles if you want them clustered<br>>>>><br>>>>> 3. Extract the first frame from the trajectory as reference for<br>>>>> removing jumps if you want to remove jumps.<br>
>>>><br>>>>> trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb<br>>>>><br>>>>> 4. Remove jumps if you want to have them removed using the first<br>>>>> frame<br>
>>>><br>>>>> trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc<br>>>>><br>>>>> 5. Center your system using some criterion. Doing so shifts the<br>
>>>> system, so don't use |trjconv -|pbc| nojump| after this step.<br>>>>><br>>>>> trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc<br>>>>><br>>>>> 6. Put everything in some box.<br>
>>>><br>>>>> trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o<br>>>>> mdwholeNOjumpCENTERbox.xtc<br>>>>><br>>>>> 7. Fit if desired and don't use any PBC related option afterwards.<br>
>>>><br>>>>> trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o<br>>>>> mdfinal.xtc<br>>>>><br>>>>><br>>>>> I used SYSTEM everywhere as output orinput. However, my ligand is still<br>
>>>> jumping like a fly around the stable protein. Do you have any suggestions?<br>>>>><br>>>>><br>>>><br>>>> Center on either the protein, the ligand, or some custom index group of<br>
>>> residues surrounding the ligand. Centering on the whole system usually<br>>>> doesn't do anything useful.<br>>>><br>>>> -Justin<br>>>><br>>><br>>> Thank you guys but...<br>
>><br>>> I am trying and it does not work... my ligand is jumping like an idiot<br>>> outside the box changing its position even two dimensions of box in one<br>>> frame. I removed -ur compact from the first line and I tried centering on<br>
>> ligand or protein (centering group: LIG or Protein, output: SYSTEM). No<br>>> results...<br>>> My ligand at the begining of the simualtion is not within the protein.<br>>> Please, help :(((( I tried this workflow with many ligands and same protein<br>
>> - it worked! Now it does not...<br>>> Here is my workflow:<br>>><br>>><br>>> 1. First make your molecules whole if you want them whole.<br>>><br>>> trjconv -f md.trr -s md.tpr -pbc whole -o mdwhole.xtc<br>
>><br>>> 2. Cluster your molecules/particles if you want them clustered<br>>><br>>> 3. Extract the first frame from the trajectory as reference for<br>>> removing jumps if you want to remove jumps.<br>
>><br>>> trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb<br>>><br>>> 4. Remove jumps if you want to have them removed using the first frame<br>>> (system)<br>>><br>>> trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc<br>
>><br>>> 5. Center your system using some criterion. Doing so shifts the system,<br>>> so don't use trjconv -pbc nojump after this step (tried centering on LIG or<br>>> PROTEIN)<br>>><br>
>> trjconv -f mdwholeNOjump.xtc -n Ligand.ndx -center -o<br>>> mdwholeNOjumpCENTER.xtc<br>>><br>>> 6. Put everything in some box.<br>>><br>>> trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc<br>
>><br>>> 7. Fit if desired and don't use any PBC related option afterwards.<br>>><br>>> trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o<br>> --<br>> Tsjerk A. Wassenaar, Ph.D.<br>
><br>> post-doctoral researcher<br>> Molecular Dynamics Group<br>> * Groningen Institute for Biomolecular Research and Biotechnology<br>> * Zernike Institute for Advanced Materials<br>> University of Groningen<br>
> The Netherlands<br>> --<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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