[gmx-users] PBC - Protein - ligand

[Tsjerk Wassenaar]

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> wrote:
>
>
> On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul <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
> mdfinal.xtc
>
> With point three, the issue is that trjconv removes the jumps from the first
> frame using the reference structure provided with -s. If the reference
> structure (run input file) is not clustered/whole, trjconv -pbc nojump will
> undo steps 1 and
>
> Steven
>
>
> ========================================
>
> 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
>
> ========================================
>>
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-- 
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