[gmx-users] PBC - Protein - ligand

[Steven Neumann]

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<http://www.gromacs.org/Documentation/Gromacs_Utilities/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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>

==============================**==========

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