[gmx-users] Re: PBC - Protein - ligand

[Steven Neumann]

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 <tsjerkw at 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.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
> --
> 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
> --
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