Steven Neumann wrote:
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...


I have no idea why the proposed protocol isn't working, but I know that one should be able to do something very simple, along the lines of the following, for this to work:

1. trjconv -s md.tpr -f md.xtc -o pbc_fix.xtc -pbc mol
2. trjconv -s md.tpr -f pbc_fix.xtc -o center.xtc -center (center on the 
protein)
3. trjconv -s md.tpr -f center.xtc -o fit.xtc -fit rot+trans (choose protein for fitting)

-Justin

Steven

On Monday, November 7, 2011, Tsjerk Wassenaar <tsje...@gmail.com <mailto: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 <mailto:s.neuman...@gmail.com>> wrote:
 >>
 >>
>> On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul <jalem...@vt.edu <mailto: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
 > --
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 >


--
========================================

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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