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

Wed Nov 9 22:40:34 CET 2011

Sounds like the ligand is near the edge of the box, so only has to move short distance then does the jumping you are observing.

The suggestion that has already been make, -pbc nojump, should stop that.

Another option is to center the box on a residue within the protein which is near the spot at which the ligand is interacting.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Steven Neumann
Sent: Tuesday, 8 November 2011 8:30 PM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Re: PBC - Protein - ligand

Thank you Justin, Mark and Tsjerk.

I used the following workflow

trjconv -s md.tpr -f md.xtc -o pbc_fix.xtc -pbc mol
trjconv -s md.tpr -f pbc_fix.xtc -n index.ndx -pbc cluster -o pbcfixcluster.xtc  (Protein+ligand group)
trjconv -s md.tpr -f pbcfixcluster.xtc -o center.xtc -center (center on the protein)

trjconv -s md.tpr -f center.xtc -o Cluster1.xtc -fit rot+trans (choose protein for
fitting)

Trajectory looks very good from the time when ligand stacked to the protein (90% of trajectory) but at the begining of the trajectory (when it is away from protein) it still jumps. I think that is the best solution I have found. If you know how to fix begining please let me know.

Steven

On Tue, Nov 8, 2011 at 8:53 AM, Steven Neumann <s.neumann08 at gmail.com<mailto:s.neumann08 at gmail.com>> wrote:

On Mon, Nov 7, 2011 at 9:47 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:

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

Thank you Justin. From this workflow my ligand is binding the protein most of the frames but sometimes it rapidly jumps to different part of the box and come back again. Then remains with protein and situation is repeated: in one frame it changes its position and come back to protein remaining. :((((((((( no clue...

Steven

On Monday, November 7, 2011, Tsjerk Wassenaar <tsjerkw at gmail.com<mailto:tsjerkw at gmail.com> <mailto:tsjerkw at gmail.com<mailto: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<mailto:s.neumann08 at gmail.com> <mailto:s.neumann08 at gmail.com<mailto:s.neumann08 at gmail.com>>> wrote:

 >>
 >>
 >> On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu<mailto: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
 > --
 > gmx-users mailing list    gmx-users at gromacs.org<mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>>

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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<http://vt.edu/> | (540) 231-9080<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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