normal MARTINI simulation of protein-protein assosiation

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7 years 10 months ago #5542 by James Starlight
Replied by James Starlight on topic MARTINI simulation of protein-protein assosiation
I was in stuck with simpler task how to make new ndx file for given .tpr file - defining chain A (this is how the smaller protein is defined) as
separate ndx group and all of the rest of the protein (rest chains which should be centred in the trajectory before calculations of grid) as another group. Assuming that during make_ndx session to select chain A I just put Chain A (or
alternatively resid 1-100 for my case) how I can define selection
'Protein and not Chain A' or 'Protein and not resid 1-100' excluding
chain A or first 100 residues from the second selection?


Thanks for help again!

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7 years 10 months ago - 7 years 10 months ago #5543 by Pim
In make_ndx you can use logical operators & (and) and | (or) and ! (not)

So Protein and not residue 1 to 100 is "Protein &! r 1-100"
Last edit: 7 years 10 months ago by Pim.

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7 years 10 months ago #5545 by James Starlight
Replied by James Starlight on topic MARTINI simulation of protein-protein assosiation
Yes, thanks !

It's strange I have done all of those steps properly
1- MERGE ALL MY TRAJECTORIES
trjcat -f resp_complex_conf1.xtc resp_complex_conf2.xtc resp_complex_conf3.xtc resp_complex_conf4.xtc resp_complex_conf5.xtc resp_complex_conf6.xtc resp_complex_conf7.xtc -o resp_complex_merged.xtc -tu ps -cat

2- gmx densmap to calculate density plots of ligand defined in new2.ndx:
gmx densmap -f resp_complex_merged.xtc -s ref.pdb -n new2.ndx -od densmap.dat -w

and in that case obtained Segmentation fault error

Group 16 ( r_1-104) has 236 elements
Group 17 (Protein_&_!r_1-104) has 4117 elements
Select a group: 16
Selected 16: 'r_1-104'
Reading frame 1800 time 708000.000 Segmentation fault

Here ref.pdb consist of only protein atoms defined in groups 16 and 17 of new2.ndx

At the same time If I chose group of receptor (17 in that case) from the same inputs - it produces normal density map. Where here might be source of the error? What are the best option for the visualization of density maps? E.g I have not found any of PDB files produced. Is it possible to upload density map to VMD together with the ref.tpr for the its visualization ?

Thanks again!
J.

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7 years 10 months ago #5546 by Pim
gmx densmap creates a density map, which is always a 2D matrix of intensities as function of x/y coordinates. You can not use it for 3D coordinates I think. As long as your trajectory has been fitted onto some reference, you should get something reasonable

If you want, you can make a PostScript image from the xpm output using xpm2ps -f file.xpm
Alternatively, you can take the .dat output and use any plotting program to make a 2D plot. I don't think you can load it into VMD.

About the first part: I have no idea. Check if perhaps one of your xtc files is broken or changes at time 708000? Unlikely, but if your xtc file is very big, maybe your computer is running out of memory and you can try to execute the operation on a trajectory without water atoms?

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7 years 10 months ago #5549 by flaviyan
Hi J,

look into the options gmx densmap options -aver this gives you the average density with respect to planes which is what you want. I am not sure about the segmentation fault.

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7 years 10 months ago - 7 years 10 months ago #5552 by James Starlight
Replied by James Starlight on topic MARTINI simulation of protein-protein assosiation
yep thanks!
By means of reducing number of the input trajectories has solved my problem.
Now will think about analysis in details.

But from the densmap.dat produced by

gmx densmap -f resp_complex_merged.xtc -s ref.tpr -n new2.ndx -od densmap.dat -aver z

it still unclear how to obtain some clues regarding possible interfaces of binging between both proteins - here it plots on X the actual distance on Z and on Y it's occupancy.
So some kind visualization of densities mapped on 3D structure might give me more insights I guess.

Might other analysis based on the merged trajectory be useful e.g something related to clusterization of binding interfaces?



Thanks again for the help!

J.
Last edit: 7 years 10 months ago by James Starlight.

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7 years 10 months ago #5556 by flaviyan
Your question is little ambiguous, but use the xpm file and see what happens.

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7 years 10 months ago #5557 by James Starlight
Replied by James Starlight on topic MARTINI simulation of protein-protein assosiation
plz see again my previous post I have edited it with more relevant part :-)

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7 years 10 months ago #5558 by flaviyan
you can map the densities in 3D with the combined trajectory but you have to write a script. I am not aware of any software that allows you to do so directly.

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7 years 10 months ago #5564 by James Starlight
Replied by James Starlight on topic MARTINI simulation of protein-protein assosiation
yes the question for me too.

I also tried to found some solution based on the co-variance matrix method e.g to make PCA of the merged trajectory 1) selecting ligand atoms as the input group for the cov matrix and 2) project snapshots on the eigenvectors to see how the trajectory will be clusterized along first PCs but in my case it seems it might be useless because usually PCA captures only the internal molecular motions and the first six eigenvectors (translation and rotation which might be degrees of freedom by which sampling of the interfaces actually is achieved) are not included to the analysis.
MB someone know some server for the visualization of binding inter-phases?

J.

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7 years 10 months ago #5568 by James Starlight
Replied by James Starlight on topic MARTINI simulation of protein-protein assosiation
today I found the script for VMD which should print residues in the contact between 2 selections from the trajectory
proc contactFreq { {sel1} {sel2} {percent 0} {outFile stdout} {mol top} } {
  if { $outFile != "stdout" } { 
     set outFile [open $outFile w]
  } 
  puts $outFile "[clock format [clock scan now]] Search started."

  set allAtoms {}
  set allCount {}
  set numberOfFrames [molinfo $mol get numframes]
  for { set i 0 } { $i < $numberOfFrames } { incr i } {
      molinfo $mol set frame $i

      set frameCount {}
      set frameAtoms [atomselect $mol "$sel1 and within 4 of ($sel2)"]
      foreach {segid} [$frameAtoms get segid] {resname} [$frameAtoms get resname] {resid} [$frameAtoms get resid] {name} [$frameAtoms get name] {
	  set atom [list $resid $resname $segid]
	  if {[lsearch $frameCount $atom] != -1} continue
	  lappend frameCount $atom
	  set loc [lsearch $allAtoms $atom]
          if { $loc == -1 } {
             lappend allAtoms $atom
             lappend allCount 1
          } else {
             lset allCount $loc [expr { [lindex $allCount $loc] + 1 } ]
          }
     }
     $frameAtoms delete
  }

  puts $outFile "[clock format [clock scan now]] Search finished."

  puts $outFile "Find interactions:"
  puts $outFile "Residue \t\tfraction" 
  #print count after sorting
  set outData {}
  foreach { a } $allAtoms { c } $allCount {
      lappend outData [concat $c $a]
  }
  foreach { data } [lsort -integer -index 1 $outData] {
      set c [lindex $data 0]
      set fraction [expr { 100*$c/($numberOfFrames+0.0) }]
      if { $fraction >= $percent } {
	 puts $outFile [format "%s-%s-%s \t\t %.2f%%" [lindex $data 3] [lindex $data 2] [lindex $data 1] $fraction]
      }
      #set beta according to the fraction, this is optional
      set atom [atomselect $mol "segid [lindex $data 3] and resname [lindex $data 2] and resid [lindex $data 1]"]
      $atom set beta $fraction
      $atom delete
  }

  if { $outFile != "stdout" } {
      close $outFile
  }

}


assuming that I uploaded the mergd trajectory to vmd
and
defined selection 1 as chain A (this is smaller protein)
and selection 2 as not chain A (this is bigger protein)
I tried to execute

contactFreq "chain A" "not chain A"

but no residues are found.
Is it possible to adapt that script for the martini trajectories?
What another contact map based solutions might be useful here?

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7 years 10 months ago #5579 by James Starlight
Replied by James Starlight on topic MARTINI simulation of protein-protein assosiation
also another suggestions regarding analysis of this system are welcome!

Briefly I need to determine binding interface (particularly to find residues which are contribute to binding from the receptor) between 2 proteins, emerged during several independent md runs (in my case all trajectories are merged together):

www.youtube.com/watch?v=u3vKKBq4G6s

I have tried to use contact maps based vizualisation aproaches in VMD and Pymol but unfortunately it was a problem with the representation of the martini atoms in both of them (e,g in vmd the sequence of martini model have not been recognized at all).

Thanks for help!

J

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7 years 10 months ago #5580 by flaviyan
Hi J,

If you are good with python I would recommend using the MDAnalysis library of tools which already has tools to calculate contact maps.

Another suggestion would be to look into the TCL script for the contactmap plugin form VMD and modify to recognize the CG protein residues.

Gromacs also has a tools to get contacts gmx mindist gmx mdmat

Hope this helps.

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7 years 10 months ago #5584 by James Starlight
Replied by James Starlight on topic MARTINI simulation of protein-protein assosiation
Hi flaviyan,

A good suggestions - thank you !
Also I guess prody python package could do the same things, right ?

Gleb

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7 years 10 months ago #5587 by James Starlight
Replied by James Starlight on topic MARTINI simulation of protein-protein assosiation
forgot to as that I have used as well special utility g_distMat installed for gromacs

trying to calculate contact maps between 2 separate groups defined in index ndx

Group 16 ( r_1-104) has 236 elements
Group 17 (Protein_&_!r_1-104) has 4117 elements

unfortunately it has also produced an empty contact map :(
mb the atom selection in ndx should be made in another fashion?

J.

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7 years 10 months ago #5588 by James Starlight
Replied by James Starlight on topic MARTINI simulation of protein-protein assosiation
update :-)

in addition I am interesting in the clusterization of binding interfaces established during MD e.g based on the position of one protein regarding another.

For my case I have performed such clusterization from MD movie plugin of CHIMERA which recognize martini's models quite well (which was based on current selection which was the atoms of smaller protein). As the result I obtained alot of overlapped clusters. Question - Is it possible here to increase accuracy of the clusterization and to remove some degrees of freedom which are not important for my case ? E.g to pre-proces trajectory by means of PCA before clusterization (e.g to discard rotation-translation from the protein) might be good or not?

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7 years 10 months ago #5589 by flaviyan
ProDy can do contact maps with in the protein i.e native contacts I am not sure about multi-protein complex. You can also try your luck with the MDAnalysis toolkit package.

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7 years 10 months ago #5590 by flaviyan
you can do the pre-processing using the trjconv options or use the Align utility part of RMSD analysis tool in the VMD

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7 years 10 months ago - 7 years 10 months ago #5591 by James Starlight
Replied by James Starlight on topic MARTINI simulation of protein-protein assosiation
Yes, thanks so much now it looks much better!

Btw besides contact maps I also interesting to track hypothesis whether the electric field made by the charged residues located on the water-exposed surface of receptor is the main attraction force responsible for the binding of smaller protein. How it could be validated in the Martini's models ? Will the analysis of electrostatic surface of MD trajectory be good for this reason? Are there any special solutions for the software (by now Chimera are better for the Martini's trajectories than the VMD)

J.
Last edit: 7 years 10 months ago by James Starlight.

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7 years 10 months ago #5593 by flaviyan
I am not aware of any software that can calculate the electrostatic field for CG protein model and i would not advice on calculating the EPS based on CG model. You can reverse map the structure back to atomistic model and do the calculations with chimera

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