Klauda Lab Simulation Wiki

By Robert Allsopp

Downolad the files from here distance_charmm_vmd.tar.gz

There are a few ways to gather the distance data. Each with different results.

   1) Using VMD with weights
   2) Using VMD without weights
   3) Using Charmm (without weights same as VMD without weights)
   4) EDP Method

Need to update the selection of the protein, PROA is the chain name and resid 1 is the first amino acid of that protein and update it for both selection lines.

set sel [atomselect top "segname PROA and resid 1" frame $i]
set mass [$sel get mass]
set data [measure center [atomselect top "segname PROA and resid 1" frame $i] weight mass]

Update the heavy atom that is going to be measured “name P” gets the phosphate, and then update the resid 61 to 120 to be either the upper or lower leaflets. Check which leaflet that the peptide actually bound to and then take the selection that falls in the correct range.

set datalip [measure center [atomselect top "segname MEMB and name P and resid 61 to 120" frame $i]]

Next it is needed to update the calculation section to flip the sign to account for upper lower leaflets.

      set distance [expr -$data + $datalip]

All of these VMD setups follow the same process.

Then adjust these lines in the .csh file the 51 is the starting .dcd file and 150 is the final .dcd file and dist_a.tcl specifies which of the .tcl files is chosen to be used. Update the paths to everything in the .tcl

   rm new.dat
   rm proa.dat
   set j = 51
   while ( $j <= 150 )
   vmd -e dist_a.tcl -args $j
   cat new.dat >> proa.dat
   @ j++
   end

The Charmm code is similar but requires more paths and to update the lines below to specify the different selections. Here segid PROA .and. resid 1 is similar to the “segname PROA and resid 1”, just add as many lines as there are residues to measure and then echo the results to the output file, in the last line below.

   coor stat sele segid MEMB .and.  type P end
   calc zA = ?zave
   coor stat sele segid MEMB .and.  type P .and. prop z lt @zA end
   calc zd = ?zave
   coor stat sele segid MEMB .and.  type P .and. prop z gt @zA end
   calc zu = ?zave
   coor stat sele segid PROA .and. resid 1 end
   calc z1 = ?zave 
   echo @zd @zu @z1

For the EDP method of position determination follow the regular EDP process and then develop a .cmp file that selects the specific atom names that are needed to be measured. A separate row for each group that needs to be labled. Follow the templates of the lipids generated in the EDP process.

Finally, use MATLAB and the code below to do the integral. Where the neg is for negative Z positions and the pos is for the positive Z from (0:end)

[

trapz(z_control_neg,dmps_control_phos_neg.*z_control_neg)/trapz(z_control_neg,dmps_control_phos_neg) trapz(z_control_pos,dmps_control_phos_pos.*z_control_pos)/trapz(z_control_pos,dmps_control_phos_pos)

]