Previous Thread
Next Thread
Print Thread
Joined: Sep 2018
Posts: 17
C
ca4930 Offline OP
Forum Member
OP Offline
Forum Member
C
Joined: Sep 2018
Posts: 17
I am attempting to move a group of ligands in a pdb so that they are within a 5 Angstrom distance cutoff from a group of residues in a protein. I know that I can use cons harm and other positional restraints to maintain this distance during a simulation, but I am not sure how to set the initial positions of the ligands. I've tried using coor orie to align the protein to the x-axis and then used coor axis to get the approximate position of the group of residues in the protein (the inferred binding site). I then added 5 to either the x, y or z axis to define a new position for the ligand by using coor set. The first problem I'm encountering is that coor set is used to specify coordinates for a single atom, so my current implementation is assigning the same coordinates to each atom in the ligand.

coor orie sele protein end
coor axis sele resid 101 .or. resid 103 .or. resid 105 end
calc xpos = ?XAXI + 5.0
set ypos = ?YAXI
set zpos = ?ZAXI
coor set xdir @xpos ydir @ypos zdir @zpos sele segid lig1 end
write coor pdb name test.pdb

Maybe I can write a loop for all the atoms in a ligand within a larger loop for all the ligands but I'm wondering if there is a better way to position ligands within a distance cutoff?

Joined: Sep 2003
Posts: 8,667
Likes: 27
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,667
Likes: 27
You can define an axis from the site to the current ligand position with a double atom selection:

coor axis sele resid 101 .or. resid 103 .or. resid 105 end sele segid lig1 end

Then you can translate along that axis by some fraction, e.g.:

calc trn = 0.5 * ?RAXIS ! 50% of the axis length
coor tran axis dist @TRN sele segid lig1 end


Rick Venable
computational chemist


Moderated by  lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.5
(Release build 20201027)
Responsive Width:

PHP: 7.3.31-1~deb10u5 Page Time: 0.009s Queries: 18 (0.007s) Memory: 0.7291 MB (Peak: 0.7701 MB) Data Comp: Off Server Time: 2024-02-24 10:02:31 UTC
Valid HTML 5 and Valid CSS