How to add a bond between two atoms in VMD?

Question

I want to add a bond between specific atoms. I found on VMD page that one can use topotools (e.g. topo addbond 1 2 ), but I have a lot of residues so this method didn't work with me. I need to select the two residues and then build a bond between the two atoms of the two different residues. Does anyone have an idea how to do this?

Answer 1

topo addbond x y should do the trick. where x is the index of the atom of an residue in which you are interested.
if you want a more automated way, then you need to know the exact atom name and the residue number.

Let's say, the residue number you are interested in is 250 and the atom name is HG1, and you want to add a bond to atom name OG1 of residue 267.

set a [atomselect top "residue 250 and name HG1"] 
set aindex [$a get index]

set a1 [atomselect top "residue 267 and name OG1"] 
set a1index [$a1 get index]

topo addbond $aindex $a1index

if you have a list of atom names and a list of residue numbers, you can just do a foreach loop and keep the above code in the loop, in that way you can add bonds to all the desired atoms at once.