VMD-L Mailing List

From: Remya Ann (remya.mathewskl_at_gmail.com)
Date: Tue Nov 27 2018 - 07:14:59 CST

Hi,
I have a molecule as shown below-
//------------------
visual.xyz file
19

C 3 3 3
He1 6 5 5
He2 6 1 5
He3 0 5 5
He4 0 1 5
He5 6 5 1
He6 6 1 1
He7 0 5 1
He8 0 1 1
P 3 5 3
P 3 1 3
A 6 5 2
B 6 5 4
A 0 5 4
B 0 5 2
A 6 1 4
B 6 1 2
A 0 1 2
B 0 1 4
//------------------
I want to add bonds between He1-He2, He1-He5, He1-He3 and so on, so as to
create a cuboid. For just one molecule it is easy to do with the "topo
addbond id id" command. I have attached the pdb and psf files of the
required molecule.

But when I have multiple molecules (say 100 molecules), it becomes a little
difficult to add the bonds based on the indices. The setbondlist example in
the topotools tutorial page talks about 1 single atom type. But as you see
I have mutilpe other atom types which makes figuring out the correct pair
of indices a little crazy.
So I was wondering is there a way to add bonds based on the atom type
within the same molecule.
Any help would be appreciated.

Thanks in advance!
Remya Ann Mathews K
Doctoral Scholar