From: Vermaas, Joshua (
Date: Mon Jul 31 2017 - 12:42:10 CDT

Hi Shivam,

Scripting it in VMD would be my solution, but that is my solution to
most things, so I might be biased. If you have one copy of your
functional group made in Avogadro or Molefacture, you would add it to
your sheet in VMD as many times as needed, merge the functional groups
to your sheet, and then add bonds and guess angles and dihedrals.
Pseudocode for a TCL script would look something like:

#Load your graphene

for { set i 0 } { $i < $numfunctionalgroups } { incr i } {
#Load your functional group

#Place your functional group
package require topotools
set newmol [::TopoTools::mergemols [molinfo list]]

#Add in the bonds between functional groups and the main sheet

topo guessangles
topo guessdihedrals

#Write out your new files.

However, before you go filling in the blanks, I'd do a bit of googling
first to see how other folks made graphene oxide in their own studies,
since you aren't the first to look at making graphene oxide, so there
may be tools that exist that I know nothing about.


On 07/31/2017 07:33 AM, wrote:
> I am trying to create a graphene oxide sheet, for that i have generated a
> graphene sheet using Nanotube builder plugin in vmd and trying to edit
> that sheet to add the functional groups,for that I tried to use vmd
> molefacture plugin but my sheet is too big for that, i even tried to use
> AVOGADRO but even it is hanging for large sheets, so can you suggest any
> open source or free molecule editor or any other method that can handle
> large number of molecules easily.
> Best regards
> Shivam Tiwari