How do I add passivated H-atom to ZGNR

From: Priyanka Mondal (pmondal_at_udel.edu)
Date: Tue Apr 30 2019 - 11:43:20 CDT

Hello NAMD users,
I am trying to create zigzag graphene nanoribbon structure with passivated
H-atom for dangling bonds at the edges. I am able to create file.psf and
file.pdb without passivated H-atom using following command :

graphene -lx 5 -ly 3 -type armchair -nlayers 2 -b 1 -a 1 -Dihedraltypes 0
-d 0
animate write psf zgnr.psf waitfor all
animate write pdb zgnr.pdb waitfor all

But I am not sure how to add passivated H-atom to the structure and
generate corresponding file.psf and file.pdb.
Since* I don't know how to add passivated H-atom using tcl script/vmd*, I
imported zgnr.xyz into quantumatk and added passivated H-atom to the
structure and then imported the new structure back zgnr_new.xyz to vmd.
Now I tried to use psfgen to get zgnr_new2.psf for this new structure with
passivated H-atom and was unable:

package require psfgen
resetpsf
topology top_all36_prot.rtf
coordpdb zgnr_new.pdb
guesscoord
writepsf zgnr_new2.psf
writepdb agnr_new2.pdb

and here is the error message I got
# ********************************************************************
psfgen) Warning: failed to set coordinate for atom C GRA:1342 SHT
psfgen) no segment SHT
psfgen) Warning: failed to set coordinate for atom C GRA:1343 SHT
psfgen) no segment SHT
psfgen) Warning: failed to set coordinate for atom C GRA:1344 SHT
psfgen) Info: guessing coordinates for 0 atoms (0 non-hydrogen)

# *********************************************************************
Alternately, I also tried using molfacture with following command to add
passivated H-atom

package require molefacture
Molefacture::molefacture_gui_aux {numbonds <=2 and x >= 19 and z >=1}
Molefacture::add_hydrogen 1

But it is replacing the bond with adjacent carbon atom with H-atom bond
instead of adding H-atom to dangling bond and I am not sure how to specify
adding a single H-atom to specific bond of a specified atom i.e. say, how
do I add H-atom to dangling bond of atom 250.
# ***********************************************************************
I shall be very thankful if someone helps me solving this issue.

%
--------------------------------------------------------------------------------------------------------------------------------------
Priyanka Mondal,
Department of Physics and Astronomy,
University of Delaware,
USA

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