Need help with psfgen : psfgen can't read file.pdb

From: Priyanka Mondal (pmondal_at_udel.edu)
Date: Mon May 06 2019 - 20:53:03 CDT

Hello all,
I am trying to create zgnr ribbon with dangling bonds passivated by
H-atoms. I created ZGNR using nanotube builder and imported zgnr.xyz to
quantumatk to add passivated H-atom and then imported final structure back
to vmd as zgnr_H.xyz. Now I created zgnr_f.pdb and zgnr_f.psf using
following command :

% **********************************************************************
mol delete all
mol load xyz zgnr_H.xyz
package require topotools
set sel [atomselect top all]
topo guessangles
topo guessdihedrals
topo guessimpropers
topo guessbonds
$sel writepsf zgnr_f.psf
$sel writepdb zgnr_f.pdb

mol delete all
mol load psf zgnr_f.psf pdb zgnr_f.pdb
% **********************************************************************

The files zgnr_f.psf and zgnr_f.pdb (just created) have fixed residue
number 1 for all res GRA (which is different from residue number increasing
in ascending order when I created zgnr.psf without H-atom directly from
nanotube builder (i.e. no quantumatk) followed by a successful MD run).

% **********************************************************************
mol delete all
mol load psf zgnr_f.psf pdb zgnr_f.pdb
set sel [atomselect top all]
$sel set segid SHT
$sel set resname GRA
animate write psf zgnr_f2.psf waitfor all
animate write pdb zgnr_f2.pdb waitfor all

mol delete all
package require psfgen
resetpsf
topology top_all27_prot_lipid.rtf
readpsf zgnr_f2.psf
coordpdb zgnr_f2.pdb
writepsf zgnr_f3.psf
writepdb zgnr_f3.pdb
% **********************************************************************

Next when I try to use psfgen to read it using above commands, the output
zgnr_f3.pdb sets all coordinates as zero. I looked up some similar
questions and tried setting segname and resname as mentioned above but
nothing worked. I am not sure how to fix it. I really hope that someone
helps me solve this issue. I am not sure what to do. Thank you.
Priyanka Mondal,
Department of Physics and Astronomy,
University of Delaware,
USA

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