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

From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Tue May 07 2019 - 01:46:43 CDT

just replace the zeros with whatever coordinate you have in the xyz.

On Mon, May 6, 2019 at 9:53 PM Priyanka Mondal <pmondal_at_udel.edu<mailto:pmondal_at_udel.edu>> wrote:
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<http://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.
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Priyanka Mondal,
Department of Physics and Astronomy,
University of Delaware,
USA

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