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

From: Priyanka Mondal (pmondal_at_udel.edu)
Date: Tue May 07 2019 - 10:05:37 CDT

Hello,
Thank you for your reply. I have file.xyz and I am trying to get file.pdb
and file.psf from that and add water and ions using solvate and autoionize.
Since file.xyz has info about coordinates but not bonds, I used topotools.
So far when I loaded the output file into vmd window, everything looked
right (atleast visually). Now when I tried adding water using "solvate"
which uses psfgen with command

solvate file.psf file.pdb -minmax {{-20 -20 -20} {20 20 20}} -o file_sol

 I see that file_sol.pdb coordinates are all zero. To be sure that it is
psfgen that's unable to read input files and hence causing the error, I
wrote the small attached script.

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

which confirmed that psfgen is not being able to read file.pdb. Your help
is much appreciated.

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

On Tue, May 7, 2019 at 9:16 AM Brian Radak <brian.radak_at_gmail.com> wrote:

> I am not a topotools expert (in fact, not even a user), but I know psfgen
> pretty well -- what is this section of the script intended to accomplish?
> It doesn't do anything useful that I'm aware of.
>
> 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
>
> Note that coordpdb is meant to read in coordinates for a *segment* and
> has a segment argument that is that segment name (or defaults to the last
> new segment, which is null here). I think what you want is instead:
>
> readpsf zgnr_f2.psf pdb zgnr_f2.pdb
>
> but again, I'm not sure why you would want/need to do this.
>
> HTH,
> BKR
>
>
> On Mon, May 6, 2019 at 9:55 PM Priyanka Mondal <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 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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