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

From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue May 07 2019 - 10:44:39 CDT

As stated in my last email, this is not the correct psfgen syntax for
reading a PSF with PDB coordinates -- the PDB should be included as an
argument to the readpsf command (this is covered in the user guide):

readpsf zgnr_f2.psf pdb zgnr_f2.pdb ;# you can also read NAMD binary
coordinates with the "namdbin" flag

Returning to my first question, I don't understand what you hope to
accomplish by reading a PSF/PDB into psfgen and then writing them out
again. Your psfgen script does not modify the input PSF/PDB in any way so
there is no obvious value in doing this.

On Tue, May 7, 2019 at 11:05 AM Priyanka Mondal <pmondal_at_udel.edu> wrote:

> 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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