VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Tue May 21 2024 - 09:03:17 CDT

Hi Roni, maybe the attachment got blocked.
Here's the script.

# Load the psfgen package
package require psfgen

# Reset psf just in case
resetpsf

# Read system using PSFGEN commands
readpsf file.psf
coordpdb file.pdb

# Load system to VMD
mol load psf file.psf pdb file.pdb

# Do some VMD tasks
set sel [atomselect top protein]
measure center $sel
measure minmax $sel

# Write the system to .psf/pdb using PSFGEN commands
writepsf all.psf
writepdb all.pdb

# To modify the system, one should use PSFGEN commands.
# Example: to remove water molecules
  # Select the water
  set water [atomselect top water]

  # Using PSFGEN commands, delete the selected atoms.
  foreach segid [$water get segid] resid [$water get resid] {
    delatom $segid $resid
  }

# Write molecule without water, using PSFGEN commands
writepsf nowater.psf
writepdb nowater.pdb

quit

On Mon, May 20, 2024 at 10:22 PM Roni Saiba <ronis_at_imsc.res.in> wrote:

> If you can share the script here or in any sharing platform, it may be
> beneficial for others in future.
> Regards,
> Roni
> Quoting DENILSON FERREIRA DE OLIVEIRA <denilson_at_ufla.br>:
>
> > Dear Diego Gomes,
> >
> > Thank you very much.
> >
> > Best regards.
> >
> > Denilson.
> >
> >
> > Em qua., 15 de mai. de 2024 às 12:58, Diego Gomes <diego.enry_at_gmail.com>
> > escreveu:
> >
> >> Hi Denilson,
> >> one should use PSFGEN commands for a complete PSF.
> >>
> >> I made you a .tcl script with comments, but Jérôme Henin gets the
> credits
> >> for this solution.
> >>
> >> Friendly,
> >> Diego.
> >>
> >> On Wed, May 15, 2024 at 7:45 AM DENILSON FERREIRA DE OLIVEIRA <
> >> denilson_at_ufla.br> wrote:
> >>
> >>> Dear Diego Gomes,
> >>>
> >>> First of all, thank you for replying to my message.
> >>>
> >>> I will send the files to your email.
> >>>
> >>> Best wishes.
> >>>
> >>> Denilson.
> >>>
> >>> Em ter., 14 de mai. de 2024 às 12:18, Diego Gomes <
> diego.enry_at_gmail.com>
> >>> escreveu:
> >>>
> >>>> Denilson,
> >>>> I can review your issue if you send me the .pdb and .psf.
> >>>>
> >>>> --
> >>>> Diego
> >>>>
> >>>>
> >>>> On Tue, May 14, 2024 at 8:52 AM DENILSON FERREIRA DE OLIVEIRA <
> >>>> denilson_at_ufla.br> wrote:
> >>>>
> >>>>> Dear all,
> >>>>>
> >>>>> 1) I generated psf and pdb files with VMD 1.9.4a57, for a protein
> >>>>> complex with a ligand, using the Charmm force field topology
> >>>>> files, which I
> >>>>> obtained on November 13, 2021, from
> >>>>>
> https://urldefense.com/v3/__http://mackerell__;!!DZ3fjg!4iqR-7mp990ZvmdFgkHu6_V63VDpl5oeSJxJI9TH7YRvzPwKgQmm8YZ0E4yxQf_1aLJEtSnHMPOrqXDWt4s$
> >>>>> <
> https://urldefense.com/v3/__http://mackerell__;!!DZ3fjg!9ySzr4oryoRSVTF8v-hjgFGDp358ZuCSPZcAOLoqhcRuf87uj1zC6vmVQKEcl0MIHu8p3NWwczr04WXB1gM$
> >.
> >>>>> umaryland.edu/charmm_ff.shtml
> >>>>> <
> https://urldefense.com/v3/__http://umaryland.edu/charmm_ff.shtml__;!!DZ3fjg!9ySzr4oryoRSVTF8v-hjgFGDp358ZuCSPZcAOLoqhcRuf87uj1zC6vmVQKEcl0MIHu8p3NWwczr0rodqqnk$
> >:
> >>>>> toppar_c36_jul21.tgz.
> >>>>>
> >>>>> 2) The ligand contains chlorine atoms. As a result, one electron pair
> >>>>> for each chlorine atom is specified in the pdb file as well as in
> the psf
> >>>>> file. Furthermore, the NUMLP NUMLPH section appears in the psf file:
> >>>>>
> >>>>> 8 24 !NUMLP NUMLPH
> >>>>> 2 1 F 1.6400 0.0000 0.0000
> >>>>> 2 4 F 1.6400 0.0000 0.0000
> >>>>> 2 7 F 1.6400 0.0000 0.0000
> >>>>> 2 10 F 1.6400 0.0000 0.0000
> >>>>> 2 13 F 1.6400 0.0000 0.0000
> >>>>> 2 16 F 1.6400 0.0000 0.0000
> >>>>> 2 19 F 1.6400 0.0000 0.0000
> >>>>> 2 22 F 1.6400 0.0000 0.0000
> >>>>> 20815 20786 20779 20816 20802 20792 20855 20826
> >>>>> 20819 20856 20842 20832 20895 20866 20859 20896
> >>>>> 20882 20872 20935 20906 20899 20936 20922 20912
> >>>>>
> >>>>> 3) After optimizing the system with Namd 3.0b6, a coor file was
> >>>>> generated. Then I used the following commands in VMD:
> >>>>>
> >>>>> mol new file.psf
> >>>>> mol addfile file.coor
> >>>>> set all [atomselect top all]
> >>>>> measure center $all
> >>>>> measure minmax $all
> >>>>> $all writepdb new.pdb
> >>>>> $all writepdb new.psf
> >>>>>
> >>>>> 4) The new.psf file does not have the NUMLP NUMLPH section described
> >>>>> above. Therefore, when using the new.psf file for a molecular
> dynamics
> >>>>> simulation with Namd 3.0b6, the electron pairs of the chlorine atoms
> fly
> >>>>> around.
> >>>>>
> >>>>> Hence the following question: is there any way to prevent VMD
> 1.9.4a57
> >>>>> from eliminating the NUMLP NUMLPH section during the generation of
> the
> >>>>> new.psf file?
> >>>>>
> >>>>> Thank you in advance for your attention.
> >>>>>
> >>>>> Best wishes.
> >>>>>
> >>>>> Denilson.
> >>>>>
> >>>>>
> >>>>>
> >>>>> O conteúdo deste e-mail e anexos são restritos aos seus
> destinatários e
> >>>>> de responsabilidade do remetente. O uso do e-mail deve estar de
> >>>>> acordo com
> >>>>> os regulamentos institucionais vigentes.
> >>>>>
> >>>>
> >>>>
> >>>> --
> >>>> Diego Enry B. Gomes, PhD
> >>>> Department of Physics at Auburn University &
> >>>> NIH Center for Macromolecular Modeling and Visualization
> >>>> Leach Science Center - Ste. 3182 - Auburn, AL
> >>>> dgomes_at_auburn.edu
> >>>>
> >>>
> >>> O conteúdo deste e-mail e anexos são restritos aos seus destinatários e
> >>> de responsabilidade do remetente. O uso do e-mail deve estar de acordo
> com
> >>> os regulamentos institucionais vigentes.
> >>>
> >>
> >>
> >> --
> >> Diego Enry B. Gomes, PhD
> >> Department of Physics at Auburn University &
> >> NIH Center for Macromolecular Modeling and Visualization
> >> Leach Science Center - Ste. 3182 - Auburn, AL
> >> dgomes_at_auburn.edu
> >>
> >
> > --
> > O conteúdo deste e-mail e anexos são restritos aos seus destinatários e
> de
> > responsabilidade do remetente. O uso do e-mail deve estar de acordo com
> os
> > regulamentos institucionais vigentes.
>
>
> 

-- 
Diego Enry B. Gomes, PhD
Department of Physics at Auburn University &
NIH Center for Macromolecular Modeling and Visualization
Leach Science Center - Ste. 3182 - Auburn, AL
dgomes_at_auburn.edu