VMD-L Mailing List

From: DENILSON FERREIRA DE OLIVEIRA (denilson_at_ufla.br)
Date: Tue May 14 2024 - 08:06:59 CDT

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!9ySzr4oryoRSVTF8v-hjgFGDp358ZuCSPZcAOLoqhcRuf87uj1zC6vmVQKEcl0MIHu8p3NWwczr04WXB1gM$ .
umaryland.edu/charmm_ff.shtml: 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.