VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Tue May 14 2024 - 10:18:44 CDT

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!865ySZWJlsusapjnK7iEUK6mEWxn9Vpg86xRYEFPet_gc6uhIKDW7huo5cWMJPPc-Vb-U3-FMXQPKx8cFGfC$ 
> <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.
>
>
>
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>
-- 
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