VMD-L Mailing List

From: DENILSON FERREIRA DE OLIVEIRA (denilson_at_ufla.br)
Date: Wed May 15 2024 - 07:07:12 CDT

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!7JhKE0eCOB6FC-CS1VjAavOQ4NPmVTkIXl3zDK66c6eKkQmxc59XvGfIl-v3mdanwGVX9pslaMK20-55vdY$
>> <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
> 

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