VMD-L Mailing List

From: DENILSON FERREIRA DE OLIVEIRA (denilson_at_ufla.br)
Date: Mon May 20 2024 - 14:05:58 CDT

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
> 

-- 
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