VMD-L Mailing List

From: Roni Saiba (ronis_at_imsc.res.in)
Date: Mon May 20 2024 - 22:22:06 CDT

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.