VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Wed May 15 2024 - 10:58:07 CDT

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!4wsN7sqBgJrl5NAXgey8m-D8uhfUkvhZocac_NjkglzaW2RQghYxI-v8Py_uYeMIdpuIAYa2X2zQ31NfriQm$
>>> <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