From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri May 22 2020 - 09:47:43 CDT
You can use "Using solvent other than water" in the Solvate plugin doc as
reference for filling a box with anything:
https://www.ks.uiuc.edu/Research/vmd/plugins/solvate/
And check the water models doc in the UG:
https://www.ks.uiuc.edu/Research/namd/2.13/ug/node24.html#6839
On Fri, May 22, 2020 at 10:28 AM HEMANTH H <hemanth.h_at_iitgn.ac.in> wrote:
> Refer CHARMM-GUI for detailed instructions on how to do it. VMD might not
> be the best tool to solvate the structure, if you need SWM4 out of the box.
>
> On Fri, May 22, 2020 at 6:09 AM Qasim Pars <qasimpars_at_gmail.com> wrote:
>
>> Dear users,
>>
>> I have the pdb file of a molecule and want to solvate that molecule with
>> SWM4 water model. Then I would run the solvated system using NAMD with
>> Drude FF after doing parameterization.
>>
>> Does anyone know how I can solvate the pdb file of a molecule with SWM4
>> water model?
>>
>>
>> Any help would be appreciated.
>>
>> Thanks,
>>
>> --
>> Qasim Pars
>>
>
>
> --
> *Hemanth H 18310019*
> Research Scholar
> IIT Gandhinagar
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Research collaborator, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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