From: Qasim Pars (qasimpars_at_gmail.com)
Date: Fri May 22 2020 - 15:42:13 CDT
@Hemanth I need to have the psf file of molecule in order to use CHARMM-GUI
but I don't have it. Note that I only have the pdb file of molecule. So I
can't use the CHARMM-GUI without having the psf file from Drude FF.
@Giacomo It seems that VMD doesn't have ability to generate Drude
topologies.
What I want is just to solvate the ligand/molecule in the pdb file with
SWM4 and generate the drude topology of solvated system.
On Fri, 22 May 2020 at 17:48, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> 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
>
-- Qasim Pars
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