Re: solvation with SWM4 water model

From: HEMANTH H (hemanth.h_at_iitgn.ac.in)
Date: Fri May 22 2020 - 20:42:58 CDT

@Qasim, you can generate the PSF file for your structure from CHARMM-GUI,
using input generator. It takes in a pdb file and gives a charmm formatted
pdb and PSF file. It can then be used to create drude FF files.

Best regards,
Hemanth

On Sat, 23 May 2020, 02:12 Qasim Pars, <qasimpars_at_gmail.com> wrote:

> @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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