Re: solvation with SWM4 water model

From: Ropón-Palacios G. (biodano.geo_at_gmail.com)
Date: Sun May 24 2020 - 14:51:36 CDT

Dear NAMD users,

Anybody please, can help me with good protocol for simulation virus
capsid?, i'm try simulate dengue virus, using protocol mentionated by 
Prof. Perilla and Prof Hadden-Perilla, but not can pass of minimization,
in this point i've two problems:

1. RETLE bad atoms

2. box turn small box. i've try several box padding 10, 15, 20, 30, 40.

my trimeric protein (3J27), is prepared using charmm-gui, fix missing
atoms and residues.  please help me.

What is good protocol. my current protocol is:

1. pdb and psf generatiosn

2. solvatation and ionization

3. minimization using harmonic restraint to backbone

4. heating from 60 to 310k

5. relax harmonics restraint

6. production without restraint

On 22/5/20 20:42, HEMANTH H wrote:
> @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
> <mailto: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 <mailto: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 <mailto: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 <mailto: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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