[gmx-users] Sulfate ion parameters

[#SUKRITI GUPTA#]

Dear Mark,

Thanks for the reply. Actually, I emailed the corresponding author but didn't get any reply. Also, it is not mentioned in the paper that the model is for a rigid system.

Regards
Sukriti


Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:erian.ntu.edu.sg




________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abraham at gmail.com>
Sent: Monday, February 29, 2016 7:04 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Sulfate ion parameters

Hi,

Such questions are why all published articles list the email address of a
"corresponding author" ;-) But first, be sure their model wasn't designed
to be rigid, and so have no internal parameters such as you are seeking.

Mark

On Mon, Feb 29, 2016 at 12:01 PM #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg>
wrote:

> Thanks for the reply.
>
> I got one paper stating non bonded parameter values for sulphate ions:
> "Sulfate Anion in Water: Model Structural, Thermodynamic, and Dynamic
> Properties", but this paper does not provide bonded parameters required for
> simulating sulfate ions, i.e. bond bending and stretching parameters. Is
> there a way to find what parameters were used in the study.
>
> Thanks and Regards
> Sukriti
>
>
>
>
> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N)
> | Nanyang Technological University
> N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:
> erian.ntu.edu.sg
>
>
>
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Christian
> Bope Domilongo <christianbope at aims.ac.za>
> Sent: Wednesday, February 24, 2016 4:43 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Sulfate ion parameters
>
> You may try to generate topology file using Topolbuilder
> http://www.gromacs.org/Downloads/User_contributions/Other_software
> Regards,
>
>
> On 24 February 2016 at 14:16, #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg>
> wrote:
>
> > Dear gromacs users,
> >
> >
> > I wanted to simulate sulphate ions in water using oplsaa force field but
> I
> > couldn't find parameters for sulphur and oxygen atoms of sulphate ions in
> > the oplsaa force field files. Can anyone suggest from where can I get
> these
> > parameters?
> >
> >
> > Charmm force field has the parameters for sulphate ions, so is it
> possible
> > to use those parameters itself for simulations? Also the partial charges
> > given in charmm force field to S and O of sulphate ions do not add up to
> > -2. (S +1.33, O -0.78) So how to select the correct partial charges here?
> >
> >
> > Thanks and Regards
> >
> > Sukriti
> >
> >
> > [
> >
> https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAAAAAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0AAAANaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D&X-OWA-CANARY=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.&retryCount=3
> > ]
> >
> > Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N
> )
> > | Nanyang Technological University
> > N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> > Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:
> > erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html>
> >
> >
> >
> > --
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>
> --
> Bope Domilongo Christian
> Ph.D candidate in Computational Biology
> Division of Structural Biology and Biochemistry
> School of Biological Sciences
> Nanyang Technological University
> Singapore
> +6590565804
> http://www.ntu.edu.sg/
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