[gmx-users] Sulfate ion parameters

[#SUKRITI GUPTA#]

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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