Re: Missing Parameters For H3O+

From: Brian Radak (brian.radak_at_gmail.com)
Date: Wed Jan 24 2018 - 09:05:36 CST

The Shen group has developed hydroxide and hydronium parameters that are
presumably compatible with CHARMM36. They are primarily used for constant
pH, but I'll let you decide if they are useful for your purposes:

http://www.cell.com/biophysj/pdf/S0006-3495(13)00745-5.pdf

On Tue, Jan 23, 2018 at 11:16 PM, Victor Kwan <vkwan8_at_uwo.ca> wrote:

> Hi Ahmed,
>
> For the topology file, read: http://www.ks.uiuc.edu/
> Training/Tutorials/namd/namd-tutorial-unix-html/node24.html
>
> VK
>
> On 23/01/2018 11:03 PM, Victor Kwan wrote:
>
> Hi Ahmed,
>
> Mixing parameters from different force fields are not recommended (unless
> you can justify it physically). That said, you can extract the H3O+
> parameters from AMBER, and add it to your charmm parameter file.
>
> Regards,
>
> VK
>
> On 23/01/2018 1:13 PM, Ahmad Kiani wrote:
>
> Dear NAMD users
>
> I'm trying to put some hydronium ions in my water box but I didn't find
> any toppalogy or parameter file for this ion. I know that people are
> using Baaden’s parameters in Amber but I’m using CHARMM. Do you know how
> can I build psf file for H3O+ to use it in NAMD?
>
> Regards
> Ahmad
>
>
>
>

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