From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jan 24 2018 - 08:41:47 CST
Hello Ahmad, using everyone's favorite search engine you can find for H3O+
in CHARMM that the big man himself says "no" in this older thread:
https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=1070
There is an even older paper that has in-house parameters that should still
work, but I haven't tried it:
https://doi.org/10.1016/S0006-3495(96)79773-4
The main reason why there isn't a mainstream CHARMM model for H3O+ is that
aside from its instability, its concentration at the pH of biologically
relevant environments is very low, and you'd have zero ions in a typical MD
water box. Due to both problems, people have usually opted for treating it
at the QM or QM/MM level.
Giacomo
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/Trainin
> g/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
>
>
>
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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