Re: Missing Parameters For H3O+

From: Ahmad Kiani (ahmadkianikaranji_at_gmail.com)
Date: Wed Jan 24 2018 - 09:27:28 CST

Thank you Victor, Giacomo and Brian. I appreciate your help.

Ahmad

On Wed, Jan 24, 2018 at 10:05 AM, Brian Radak <brian.radak_at_gmail.com> wrote:

> 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/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
>>
>>
>>
>>
>

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