Re: Topology and parameters for nitrate and nitrite ion

From: amin_at_imtech.res.in
Date: Mon Jul 01 2013 - 02:39:44 CDT

Sadly, I didn't find any CHARMM parameters for nitrate or nitrite in the
literature. I did find amber and opls parameters for nitrate but not for
nitrite. As you are actively involved in CHARMM development I would request you
to consider these two ions whenever possible as these ions are really important
in biological systems.

Warm Regards.
Amin.

> So you didn't find anything in the literature, then? Because that's where
> most people get their small ion parameters in practice. It would surprise
> me if nobody made an attempt at parameterizing nitrate before...
>
> Also, I'd like to emphasize that if you only want to have the ion present
> in an active site, and are not interested in studying binding/unbinding,
> then even a very crude model just might be good enough. I'm in the group
> that is responsible for the majority of the official CHARMM force field
> development, and even we have on occasion knowingly used a very crude and
> imperfect model for an active site ion. (Did I mention ions are
> difficult?) I believe we even needed distance restraints to keep the darn
> thing in place (not sure at all, it wasn't my project). As long as you
> fully realize it's a crude model and you interpret and present your
> results accordingly, I would say it's OK. That's the pragmatic side of things.
>
>
> On 07/01/2013 12:00 AM, amin_at_imtech.res.in wrote:
>> Thanks for the detailed answer. Actually I had followed the swissparam
>> approach
>> a few days ago. But reading your earlier post made me realize that this may
>> not
>> be an accurate way of doing it. Overall it looks too specialized a job for me
>> to
>> attempt. Hoping some person with the required skill set will do this in near
>> future.
>>
>> Regards.
>> Amin.
>>
>>
>>> - small anorganic ions usually require special dedicated L-J parameters.(*)
>>>
>>> - as far as I know, CHARMM does not officially have L-J parameters for
>>> nitrate and nitrite.
>>>
>>> - Swissparam uses the L-J parameters from the official CHARMM release so
>>> it doesn't have them either. Hence, it cannot be expected to do a good job
>>> at this assignment.(+)
>>>
>>> - Charges that are directly derived from QM calculations generally cannot
>>> be combined with the CHARMM L-J parameters; see:
>>> http://mackerell.umaryland.edu/~kenno/cgenff/faq.html#esp
>>> A relevant 3rd party study illustrating this point is
>>> A. Ahmed, S. I. Sandler; J. Chem. Theory Comput. 2013, 9 (6), 2774–2785
>>>
>>> - 3rd party nitrate and nitrite parameter sets that claim to be
>>> compatible with CHARMM may be found in the literature. Their degree of
>>> actual CHARMM compatibility and their quality may vary widely. Depending
>>> on your purpose, they may or may not be good enough for you. If you
>>> require the ion to remain bound in an enzyme active site, quality is less
>>> critical than if you plan to allow it to unbind. To gauge the quality,
>>> look for MD validation runs using the TIP3P water model, aiming to
>>> reproduce solution-phase experimental data that are relevant for your
>>> purpose.
>>>
>>> Cheers,
>>>
>>> Kenno.
>>>
>>> (*) Parameterization of small anorganic ions is extremely specialized
>>> work, requiring (among other things) the calculation of Radial
>>> Distribution Functions of different salt solutions and comparison with
>>> experiment. Usually, in the additive force field, special NBFIX terms are
>>> required for correct solution-phase behavior in the presence of different
>>> counterions. Within the CHARMM community, the authority on ion
>>> parametrization is Benoît Roux; see his work.
>>>
>>> (+) More generally spoken, the Swissparam approach of combining CHARMM L-J
>>> parameters with MMFF94 charges and dihedrals is flawed; see my post of a
>>> few days ago. The Swissparam developers advertise their work as a tool for
>>> obtaining very rough models for large-scale virtual screening, not for
>>> detailed MD studies.
>>>
>>>
>>>
>>> On 06/30/2013 03:02 PM, flavio seixas wrote:
>>>> Hi,
>>>>
>>>> Download the *.mol2 version of nitrite and nitrate molecules from zinc
>>>> database: *zinc*.docking.org/
>>>> Special attention to protonated state of molecules at pH 7.0 (or other
>>>> desired pH).
>>>> Submit each of them to www.*swissparam*.ch/
>>>>
>>>> Download toppar and param files in Charmm format (*.zip).
>>>>
>>>> If you want accurate force fields, optimize molecules with
>>>> B3LYP/6-31G++(d,p) level of theory and replace partial charges at toppar
>>>> files generated by Swissparam.
>>>>
>>>> Regards,
>>>> -------------------------------------
>>>> Flavio Augusto Vicente Seixas
>>>> Laboratory of Structural Biochemistry
>>>> Department of Biochemistry
>>>> Universidade Estadual de Maringá, PR, Brazil
>>>> http://www.uem.br
>>>> --------------------------------------------------------------------------
>>>> *From:* "amin_at_imtech.res.in" <amin_at_imtech.res.in>
>>>> *To:* namd-l_at_ks.uiuc.edu
>>>> *Sent:* Saturday, June 29, 2013 2:51 PM
>>>> *Subject:* namd-l: Topology and parameters for nitrate and nitrite ion
>>>>
>>>> Dear NAMD users,
>>>> I want to run a simulation of a protein with bound nitrite and nitrate
>>>> ions. Can
>>>> someone please guide me on how/where to obtain the topology and parameter
>>>> files
>>>> for these ions? Any suggestions will be highly appreciated.
>>>>
>>>> Regards.
>>>> Amin.
>>>>
>>>> ______________________________________________________________________
>>>> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
>>>> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
>>>> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
>>>> पिन कोड/PIN CODE :160036
>>>> दूरभाष/EPABX :0172 6665 201-202
>>>>
>>>>
>>>>
>>>
>>>
>>
>> ______________________________________________________________________
>> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
>> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
>> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
>> पिन कोड/PIN CODE :160036
>> दूरभाष/EPABX :0172 6665 201-202
>>
>
>

______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202

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