Re: Topology and parameters for nitrate and nitrite ion

From: Kenno Vanommeslaeghe (
Date: Sun Jun 30 2013 - 23:47:57 CDT

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, 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:
>> 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*
>>> 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
>>> --------------------------------------------------------------------------
>>> *From:* "" <>
>>> *To:*
>>> *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.
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> ______________________________________________________________________
> 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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