Re: Topology and parameters for nitrate and nitrite ion

From: Kenno Vanommeslaeghe (
Date: Sun Jun 30 2013 - 19:17:40 CDT

- 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.



(*) 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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