Re: Topology and parameters for nitrate and nitrite ion

From: amin_at_imtech.res.in
Date: Sun Jun 30 2013 - 23:00:29 CDT

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

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:24 CST