From: Massimiliano Porrini (m.porrini_at_iecb.u-bordeaux.fr)
Date: Mon Jul 01 2013 - 06:41:12 CDT
Dear Kenno and Amin,
I am very interested to this discussion too.
I had already read in Charmm forum that OPLS parameters
for non-bonded interactions implement well within CHARMM FFs.
However, I have a concern about the combination rules of Lennard-Jones (LJ)
parameters.
In fact, OPLS FF uses a *geometric* combination rule both
for LJ interaction strength (\epsilon) and for size of atoms (\sigma),
whereas CHARMM FFs use Lorentz-Berthelot combining rules, that is
geometric for \epsilon and arithmetic for \sigma.
Is there any workaround about this different way of implementing LJ
parameters?
For instance: can one somehow specify a \sigma geometric combination rule
only for those atoms for which OPLS FF parameters are implemented?
Or it has already been demonstrated that using OPLS LJ parameters
within CHARMM, implementing Lorentz-Berthelot combination rules, is not
harmful
for the results of the simulations?
Many thanks in advance for any comment about this.
Best regards,
On 1 July 2013 09:52, Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu>wrote:
> Then you're in luck; OPLS parameters for small molecules with no rotatable
> bonds often perform well when transferred to CHARMM, because the CHARMM
> nonbonded parameters are historically based on OPLS ones. Disclaimer: this
> is true of no other force field than OPLS!
>
>
>
> On 07/01/2013 03:39 AM, amin_at_imtech.res.in wrote:
>
>> 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.
>>>>>>
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>>>>>>
>>>>>
>>>>>
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>>>
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>>
>> ______________________________**______________________________**
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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
>>
>>
>
>
--
Dr Massimiliano Porrini
Institut Européen de Chimie et Biologie (IECB)
CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN)
2, rue Robert Escarpit
33607 Pessac Cedex
FRANCE
Tel : 33 (0)5 40 00 30 31
Fax : 33 (0)5 40 00 22 00
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Emails: m.porrini_at_iecb.u-bordeaux.fr
M.Porrini_at_ed.ac.uk
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