Re: tools for Charmm

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Thu Feb 20 2014 - 14:06:28 CST

Oh, sorry, I forgot to mention that optimization is generally not required
for the biomolecular force fields (including the carbohydrate force field
as used by Glycan Reader), because the chemical environment in which a
chemical group will find itself is always more or less the same in a
biopolymer, and the groups (actually residues in this context) are already
parameterized specifically for that chemical environment. This is why we
don't allow people to use CGenFF for biomolecules; the biomolecular parts
of the CHARMM force field are far better for that purpose and suffer much
less from transferability problems.

On 02/20/2014 02:59 PM, Kenno Vanommeslaeghe wrote:
> Hi Gianluca,
>
> I'm probably telling you a lot of things you know already, but no general
> force field has parameters for every single organic molecule it will
> encounter. At best, it will have coverage of a comprehensive set of basic
> chemical groups, parametrized in a generic context. It is implicitly
> assumed that these generic parameters will keep on performing well if the
> same chemical group is placed in an actual molecule, adjacent to other
> chemical groups. However, in reality, this assumption of [parameter]
> transferability is often problematic, especially when it comes to dihedral
> parameters and charges in additive force fields. So for a significant
> percentage of molecules, the force field can (and sometimes even needs to)
> be made more accurate by optimizing the parameters specifically for that
> molecule. This is a non-trivial thing to do, not only because it's
> somewhat complicated, but also because a methodology should be followed
> that is rigorously consistent with the rest of the force field, else
> strange things may happen. Knowing this, we released a standard
> methodology for use with the CHARMM (General) Force Field. That's the
> "refinement" I was talking about in my e-mail re: "namd-l: tools for
> Charmm" earlier today; all the information is in there. Further questions
> about the parameterization procedure (but not about how to use it with
> NAMD) can be directed to CHARMM's "Parameter Set Discussion" forum:
> http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=29297
>
> Cheers,
>
> Kenno.
>
>
> On 02/20/2014 02:15 PM, Gianluca Interlandi wrote:
>> Hi Kenno,
>>
>> I used CHARMM-GUI's Glycan Reader a few weeks ago. Extremely valuable! I'm
>> just curious: do you mind sharing some tips about the "optimization" part
>> that you mention?
>>
>> Gianluca
>>
>> On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote:
>>
>>> Yes, CHARMM-GUI does use our CGenFF program in the back-end when it
>>> encounters non-biomolecules. So it does parameter assignment. Though
>>> some people use different terminology, we define parameterization :=
>>> (parameter assignment + optimization). CHARMM-GUI does not do
>>> optimization.
>>>
>>> As an aside, CHARMM-GUI also has a unique and powerful function to
>>> generate carbohydrate structures: Glycan Reader (but that one doesn't
>>> generate parameters in the process).
>>>
>>>
>>>
>>> On 02/20/2014 01:08 PM, Gianluca Interlandi wrote:
>>>> Have a look at
>>>>
>>>> charmm-gui.org
>>>>
>>>> On Thu, 20 Feb 2014, Peter Reinke wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> Any suggestions of tools to parameterize molecules with Charmm force
>>>>> field?
>>>>>
>>>>> Thanks for your attention,
>>>>> Peter
>>>>>
>>>>>
>>>>
>>>> -----------------------------------------------------
>>>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>>>> +1 (206) 685 4435
>>>> http://artemide.bioeng.washington.edu/
>>>>
>>>> Research Scientist at the Department of Bioengineering
>>>> at the University of Washington, Seattle WA U.S.A.
>>>> -----------------------------------------------------
>>>>
>>>
>>>
>>
>> -----------------------------------------------------
>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>> +1 (206) 685 4435
>> http://artemide.bioeng.washington.edu/
>>
>> Research Scientist at the Department of Bioengineering
>> at the University of Washington, Seattle WA U.S.A.
>> -----------------------------------------------------

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