[gmx-users] charge atoms

[Tsjerk Wassenaar]

Hi,

When the question is "what's the dynamics of a GlcN chain?", it is
quite important to have a proper set of parameters. If the question is
"what would a protein do when something resembling a GlcN chain is
inserted (e.g. Lysozyme)?" then you may get away using a set of
parameters derived from available building blocks with similar groups,
using "chemical intuition". In particular, this would apply to
simulations aimed at comparing behaviour... at a qualitative level.

Cheers,

Tsjerk

On Tue, Sep 2, 2008 at 8:45 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> cesteban at unsl.edu.ar wrote:
>>
>> Hi All
>> I am trying to analyze the dynamics of polymer of GlcN residues using
>> ffG53a6 force field.
>> I made a new building block in .rtp file, but I haven´t the charge of some
>> atoms.
>> Which is the best procedure to obtein new charges?
>
> For some general information, refer here:
>
> http://wiki.gromacs.org/index.php/Parameterization
>
> With empirical force fields like Gromos96, a reasonable starting point is to
> identify similar functional groups from other molecules (those that have
> been parameterized already), and apply them to your molecule.
>
> The extent of the validation is up to you, but rigorous verification of the
> parameters typically involves some sort of free energy calculations.  I have
> seen several instances in the literature where investigators have molecules
> that are very similar to existing compounds in the force field, and they
> have skipped the validation steps.  Whether or not that is acceptable is up
> to you...
>
> -Justin
>
>> Someone has experience about this?
>> Any help would be appreciated
>> Carmen
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623