From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Thu Jun 19 2014 - 02:38:50 CDT
If you have trajectories of the two monomers in isolation you may want to
consider MM/PBSA which is more accurate than plain interaction energy, as
it also considers the desolvation penalty of dimer formation.
On 18 June 2014 20:59, Fotis Baltoumas <fbaltoumas_at_biol.uoa.gr> wrote:
> Dear NAMD users,
>
> Having performed a number of MD simulations on protein-protein complexes
> with NAMD, I am currently attempting an evaluation of interaction energy
> values with VMD's NAMD Energy plugin. In my simulations I defined periodic
> boundary conditions and used the Particle Mesh Ewald method for full
> electrostatics.
> My question is: should I also use PME in the calculation of electrostatic
> interaction energy, or should I use the default settings, and calculate
> with Coulomb's law and the defined cutoff? I have attempted both and,
> although for some complexes the results are similar, in other cases the
> changes are dramatic. For one particular example the results are:
> Electrostatics without PME: -26.22 kcal/mol (Std. Dev.=10.16)
> Electrostatics with PME: -204.58 kcal/mol (Std. Dev.=10.53)
> In your opinion, which value should I trust as "biologically relevant"?
> Can the PME result be interpreted as the influence of distant charged
> groups to my complex, or should I use the non-PME result instead?
>
> Thank you,
> Fotis Baltoumas
>
>
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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