As far as I am aware there are still only two methods to compute the
entropy (your link doesn't say otherwise). The question is whether the
single trajectory approach is really appropriate given the
possible flexible nature of your system. Remember, that in the single
trajectory approach you assume that receptor and ligand have compatible
conformations just as you would obtain from separate simulations. In
fact, this may not be true and may have a tremendous effect on your
final binding energies. We played around with rather largish
systems and found that predicted relative binding energies would have
opposite signs (DOI: 10.1002/prot.24339). But then one might ask how
reliable results for a large protein-peptide complex really are...
On Fri, 21 Feb 2014 16:38:55 +0100
Fernando Martín García <fmgarcia.cbm.uam.es> wrote:
>
>
> Dear Amber users,
>
> I'm trying to calculate the binding energy of a
> system composed by a protein (homodimeric) and a 20-mer DNA using
> MMPBSA.py. After reading this topic in the Amber mail list:
>
>
> http://archive.ambermd.org/201012/0545.html
>
> I have deduced that
> entropy calculation can be introduced using three methods: a
> quasi-harmonic method (entropy=1), using normal modes for receptor and
> ligand or using two alternatives dynamics, one of the ligand and other
> of the receptor, separately in order to introduce this entropy energy
> element. This is where I have some doubts: these two dynamics are
> completely independent of the original complex dynamic or are
> extracted with some option (ambermask?) during the simulation?
>
> On the other
> hand, could I have some problems if I define a complete DNA (20-mer)
> as ligand and this homodimeric protein as receptor, considering I
> have some "gaps" in the sequence?. I have some energy errors (my
> mutant binds strongly than my wild-type protein) and I don't know if
> I have some mistake .
>
> Thank you,
>
> Best regards,
>
> Fernando
>
> --
>
> ==============================================
> Fernando Martín
> García, PhD.
> Molecular Modeling Group - Lab 312.1
> Molecular Biology
> Center "Severo Ochoa"
> C/ Nicolás Cabrera, 1.
> UAM University.
> Cantoblanco, 28049 Madrid. Spain.
> TEL: (+34) 91-196-4662 FAX: (+34)
> 91-196-4420
> Web:
> http://fertoledo.wordpress.com/
> ==============================================
>
>
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Received on Fri Feb 21 2014 - 08:30:02 PST
