On Tue, 2014-04-08 at 22:26 +0800, jinfenghuang wrote:
> Dear Amber users, These days I try to use the MM_PBSA.py module to
> calculate the energy of the H2O and H3O+, but there exists a problem
> that puzzled me a lot. Firstly, I download the H3O+ parameters from
> the website http://www.pharmacy.manchester.ac.uk/bryce/amber.
> According to the parameters ,I generate the H2O parameters which have
> the same frcmod file as the H3O+. But things goes strange, when I use
> the sander module of AMBER11 to calculate the gas energy of two
> molecule, the H3O+ has electrostatic energy while the H2O doesn't
> have.Results are as follows:
> H2O
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 4.9643E-05 1.1479E-01 2.1413E-01 O 1
>
>
> BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
> VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
>
>
> H3O+
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.9759E+02 3.8746E+01 7.0478E+01 Hw2 4
>
>
> BOND = 0.0002 ANGLE = 0.0000 DIHED = 0.0000
> VDWAALS = 0.0000 EEL = 197.5904 HBOND = 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
>
>
> Why the sander module recived the different gas energy of H3O+ and H2O
> which have the same frcmod file ?
They are different molecules! Consider an alanine tripeptide and an
alanine dipeptide modeled by the same force field. You certainly would
not expect their gas phase energies to be the same since they are
different systems and form different interactions.
> At the same tme, I'm sure that the three atoms of H3O+ are bonded to
> the oxgen.
If all you have is a single H3O+ molecule in which the oxygen is bound
to all 3 hydrogens, it's impossible to have a EEL value that is
non-zero. The reason is that nonbonded interactions between atoms that
are separated by 1 or 2 bonds (that form bonds or angles) is omitted
from the calculation. In H3O+, all atoms are separated by 2 bonds or
fewer, which means that no nonbonded interactions are computed.
Therefore, at least one of the hydrogens must not have a physical bond
to the oxygen. You can use the "printBonds" command in ParmEd to get a
full listing of the bonds that are present in the topology file.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 08 2014 - 09:00:02 PDT
