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 ? At the same tme, I'm sure that the three atoms of H3O+ are bonded to the oxgen.
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Received on Tue Apr 08 2014 - 07:30:03 PDT
