I have never started from a PDB file to fully determine the description of a molecule including new bond types. Because basically what I need is the MOD4 entry for the atom type of O in O2, kb and b0 for O-O bond and the partial charge of O. what I know is b0=1.23 and partial charge =0. could you explain or direct me to a howto/manual how to get kb and LJ terms?
thank you very much.
max
On Wed, Sep 30, 2015 at 1:04 PM, Ebert Maximilian <m.ebert.umontreal.ca<mailto:m.ebert.umontreal.ca>>
wrote:
Hi there,
I am looking for di-oxygen parameters for AMBER99SB-ILDN. I found an old
post here in the mailing list with the suggestion to derive them but I
wanted to know if somebody has some maybe already ready to share. Otherwise
I found in the GROMOS FF a definition for O-O using ideal bond length of
1.23 Å and force constant of 1.66 107 kJ mol-1nm-2. Could I just use
this?
Probably, provided that you convert to kcal/mol/angstrom**2. Bond force
constants are, I believe, frequently transferable because they just come
from a QM frequency calculation.
On the whole, O2 parameters are not particularly challenging outside of the
L-J terms. The charge is just 0 and the bond vibration *is* the only
vibrational mode in the molecule.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 30 2015 - 11:00:03 PDT
