Dear Amber developers,
Recently I am doing molecular dynamics simulation for a molecule
which contains a fully protonated phosphate group. The Antechamber is used
to generate the parameters for the molecule.The atomic charges are fitted
using RESP method in HF/6-31G* level. However, when I used these parameters
to minimize the molecule, the hydroxylic hydrogen atom always had a bad
contact with its neighboring oxygen atom which double bonded to the
phosphorus atom. And this lead to the failure of MD simulation. I tried the
BCC charges, but this problem was still existed. The initial structure of
the molecule is 100% OK. So, can anyone tell me how to solve this problem ?
Thanks in advance.
Best,
Jinfeng
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Received on Sun Nov 20 2016 - 19:00:02 PST
