Hello,
I am minimizing a complex synthetic compound, which also has phosphonic acid groups attached to it:
OH
|
R - P = O
|
OH
The automatic atom type assignment (gaff) put (py) atom type for central P, (o) for double bond O, (oh) for O in OH fragment, and (ho) for H in OH fragment.
I did not put any restrictions for minimization, and within fist 1000 steps hydrogens collapsed onto neighboring oxygens, which is not supposed to happen.
I wonder if there is something wrong with my parametrization or minimization script.
Any ideas or suggestions?..
additional info:
Partial charges were assigned by mulliken method (resp didn't work well with the rest of this compound).
With best regards, Maria Minakova.
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Received on Thu Jul 12 2012 - 15:30:02 PDT
