If the HO type has 0 vdw radius, you may want to use a type that
has > 0 radius to prevent it moving through the OH vdw.
Bill
> > 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).
>
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Received on Thu Jul 12 2012 - 16:30:03 PDT
