I would create another type of H (e.g. HX), like HO in all respects but vdw.
Bill
Maria Minakova <mariabiophysics.gmail.com> wrote:
> Oh I see. I will think about other options, though concern is that this particular atom type is designed for OH hydrogen, while others might have different bond, angles and etc. parameter values.
> Would you suggest to modify the definition of ho to give it nonzero wdv radious via frcmod?
>
> With best regards, Maria.
>
> On Jul 12, 2012, at 7:20 PM, Bill Ross wrote:
>
> > 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 - 17:30:02 PDT
