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 - 17:00:03 PDT
