AMBER Archive (2007)

Subject: Re: AMBER: Energy minimization problem of -SO3H group

From: Eddie Men (pckboy_at_gmail.com)
Date: Tue Nov 06 2007 - 23:52:09 CST

Are the ATP and GTP molecules in the database?.

The best way you can "optimize" such a small molecule is by runing a
gaussian job and generating
RESP charges, then you simulate the bigger thing. You can also do
QM/MM method

Cheers

Eddie
David A. Case wrote:
> On Tue, Nov 06, 2007, Takao Kobayashi wrote:
>
>> I tried to optimize the structure of CH3-SO3H, but it failed,
>> where H of S-O-H is overlapped on O of S=O.
>>
>
> This happens with phosphates as well. As far as I know, you will have to
> correct this by hand, either by given non-zero vdW parameters to the
> hydrogen, or by including an artificial S--H bond (say) to keep the proton
> away from nearby oxygens. You might want to look to see how the ATP/GTP
> parameters in the contributed parameters database handle this problem.
>
> ..good luck...dac
>
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