AMBER Archive (2007)

Subject: Re: AMBER: a problem of surface area calulated by MM/PBSA

From: David A. Case (case_at_scripps.edu)
Date: Mon Apr 30 2007 - 10:20:43 CDT

On Mon, Apr 30, 2007, Chengwen Chen wrote:
>
>
> I got the no error when doing MM/PBSA calculation with this 2 compounds, the
> difference between them is b has 3 more carbon than a.
> a, C4H14Cl2N2PtSi Platinum, dichloro[dimethylsilylenebis (methanamine)]-,
> (SP-4-2); b, C7H18Cl2N2PtSi [Bis
> (aminomethyl)cyclopentamethylenesilane]dichloroplatinum (II);

First, try running molsurf by hand on each of these structures; check
carefully what radius is used for Pt: Amber often does a poor job with metals.

Second, try some other program (like MSMS) to see what you get.

...good luck...dac

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