AMBER Archive (2009)

Subject: Re: [AMBER] [Fwd: problem with minimization]

From: Bill Ross (
Date: Thu Oct 22 2009 - 11:49:45 CDT

> WARNING: There is a bond of 30.500389 angstroms between:
> ------- .R<RA3 712>.A<N7 16> and .R<RA3 712>.A<C5 17>
> WARNING: There is a bond of 31.529394 angstroms between:
> ------- .R<RA3 712>.A<C8 14> and .R<RA3 712>.A<N7 16>

That is worth figuring out.

> WARNING: The unperturbed charge of the unit: -0.999880 is not zero.

It looks like if there are as manya s 153 ions, rounding errors in the
charge calculation mean you are coming out an ion short. You can add
this explicitly with another addions cmd for now.

The bond length thing seems the more likely cause of minimization


AMBER mailing list