AMBER Archive (2009)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Oct 23 2009 - 12:40:57 CDT

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

> I removed the short contacts

What about the long bonds?

> and the minimisation
> and equillibration showed no error. But the simulation blew up in the
> very first step.

What equilibration did you do? I forget if you sent them already, but
I would have to see mdin files for equil and production to guess what's up.

> I have tried varying the solvent box sizes (increase) but then the
> minimization itself blows up.

What were your original and second box clearances?

Bill

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