AMBER Archive (2006)

Subject: Re: AMBER: basic minimize question

From: David A. Case (case_at_scripps.edu)
Date: Wed Feb 01 2006 - 18:09:11 CST

On Wed, Feb 01, 2006, A D wrote:

> when I try to run mimizations using the command they seem to take
> forever...I opened up one of the generated output files and saw this..
>
>
> Here is the input file:
>
> Initial minimisation of our structures
> &cntrl
> imin=1, maxcyc=500, ncyc=200,
> ntb=1, igb=0, ntc=2, ntf=2, cut=9
> /
>
> | Flags:
> getting new box info from bottom of inpcrd
> | peek_ewald_inpcrd: Box info not found in inpcrd
> |Largest sphere to fit in unit cell has radius = 0.000

You are asking for a periodic simulation (ntb=1), but it looks like you did
not set up the system in LEaP to be periodic. It is hard to be more specific
without more information. Try to find one of the test cases that most closely
matches what you want to do, and see if you can use that as a template.

...good luck...dac

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