AMBER Archive (2006)

Subject: Re: AMBER: basic minimize question

From: A D (nkomli_at_gmail.com)
Date: Wed Feb 01 2006 - 17:35:38 CST

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..

>>>>>>>
| Run on 02/01/2006 at 15:11:20
  [-O]verwriting output

File Assignments:
| MDIN: x.in
| MDOUT: WTA.out
|INPCRD: WTA.00.rst
| PARM: WTA.parm7
|RESTRT: WTA.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 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
 /

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| 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

anyone know how to fix the problem?

Thanks...

On 2/1/06, Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> Yes.
>
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.
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>
>
> ________________________________
   From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu]
On Behalf Of A D
> Sent: Wednesday, February 01, 2006 14:51
> To: amber_at_scripps.edu
> Subject: AMBER: basic minimize question
>
>
> $AMBERHOME/exe/sander -O -i x.in -o WTB.out -c WTB.00.rst -p WTB.parm7 -r WTB.rst
>
> I'm doing a minimization...does this file order look fine as a sander command?
>
>
> thanks
>
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