You are using periodic boundaries (ntb=1) but your coordinate file does not
contain any box information. Do you want to run a gas phase simulation? If
so then set ntb=0.
If you want to run a periodic simulation then you need to go back to leap
and re-create your prmtop and inpcrd files and make sure that you use one of
the solvate commands to create a periodic system..
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.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.
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of A D
> Sent: Wednesday, February 01, 2006 15:36
> To: amber.scripps.edu
> Subject: Re: AMBER: basic minimize question
>
> 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.rosswalker.co.uk> wrote:
> >
> > Yes.
> >
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | Department of Molecular Biology TPC15 |
> > | The Scripps Research Institute |
> > | Tel: +1 858 784 8889 | EMail:- ross.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.
> >
> >
> >
> > ________________________________
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu]
> On Behalf Of A D
> > Sent: Wednesday, February 01, 2006 14:51
> > To: amber.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
> >
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
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Received on Thu Feb 02 2006 - 06:10:07 PST
