Dear Robyn, Ross, and Linda,
Thank you very much for your advices.
Setting the NCYC parameter works well
and output appears fine.
Sincerely,
Mineyuki
----- Original Message -----
From: "Robyn Ayscue" <kajsicat.yahoo.com>
To: <amber.scripps.edu>
Sent: Thursday, June 10, 2004 8:52 PM
Subject: Re: AMBER: LINMIN failure
> Hi! I looked at your .in file, and it looks like you
> don't have anything set for the NCYC variable, so
> Sander sets the default at NCYC=10, meaning that after
> 10 cycles conjugate gradient minimization will be
> turned on. When you have a solvated system then the
> conjugate gradient method can overwhelm Sander and
> it'll often give you that LINMIN error. To avoid it,
> try including a tag in your .in file of NCYC=500. As
> long as you keep NCYC greater than MAXCYC, the
> conjugate gradient is never turned on.
>
> Yours,
> Robyn Ayscue
>
> --- Mizuguchi Mineyuki <mineyuki.ms.toyama-mpu.ac.jp>
> wrote:
> > Hello, Amber
> >
> > I am energy-minimizing the system containing a
> > protein and TIP3 water
> > moleclues.
> > But something is wrong, and the output file says
> > 'LINMIN FAILURE'.
> > Attached files are input and output files. Could
> > someone advise and help
> > me?
> >
> > Sincerely,
> >
> > Mineyuki
> >
>
> > ATTACHMENT part 2 application/octet-stream
> name=ttr_min_wat.out
>
>
> > ATTACHMENT part 3 application/octet-stream
> name=min.in
>
>
>
>
>
>
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Received on Fri Jun 11 2004 - 04:53:00 PDT
