AMBER Archive (2004)

Subject: Re: AMBER: LINMIN failure

From: Mizuguchi Mineyuki (mineyuki_at_ms.toyama-mpu.ac.jp)
Date: Thu Jun 10 2004 - 21:58:24 CDT

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_at_yahoo.com>
To: <amber_at_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_at_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
>
>
>
>
>
>
> __________________________________
> Do you Yahoo!?
> Friends. Fun. Try the all-new Yahoo! Messenger.
> http://messenger.yahoo.com/
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu