Dear Mineyuki,
If the output file you attached to the email below is the one from when you
set the NCYC parameter then it is definitely NOT fine. Just look at the
first couple of steps:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NAN NAN 6.4076E+04 C 6998
BOND = 4558117.6476 ANGLE = 1310.8486 DIHED =
3688.2075
VDWAALS = nan EEL = nan HBOND =
0.0000
1-4 VDW = 2028.5963 1-4 EEL = 22119.3049 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
5 NAN NAN 0.0000E+00 N 1
BOND = nan ANGLE = nan DIHED =
nan
VDWAALS = -1315.8256 EEL = nan HBOND =
0.0000
1-4 VDW = nan 1-4 EEL = nan RESTRAINT =
nan
EAMBER = nan
All of those "nan"'s stand for Not a Number, this is typically what happens
when you divide by zero! Thus something is very very wrong with your initial
structure. Somewhere you are getting a divide by zero, probably a distance
between two atoms, that is leading to you having infinite energy. It doesn't
matter how long you minimise this for you are not going to fix it. As soon
as you switch to molecular dynamics your system is going to blow up. I
suggest you take a good look at your starting structure.
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 |
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Mizuguchi Mineyuki
> Sent: 10 June 2004 19:58
> To: amber.scripps.edu
> Subject: Re: AMBER: LINMIN failure
>
> 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 - 07:53:00 PDT
