AMBER Archive (2004)

Subject: RE: AMBER: Cannot read in sander

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed May 26 2004 - 20:08:48 CDT

Dear Bo,

Are the ^M control characters really at the end of each line in your input
file? If so then you have a DOS formatted text file which has a Carriage
return and a line feed at the end of each line of text instead of just a
line feed. This is most likely confusing Sander. Try converting it to a unix
format text file:

dos2unix myfile.in (Assuming dos2unix exists on your machine)

Also, you may have a problem if the &cntrl flag is in the wrong place. The &
character has to be in the SECOND column of the file. E.g your file should
look like this (Assuming email formatting doesn't muck this up):

TITLE FOR JOB
 &cntrl
   imin=1,
   maxcyc=200,
   ntpr=5,
 /

(You can use &end instead of the / but some machines don't like this. The /
should work on everything)

If you still get a problem try attaching the input file to your email.

All the best
Ross

/\
\/
|\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 |

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of bybaker_at_itsa.ucsf.edu
> Sent: 26 May 2004 17:48
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Cannot read in sander
>
>
> Hello, Dac:
>
> Thank you for the suggestions. I guess that the problem was related to
> the quota limitation of my account. I had my account size
> increased, and
> the sander went through. But I got another problem, no result from the
> test run. I don't know what happened. The 'model1-1.inpcrd' and
> 'model1-1.prmtop' contain the data, and my min.in is
> 'Minimization Test
> run1^M &cntrl^M imin=1, maxcyc=200^M ntpr=5^M &end'. The amber said
> 'Could not find cntrl namelist', I don't know what this mean.
>
> Please help!
>
> Bo Yang
>
> The follows are what I did for the sander run:
>
> -----
> guanine.22% sander -O -i /home/spin/bybaker/Testrun1min.in -o
> Testrun1min.out -c model1-1.inpcrd -p model1-1.prmtop -r
> Testrun1min.rst
>
> guanine.23% ls
> Testrun1min.out leap. model0.pdb
> model1min.out polyAT_vac_init_min.out
> built.lib leap.log
> model1-1.inpcrd nuc.out
> help mdout
> model1-1.prmtop out.min
>
> guanine.24% less Testrun1min.out
>
> -------------------------------------------------------
> Amber 7 SANDER Scripps/UCSF 2002
> -------------------------------------------------------
>
> | Wed May 26 17:15:10 2004
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: /home/spin/bybaker/Testrun1min.in
>
> | MDOUT: Testrun1min.out
>
> |INPCRD: model1-1.inpcrd
>
> | PARM: model1-1.prmtop
>
> |RESTRT: Testrun1min.rst
>
> | REFC: refc
>
> | MDVEL: mdvel
>
> | MDEN: mden
>
> | MDCRD: mdcrd
>
> |MDINFO: mdinfo
>
> |INPDIP: inpdip
>
> |RSTDIP: rstdip
>
>
>
> Here is the input file:
>
> Minimization Test run1^M &cntrl^M imin=1, maxcyc=200^M
> ntpr=5^M &end
> Could not find cntrl namelist
>
> (END)
>
>
>
>
>
>
> On Wed, 26 May 2004 09:14:52 -0700 "David A. Case" wrote:
>
> > On Tue, May 25, 2004, bybaker_at_itsa.ucsf.edu wrote:
> > >
> > > I tied to run 'sander' for initial testing. But I got an
> error massage
> > > saying that floating point exception. The follows are
> what I typied in
> > > 'sander':
> > >
> > > ----
> > > Guanine.10% sander -O -i /home/spin/bybaker/model1min.in -o
> > > model1-1min.out -c model1-1.crd -p model1-1.top -r model1-1min.rst
> > > ---
> > >
> > > and this is what I received:
> > >
> > > ---
> > > forrtl: error(75): floating point exception
> > > cannot read in sander
> > > ---
> >
> > (1) I'm assuming that the test cases pass.
> > (2) What is in the file model1-1min.out?
> > (3) This sometimes comes from a bad initial structure; use the
> > "checkoverlap"
> > command in ptraj to see if you have any bad atom-atom contacts.
> >
> > ...good luck...dac
> >
> > --
> >
> > ==================================================================
> > David A. Case | e-mail: case_at_scripps.edu
> > Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> > The Scripps Research Institute | phone: +1-858-784-9768
> > 10550 N. Torrey Pines Rd. | home page:
> > La Jolla CA 92037 USA | http://www.scripps.edu/case
> > ==================================================================
> >
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>
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