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.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.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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Received on Thu May 27 2004 - 10:53:02 PDT
