AMBER Archive (2004)

Subject: Re: AMBER: Cannot read in sander-again

From: bybaker_at_itsa.ucsf.edu
Date: Thu May 27 2004 - 17:05:22 CDT

('binary' encoding is not supported, stored as-is) Hello,

Thanks for the suggestions.

I did change 'cntr1(one)' to 'cntrl', but ending up to other bad condition:

'forrtl: error (75): floating point exception
 cannot read in sander
 core dumped'

I use Mactosh Terminal to have remote connection to socrates at
cgl.ucsf.edu. I changed '/' to '&end', but this does not change the
result. I either get 'could not read cntr1 namelist', or the 'core dumped
(with &cntrl (not one)).

Please help! Thank you

regards

Bo yang

On Thu, 27 May 2004 17:28:39 -0400 Guanglei Cui wrote:

> you have cntr1(one), not cntrl. some other font might help
>
> bybaker_at_itsa.ucsf.edu wrote:
>
> > Hello, Amber:
> >
> > I check the output file again, it does show the massage 'Could not find
> > cntrl namelist' and the input file. Sorry for the mess.
> >
> > I don't know why sander could not find cntr1 namelist. Please help.
> >
> > Bset regards
> >
> > Bo Yang
> >
> >
> >
> > The follows are the result from sander run:
> >
> > ------ start ----
> >
> > guanine.20% sander -O -i test1amin.in -o test1amin.out -c
> > /home/spin/bybaker/model1-1.crd -p /home/spin/bybaker/model1-1.top -r
> > test1amin.rst
> > guanine.21% ls
> > Run1min.out model0.pdb run1min.in
> > built.lib model1-1.inpcrd test1amin.in
> > help model1-1.prmtop test1amin.out
> > leap. nuc.out test1min.in
> > leap.log out.min test1min.out
> > mdout polyAT_vac_init_min.out
> >
> >
> >
> > guanine.23% ls
> > Run1min.out model0.pdb run1min.in
> > built.lib model1-1.inpcrd test1amin.in
> > help model1-1.prmtop test1amin.out
> > leap. nuc.out test1min.in
> > leap.log out.min test1min.out
> > mdout polyAT_vac_init_min.out
> >
> >
> > guanine.24% more test1amin.out
> >
> > -------------------------------------------------------
> > Amber 7 SANDER Scripps/UCSF 2002
> > -------------------------------------------------------
> >
> > | Thu May 27 13:37:43 2004
> >
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN: test1amin.in
> > | MDOUT: test1amin.out
> > |INPCRD: /home/spin/bybaker/model1-1.crd
> > | PARM: /home/spin/bybaker/model1-1.top
> > |RESTRT: test1amin.rst
> > | REFC: refc
> > | MDVEL: mdvel
> > | MDEN: mden
> > | MDCRD: mdcrd
> > |MDINFO: mdinfo
> > |INPDIP: inpdip
> > |RSTDIP: rstdip
> >
> >
> > Here is the input file:
> >
> > initial minimization test1a
> > &cntr1
> > imin=1
> > maxcyc=200
> > ntpr=5
> > /
> >
> > Could not find cntrl namelist
> >
> > ----end----
> >
> >
> > -----------------------------------------------------------------------
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