('binary' encoding is not supported, stored as-is)
Dear Ross and Dac:
Thanks for the suggestions. I created the min.in file (named as
test1amin.in) from unix, and saved it into the local directory. This
time, there was no message such as 'cannot read &cntr1'. Instead, no
result at all. from the min.out, there is no descrption about my input
..in file. While before, the message showed the input .in file. I don't
know which part is wrong.
Could you please help! Thank you.
Bo Yang
Department of Pediatric, UCSF, San Francisco
The follows are my input and output files:
-----
guanine.9% ls
Run1min.out mdout out.min
built.lib model0.pdb polyAT_vac_init_min.out
help model1-1.inpcrd run1min.in
leap. model1-1.prmtop test1amin.in
leap.log nuc.out test1min.in
guanine.12% less test1amin.in
initial minimization test1a
&cntr1
imin=1
maxcyc=200
ntpr=5
/
test1amin.in (END)
guanine.10% setenv AMBERHOME /usr/local/amber7
guanine.11% unlimit
guanine.17% sander -O -i test1amin.in -o test1amin.out -c model1-1.inpcrd
-p model1-1.prmtop -r test1amin.rst
guanine.18% 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.19% less test1amin.out
-------------------------------------------------------
Amber 7 SANDER Scripps/UCSF 2002
-------------------------------------------------------
| Thu May 27 13:34:30 2004
[-O]verwriting output
File Assignments:
| MDIN: test1amin.in
| MDOUT: test1amin.out
|INPCRD: model1-1.inpcrd
| PARM: model1-1.prmtop
|RESTRT: test1amin.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
------end
On Wed, 26 May 2004 18:08:48 -0700 "Ross Walker" wrote:
> 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.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 bybaker.itsa.ucsf.edu
> > Sent: 26 May 2004 17:48
> > To: amber.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.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
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Received on Thu May 27 2004 - 22:53:01 PDT
