Use the following input file:
molecular dynamics run
&cntrl
imin=1,maxcyc=100,
ntpr=1,
/
Then let me know what the error is, if there is one.
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 |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of ygao.phase1.unl.edu
> Sent: 20 January 2005 14:10
> To: amber.scripps.edu
> Subject: RE: AMBER: sander failure
>
> Thanks for your reply.But it looks like the program never
> launch at all.
> The output file is as follows:
>
> -------------------------------------------------------
> Amber 8 SANDER Scripps/UCSF 2004
> -------------------------------------------------------
>
> | Run on 01/20/2005 at 16:12:46
> [-O]verwriting output
>
> File Assignments:
> | MDIN: min.in
> | MDOUT: min.out
> |INPCRD: hepta-water.crd
> | PARM: hepta-water.top
> |RESTRT: hepta-water.rst
> | REFC: refc
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: mdcrd
> |MDINFO: mdinfo
> |INPDIP: inpdip
> |RSTDIP: rstdip
>
>
> Here is the input file:
>
> molecular dynamics run
> &cntrl
> imin=1,maxcyc=100,
> nptr=1,
> &end
> END
>
>
> I've only launched it on single CPU, but get the same errors.
>
> Yi
>
>
> On Thu, 20 Jan 2005, Ross Walker wrote:
>
> > Dear Yi,
> >
> > > molecular dynamics run
> > > &cntrl
> > > imin=1,maxcyc=100,
> > > nptr=10,
> > > &end
> > > END
> >
> > Change nptr to ntpr and try again...
> >
> > Note: It is often best to test out your job on a single cpu
> first to ensure
> > it works before running it in parallel. Error messages are
> often more vague,
> > or lost all together when running in parallel.
> >
> > 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 |
> >
> > Note: Electronic Mail is not secure, has no guarantee of
> delivery, may not
> > be read every day, and should not be used for urgent or
> sensitive issues.
> >
> >
> --------------------------------------------------------------
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> > To post, send mail to amber.scripps.edu
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> >
>
> __________________________________________________________
>
> Department of Chemistry
> University of Nebraska -- Lincoln
> Lincoln, NE, USA 68508
>
> Phone: 1-402-472-9982 (O)
> 1-402-310-4155 (M)
> Email: ygao.phase1.unl.edu
>
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Received on Thu Jan 20 2005 - 22:53:00 PST
