AMBER Archive (2005)

Subject: RE: AMBER: sander failure

From: ygao_at_phase1.unl.edu
Date: Thu Jan 20 2005 - 16:31:37 CST

Now the output is

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:

 &cntrl
  imin=1,maxcyc=100,
  nptr=1,
 /

 Could not find cntrl namelist

Thanks!

Yi

On Thu, 20 Jan 2005, Ross Walker wrote:

> 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_at_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_at_scripps.edu
> > [mailto:owner-amber_at_scripps.edu] On Behalf Of ygao_at_phase1.unl.edu
> > Sent: 20 January 2005 14:10
> > To: amber_at_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_at_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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> >
> > __________________________________________________________
> >
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> > University of Nebraska -- Lincoln
> > Lincoln, NE, USA 68508
> >
> > Phone: 1-402-472-9982 (O)
> > 1-402-310-4155 (M)
> > Email: ygao_at_phase1.unl.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_at_phase1.unl.edu

__________________________________________________________
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