AMBER Archive (2005)

Subject: Re: AMBER: sander failure

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Jan 20 2005 - 16:20:00 CST

you also might want to try running the test cases before
trying your own inputs and scripts.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

ygao_at_phase1.unl.edu wrote:

>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 |
>>
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>>
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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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