did you runn the tests successfully?
did you use real filenames, or did they really say "***" in the file name?
try running locally instead of using the batch system.it may
be easier to see the error message.
have you run any other jobs successfully on the batch system?
wendy wrote:
> I start sander like this "sander -O -i ***.in -o ***.out -c ***.inpcrd -p
> ***.prmtop -r ***.rst". I have try to use my ".in" input file to minimize
> the DNA structure in tutorial 1 and get normal output file.
>
> By the way, I run sander in remote computer by sending the jobs by remote
> logon. And I didn't find out batch output file.
>
> Thank you !
>
>
>
> ----- Original Message ----- From: "wendy" <chenchengwen.gmail.com>
> To: <amber.scripps.edu>
> Sent: Monday, June 06, 2005 12:59 PM
> Subject: Re: AMBER: fail of minimization in sander
>
>
>> I start sander like this "sander -O -i ***.in -o ***.out -c
>> ***.inpcrd -p ***.prmtop -r ***.rst". I have try to use my ".in"
>> input file to minimize the DNA structure in tutorial 1 and get normal
>> output file.
>>
>> By the way, I run sander in remote computer by sending the jobs by
>> remote logon. And I didn't find out batch output file.
>>
>> Thank you !
>>
>>
>> ----- Original Message ----- From: "Bill Ross" <ross.cgl.ucsf.edu>
>> To: <amber.scripps.edu>
>> Sent: Monday, June 06, 2005 11:50 AM
>> Subject: Re: AMBER: fail of minimization in sander
>>
>>
>>>> when I begin minimization with sander, =
>>>> the output file contain nothing.
>>>
>>>
>>> How do you start sander? Is there any output to the screen
>>> or batch output file or -?
>>>
>>> Bill
>>> -----------------------------------------------------------------------
>>> The AMBER Mail Reflector
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>>
>>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
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--
===================================================================
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.stonybrook.edu
===================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Jun 06 2005 - 12:53:01 PDT
