I have run the tests successfully by use the DNA structure in Amber Tutoral
1. So I think it is not the problem of the batch system. I suspect the Pt
Atom I added is doing something wrong.
I use the real filename instead of ***. I am sorry for the confusing
character. :)
I do not have licence to run Amber on my own computer. I am using cluster
which is using LoadLeveler V3.2 for submitting jobs. My batch file is listed
below.
Thank you very much!
#!/bin/csh
# . job_type = parallel
# . node = 1
# . tasks_per_node = 4
# . class = q1n4g
# . node_usage = not_shared
# queue the program
# . queue
setenv hostlist hostlistfile
setenv K5MUTE 1
rm -f $hostlist
echo $LOADL_PROCESSOR_LIST > templist
awk '{gsub (/.itsc.cuhk.edu.hk/,"");print $1}' templist | tr " " "\n" >
$hostlist
/usr/local/bin/wipe $hostlist
/usr/local/bin/lamboot $hostlist
/usr/local/bin/mpirun -np 4 sander -O -i 1AIO-1D4-min.in -o
1AIO-1D4-min.out -c 1AIO-1D4.inpcrd -p 1AIO-1D4.prmtop -r 1AIO-1D4-min.rst
< /dev
/null
/usr/local/bin/wipe $hostlist
----- Original Message -----
From: "Carlos Simmerling" <carlos.ilion.bio.sunysb.edu>
To: <amber.scripps.edu>
Sent: Monday, June 06, 2005 7:24 PM
Subject: Re: AMBER: fail of minimization in sander
> 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 -O -i ***.in -o ***.out -c ***.inpcrd -p
>> ***.prmtop -r ***.rst". I have try to use my ".in" input file tlike this
>> "sander o 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
>>>> To post, send mail to amber.scripps.edu
>>>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>>
>>>
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
>
> --
> ===================================================================
> 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
-----------------------------------------------------------------------
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 - 17:53:00 PDT
