AMBER Archive (2005)

Subject: Re: AMBER: fail of minimization in sander

From: wendy (chenchengwen_at_gmail.com)
Date: Mon Jun 06 2005 - 10:57:08 CDT

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_at_ilion.bio.sunysb.edu>
To: <amber_at_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_at_gmail.com>
>> To: <amber_at_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_at_cgl.ucsf.edu>
>>> To: <amber_at_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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>>>
>>>
>>
>> -----------------------------------------------------------------------
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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_at_stonybrook.edu
> ===================================================================
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
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