AMBER Archive (2005)

Subject: Re: AMBER: fail of minimization in sander

From: wendy (chenchengwen_at_gmail.com)
Date: Mon Jun 06 2005 - 11:13:10 CDT

I have run the test file in Amber tutorial 1, and get normal output file. I
don't have

I am wondering if the Pt atom in my struture do something wrong. I modified
the amber force field to make Xleap recongnize my Pt atom in my structure.
How to check the validity of the ".protop" and ".inpcrd" file?

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: "Bill Ross" <ross_at_cgl.ucsf.edu>
To: <amber_at_scripps.edu>
Sent: Monday, June 06, 2005 10:34 PM
Subject: Re: AMBER: fail of minimization in sander

>> I run sander in remote computer by sending the jobs by remote
>> logon. And I didn't find out batch output file.
>
> Have you run other programs this way? Is there normally a
> batch output file in such cases? What if you run it directly
> from the command line? Is there a core file?
>
> Bill
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