AMBER Archive (2005)

Subject: RE: AMBER: fail of minimization in sander

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jun 06 2005 - 12:25:26 CDT


Hi Wendy,

See if you can get an interactive shell on the cluster machine. Some systems
let you do this. With pdb you do "qsub -i".

If you want to check that your topology file is not corrupt you can run it
through Amber's rdparm. This will give you an error if there are problems
with the prmtop file. I doubt this is the problem though. Even if your Pt
parameters were complete trash you'd still get some form of output. Just the
results would be pretty meaningless.

Also try redirecting standard out and standard error to a log file you can
get at. E.g.

/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 >& 1AIO.log

Some queue systems let you do this, other don't...

> /usr/local/bin/wipe $hostlist

I'm not sure what this command does? Is it possibly deleting any log files
containing errors?

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of wendy
> Sent: 06 June 2005 09:13
> To: amber_at_scripps.edu
> Subject: Re: AMBER: fail of minimization in sander
>
> 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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