On Thu, Feb 19, 2015 at 4:20 PM, Nicole Ippolito <
ippolito.nicole89.gmail.com> wrote:
> Here is the output I am getting. I think it has to do with the atoms not
> matching as there are two substrates in one of the strucutres. However,
> even when I strip the substrate it still produces this message.
>
> ####################################################################
> # Alabama Supercomputer Center - PBS Prologue
> # Your job id is : 36951
> # Your job name is : RMSD2cshAMBER
> # Your job's queue is : medium-serial
> # Your username for this job is : aubndi
> # Your group for this job is : aubchem
> # Your job was allocated:
> # 1 CPU on dmc81
> # Your job started at : Thu Feb 19 15:14:31 CST 2015
> ####################################################################
> setting dmc scratch directory
>
> ============================================================
> ===== Summary of your amber script job =====
> ============================================================
> The script file is: RMSD_2.csh
> The time limit is 90:00:00 HH:MM:SS
> The target directory is:
> /home/aubndi/Monoxygenase/FMR_OCS/Analysis/RMSD_Apo
> The memory limit is: 16gb
> The number of CPUs is: 1
> The job will start running after: 201502191513.44
> Look for: RMSD2cshAMBER in queue: medium-serial
>
> Directory /scratch-local/aubndi.RMSD2cshAMBER.36951 already exists
> AMBER for the DMC
> mkdir: cannot create directory `/scratch/aubndi': File exists
> Error: parm matches no files.
> Error: 'parm' matches no files.
>
This is a pretty straight-forward error message (about as clear as Amber
gets). You have no file named "parm". If you think this is a mistake,
then one of two things is happening:
1. The machine your queuing system assigned to you does not have the
current directory you submitted the job from mounted, so those files are
not available.
2. Your submitted job does not go to the correct directory after starting
and you don't change to there.
Most queuing systems have some kind of default path where jobs are run
from, and you have to cd to the correct directory. With Torque, this often
looks something like:
cd $PBS_O_WORKDIR
It will differ based on your queuing system. You should consult one of the
experts or system administrators of the cluster you are using for help with
this (or, better yet, maybe the machine has documentation that will help).
If, on the other hand, "parm" is not the name of your prmtop file, you
need to review the cpptraj syntax to make sure you have it correct. The
manual helps here.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 19 2015 - 14:00:02 PST
