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.
CPPTRAJ: Trajectory Analysis. V14.01
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
TIME: Total execution time: 0.0001 seconds.
####################################################################
# Your job finished at : Thu Feb 19 15:14:49 CST 2015
# 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 requested :
cput=90:00:00,mem=16gb,neednodes=1,nodes=1,walltime=126:00:00
# Your job used : cput=00:00:01,mem=4276kb,vmem=36272kb,walltime=00:00:18
# Your job's cpu utilization : 5%
# Your job's memory utilization (mem) : 0.03%
# Alabama Supercomputer Center - PBS Epilogue
####################################################################
On Thu, Feb 19, 2015 at 2:00 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Thu, Feb 19, 2015 at 11:09 AM, Nicole Ippolito <
> ippolito.nicole89.gmail.com> wrote:
>
> > parm parm0
> > parm parm1
> > trajin
> /home/aubndi/Monoxygenase/Apo/Analysis/Cluster/Apo_mon_aMD_avg_0_1000ns.crd.gz
> parmindex
> > 0
> > trajin
> /home/aubndi/Monoxygenase/FMP_OCS/Analysis/Cluster/FMP_OCS_mon_aMD_avg_0_1000ns.crd.gz
> parmindex
> > 1
> > reference Apo_mon_aMD_avg_0_1000ns.crd.gz parmindex 0
> > rms first out FMP_OCS_mon_RMSD_aPO.out time 0.005 :1-363
> >
> > It is telling me that the prmtop files do not match; however, they worked
> >
>
> It would be better here if you posted the exact error message. The key with
> the RMSD calculation is the number of atoms and the atom ordering must
> match between the reference and target structures. So if both your target
> and reference have the exact same residues between 1 and 363 this should
> work. Can you either paste or attach your complete cpptraj output so I can
> take a look? Thanks
>
> -Dan
>
> PS - You may be interested in the RMSD-related cpptraj tutorial here:
> http://ambermd.org/tutorials/analysis/tutorial1/
>
>
> > fine when just doing the RMSD for the individual proteins. I am assuming
> it
> > is something I am doing with my commands. If you have any advice that
> > would be great.
> >
> > Thank you,
> > Nicole Ippolito
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Feb 19 2015 - 13:30:02 PST
