Hi,
OK, to really figure this out we need to see your entire job script as well
as your cpptraj input. It seems like you might have something like this in
your input:
parm parm
If the file 'parm' exists then perhaps it's not where you think it is?
-Dan
On Thu, Feb 19, 2015 at 2:20 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.
>
> 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
> >
> _______________________________________________
> 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)
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Received on Thu Feb 19 2015 - 14:00:03 PST
