Dear Dr. Daniel
Thank you for the suggestion; I successfully updated to 'CPPTRAJ:
Trajectory Analysis. V14.22'
But, again previous error message (as you answered in the first time)
appeared as
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Using the formula you gave me, the space requirement is 23GB but I have
enough memory (400GB) in my external drive where I run the 'cpptraj'
command.
Thank you for help,
Mahendra Thapa
University of Cincinnati,OH
On Fri, Jan 2, 2015 at 2:01 PM, Thapa, Mahendra (thapamb) <
thapamb.mail.uc.edu> wrote:
>
>
>
> ________________________________________
> From: Daniel Roe
> Sent: Friday, January 2, 2015 1:00:45 PM (UTC-06:00) Central America
> To: AMBER Mailing List
> Subject: Re: [AMBER] FW: clustering problem in ambertool14
>
> Hi,
>
> According to your log output you haven't applied all updates. The very
> first line of output is:
>
> CPPTRAJ: Trajectory Analysis. V14.00
>
> You need at least 14.17 for clustering with the traj data set to work
> properly (and really you should have 14.22). After updates are applied
> the code must be recompiled. Also if you are not using the full path
> to cpptraj when executing make sure that the cpptraj you are actually
> using is the up-to-date one (with e.g. the command 'which cpptraj`).
>
> Hope this helps,
>
> -Dan
>
>
> On Fri, Jan 2, 2015 at 9:08 AM, Mahendra B Thapa <thapamb.mail.uc.edu>
> wrote:
> > Dear Dr.Daniel
> > Memory issues were solved when I followed the steps you suggested; thank
> > you for that.
> >
> > A new problem appeared as seen in the screen:
> >
> > Internal Error: Metric is COORDS base but data set is not.
> > Error: in Analysis # 0
> > 1 errors encountered reading input.
> >
> > {{ Note: I have already fixed bugs for ambertool 14
> > http://ambermd.org/bugfixes/AmberTools/14.0/update.17
> > }}
> >
> > DATAFILES:
> > cluster_out (Standard Data File): Cnum_00001
> > Warning: Set 'Cnum_00001' contains no data.
> > Warning: File 'cluster_out' has no sets containing data.
> >
> > Are these errors due to (i) a large numbers of frames (250000) and number
> > of atoms (7584 atoms) ?
> >
> > In the previous post (http://archive.ambermd.org/201408/0214.html),
> there
> > is some discussion but I am assuming that I have been using stripped
> > topology file to run cpptraj. I have attached the screen shot ( text
> > file:TEST_LOG) with this email.
> >
> > Thank you for help,
> > Mahendra Thapa
> >
> >
> > On Tue, Dec 16, 2014 at 3:20 PM, Thapa, Mahendra (thapamb) <
> > thapamb.mail.uc.edu> wrote:
> >
> >>
> >>
> >>
> >> ________________________________________
> >> From: Daniel Roe
> >> Sent: Tuesday, December 16, 2014 2:19:51 PM (UTC-06:00) Central America
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] clustering problem in ambertool14
> >>
> >> Hi,
> >>
> >> Usually when you get this error message during a command that uses a
> >> COORDS data set (cluster, 2drms, crdfluct etc) it's because you ran
> >> out of memory. Here is a formula to estimate the amount of memory you
> >> will need to hold a COORDS data set:
> >>
> >> memory_in_bytes = (F * A * 3) * 4
> >>
> >> where F is the number of frames, A is the number of atoms (after
> >> stripping in this case), the 3 is from # of coords per atom and 4 is
> >> bytes (COORDS are single precision). Divide by 1048576 to get the
> >> result in MB. Add 6 to (F * A *3) if you have box coordinates, double
> >> if you have velocities as well.
> >>
> >> However, in place of a COORDS data set cpptraj also lets you use what
> >> is called a TRAJ data set (which leaves data on-disk). The only issue
> >> with this is because it remains on the disk you cannot modify a TRAJ
> >> data set, so you will have to pre-process your trajectory (i.e.
> >> strip/image) first. This is a good idea to do in general since it will
> >> make subsequent analyses faster. Here is some input as an example.
> >>
> >> # Step 1 - Preprocess
> >> parm myparm.parm7
> >> trajin mytraj.nc
> >> strip :Na+,WAT nobox outprefix strip
> >> autoimage
> >> rms first mass .C,CA,N
> >> trajout strip.mytraj.nc nobox
> >>
> >> A few things to note here. First is that I put the 'strip' command
> >> before everything else; this way subsequent commands will be faster
> >> because there are less atoms to deal with. Also note in my 'strip'
> >> command I'm writing out a stripped topology for use with my stripped
> >> trajectory. Finally and most importantly, because you are rms-fitting
> >> you will no longer be able to image anyway, so I'm getting rid of any
> >> box coordinates.
> >>
> >> # Step 2 - Cluster
> >> parm strip.myparm.parm7
> >> trajin strip.mytraj.nc
> >> loadtraj name MYTRAJ
> >> cluster crdset MYTRAJ :1-291.CA,N,C,O mass clusters 10 out cluster_out
> >> nofit averagelinkage \
> >> summary summary_out info Cluster_info repout box2.rep repfmt pdb
> >> clusterout cluster.nc clusterfmt netcdf
> >>
> >> The 'loadtraj' command in this case is taking all loaded trajectories
> >> from 'trajin' statements and putting them into a TRAJ data set named
> >> MYTRAJ, which stays on-disk and can subsequently be used by the
> >> 'cluster' command.
> >>
> >> One more thing to keep in mind is that even though the coordinates
> >> will be kept on disk, you will still need enough memory to hold the
> >> pairwise distance matrix:
> >>
> >> memory_in_bytes = ((F * (F-1)) / 2) * 4
> >>
> >> If you don't have enough memory to hold the pairwise distance matrix
> >> try using the 'sieve' keyword to reduce the number of frames being
> >> clustered in the first pass. This will also speed up the actual
> >> clustering a bit. Last and most importantly make sure you are using
> >> the most up-to-date version of cpptraj (14.22).
> >>
> >> Hope this helps,
> >>
> >> -Dan
> >>
> >> On Tue, Dec 16, 2014 at 11:28 AM, Mahendra B Thapa <thapamb.mail.uc.edu
> >
> >> wrote:
> >> > Dear Amber users
> >> > I used following command for clustering 50ns all-atom simulated data.
> >> > cpptraj -i input_file -p para_top
> >> > where 'input_file' consists of
> >> >
> >> > trajin mdcrd_files
> >> > autoimage
> >> > rms first mass .C,CA,N
> >> > strip :Na+,WAT
> >> > cluster :1-291.CA,N,C,O mass clusters 10 out cluster_out nofit
> >> > averagelinkage \
> >> > summary summary_out info Cluster_info repout box2.rep repfmt pdb
> >> > clusterout cluster.nc clusterfmt netcdf
> >> > go
> >> >
> >> > After running the command, I got following message without any output
> >> files:
> >> >
> >> > 1]terminate called after throwing an instance of 'std::bad_alloc'
> >> > what(): std::bad_alloc
> >> > Aborted
> >> >
> >> > 2] Warning: One or more analyses requested creation of default COORDS
> >> > DataSet.
> >> > CREATECRD: Saving coordinates from Top to file to "_DEFAULTCRD_"
> >> >
> >> >
> >> > 3]Warning: Coordinates are being rotated and box coordinates are
> present.
> >> > Warning: Unit cell vectors are NOT rotated; imaging will not be
> possible
> >> > Warning: after the RMS-fit is performed.
> >> >
> >> > Any comments and suggestion will be very useful.
> >> >
> >> > Thank you,
> >> > Mahendra Thapa
> >> > University of Cincinnati
> >> > _______________________________________________
> >> > 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jan 02 2015 - 13:00:02 PST
