Re: [AMBER] FW: FW: FW: FW: clustering problem in ambertool14

From: Mahendra B Thapa <thapamb.mail.uc.edu>
Date: Fri, 23 Jan 2015 09:24:53 -0500

 Dear Dr. Daniel

I have attached the input file (input_for_test-cpptraj_openMP) for
cpptraj and the message what I got after running cpptraj in openMP (
output_message_on_screen.txt). There was no problem with the input file
when cpptraj was run in series mode instead of openMP.
I was trying these tests in dual core machine and I had allocated 500 GB
space (but not 500 GB of RAM).

Thank you for help,
Mahendra Thapa
University of Cincinnati,OH


On Tue, Jan 20, 2015 at 1:00 PM, Thapa, Mahendra (thapamb) <
thapamb.mail.uc.edu> wrote:

>
>
>
> ________________________________________
> From: Daniel Roe
> Sent: Tuesday, January 20, 2015 11:59:42 AM (UTC-06:00) Central America
> To: AMBER Mailing List
> Subject: Re: [AMBER] FW: FW: FW: clustering problem in ambertool14
>
> Hi,
>
> On Sun, Jan 18, 2015 at 9:01 AM, Mahendra B Thapa <thapamb.mail.uc.edu>
> wrote:
> > When I tried to test ' cpptraj.OMP' with 5000 frames for clustering, I
> got
> > the following error message:
> > *Floating point exception*
>
> It's much easier for us to help if you can paste or attach your entire
> input and output. A floating point exception message with no context
> will be impossible to debug without more information.
>
> > I had enough space (500GB) while running it and I did not get that error
> > message while running 'cpptraj' in series even with 250000 frames.
>
> You have 500 GB of RAM? Again, remember it is RAM that matters for the
> pairwise matrix calculation, not disk space. The OpenMP version will
> use a bit more memory than the serial version but not a huge amount
> more. At any rate I don't think memory is the issue here. Send me the
> entire output off-list and I'll see what I can find.
>
> -Dan
>
> >
> > Thank you for help,
> > Mahendra Thapa
> > University of Cincinnati,OH
> >
> >
> > On Sat, Jan 17, 2015 at 7:00 PM, Thapa, Mahendra (thapamb) <
> > thapamb.mail.uc.edu> wrote:
> >
> >>
> >>
> >>
> >> ________________________________________
> >> From: Daniel Roe
> >> Sent: Saturday, January 17, 2015 5:58:55 PM (UTC-06:00) Central America
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] FW: FW: clustering problem in ambertool14
> >>
> >> Hi,
> >>
> >> The information in that post is unfortunately several years out of
> >> date. The OpenMP-enabled cpptraj is built with the usual OpenMP
> >> AmberTools build that you configure with the '-openmp' flag. This will
> >> install cpptraj.OMP in the $AMBERHOME/bin directory. When you run it
> >> you will see this at the top of the output:
> >>
> >> CPPTRAJ: Trajectory Analysis. V14.22 OpenMP
> >>
> >> -Dan
> >>
> >>
> >> On Sat, Jan 17, 2015 at 9:01 AM, Mahendra B Thapa <thapamb.mail.uc.edu>
> >> wrote:
> >> > Dear Dr. Daniel,
> >> >
> >> > After compiling cpptraj in parallel, as mentioned in AMBER manual 14
> and
> >> > previous post "http://dev-archive.ambermd.org/201107/0005.html",
> cpptraj
> >> > looks working well without any error message ( though it is not
> completed
> >> > yet for my system). How do I know that cpptraj is running in parallel
> >> mode
> >> > instead of series? I issued the same command as
> >> > cpptraj -i input_file -p test.top
> >> >
> >> > Thank you for help,
> >> > Mahendra
> >> >
> >> >
> >> >
> >> > On Tue, Jan 6, 2015 at 6:25 PM, Thapa, Mahendra (thapamb) <
> >> > thapamb.mail.uc.edu> wrote:
> >> >
> >> >>
> >> >>
> >> >>
> >> >> ________________________________________
> >> >> From: Daniel Roe
> >> >> Sent: Tuesday, January 6, 2015 5:24:28 PM (UTC-06:00) Central America
> >> >> To: AMBER Mailing List
> >> >> Subject: Re: [AMBER] FW: clustering problem in ambertool14
> >> >>
> >> >> Hi,
> >> >>
> >> >> On Tue, Jan 6, 2015 at 3:47 PM, Mahendra B Thapa <
> thapamb.mail.uc.edu>
> >> >> wrote:
> >> >> > With the use of 'sieve 10' , the 'cpptraj' command has been
> running
> >> >> > without any complain but the analysis is very slow for my case
> (50000
> >> >> > frames, 511 residues with 7584 atoms in each frame). A section of
> the
> >> >> > screenshot *after 24 hours *is as follows:
> >> >>
> >> >> This is an inherently time-consuming process, since you need to run
> >> >> N*(N-1) / 2 calculations (roughly 12.5 M). Depending on your
> processor
> >> >> speed this can take a long time, particularly if you have a big
> >> >> system. I typically use OpenMP-compiled cpptraj for this, since the
> >> >> pairwise calc is one of the things that is parallelized. To give you
> >> >> an idea of what timings I see, for 22084 sieved frames with 8 threads
> >> >> I can complete the pairwise portion of the calculation (RMSD
> selecting
> >> >> 67 atoms) in 97 seconds (CPU is 2x Xeon X5660 . 2.8 GHz).
> >> >>
> >> >> Your best bet is to first use a very small number of frames (as a
> >> >> test) to get an idea of how long things will take, and also to make
> >> >> sure that when your clustering completes you get all the output you
> >> >> are expecting. It's pretty awful when you do an expensive clustering
> >> >> calc and realize you forgot you wanted cluster numbers vs time etc.
> >> >>
> >> >> One thing that can help speed up subsequent clustering calcs is to
> use
> >> >> the loadpairdist/savepairdist keywords to re-use calculated pairwise
> >> >> distances. Some care must be taken when doing this though -
> everything
> >> >> pertaining to the distance metric (sieve, mask, etc) MUST remain the
> >> >> same or you will get bad results. Cpptraj does some checking for this
> >> >> but can't always catch everything.
> >> >>
> >> >> Hope this helps,
> >> >>
> >> >> -Dan
> >> >>
> >> >> >
> >> >> > ANALYSIS: Performing 1 analyses:
> >> >> > 0: [cluster crdset MYTRAJ :1-511.CA,N,C,O mass clusters 10 out
> >> >> > cluster_out nofit averagelinkage summary summary_out info
> Cluster_info
> >> >> > sieve 10 repout box2.rep repfmt pdb clusterout cluster.nc
> clusterfmt
> >> >> netcdf]
> >> >> > Starting clustering.
> >> >> > Mask [:1-511.CA,N,C,O] corresponds to 2044 atoms.
> >> >> > Calculating pair-wise distances.
> >> >> > Pair-wise matrix set up with sieve, 50000 frames, 5000 sieved
> >> frames.
> >> >> > 0%
> >> >> >
> >> >> > Thank you for help,
> >> >> > Mahendra Thapa
> >> >> > University of Cincinnati,OH
> >> >> >
> >> >> >
> >> >> > On Fri, Jan 2, 2015 at 4:35 PM, Thapa, Mahendra (thapamb) <
> >> >> > thapamb.mail.uc.edu> wrote:
> >> >> >
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> ________________________________________
> >> >> >> From: Daniel Roe
> >> >> >> Sent: Friday, January 2, 2015 3:35:17 PM (UTC-06:00) Central
> America
> >> >> >> To: AMBER Mailing List
> >> >> >> Subject: Re: [AMBER] clustering problem in ambertool14
> >> >> >>
> >> >> >> Hi,
> >> >> >>
> >> >> >> I suspect that if you are running out of memory even after using
> >> >> >> 'loadtraj', the issue may be with the pairwise distance matrix.
> >> >> >>
> >> >> >> To reduce the amount of memory needed by the pairwise distance
> matrix
> >> >> use
> >> >> >> the 'sieve' keyword. Try 'sieve 10' to start. Increase the sieve
> >> value
> >> >> as
> >> >> >> necessary.
> >> >> >>
> >> >> >> -Dan
> >> >> >>
> >> >> >> On Friday, January 2, 2015, Mahendra B Thapa <thapamb.mail.uc.edu
> >
> >> >> wrote:
> >> >> >>
> >> >> >> > 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 <javascript:;>> 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
> >> >> >> > <javascript:;>>
> >> >> >> > > 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 <javascript:;>> 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 <javascript:;>
> >> >> >> > > >
> >> >> >> > > >> 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 <javascript:;>
> >> >> >> > > >> > 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 <javascript:;>
> >> >> >> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> > > >>
> >> >> >> > > >
> >> >> >> > > > _______________________________________________
> >> >> >> > > > AMBER mailing list
> >> >> >> > > > AMBER.ambermd.org <javascript:;>
> >> >> >> > > > 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 <javascript:;>
> >> >> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> > >
> >> >> >> > _______________________________________________
> >> >> >> > AMBER mailing list
> >> >> >> > AMBER.ambermd.org <javascript:;>
> >> >> >> > 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
> >> >>
> >> > _______________________________________________
> >> > 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 23 2015 - 06:30:04 PST
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