Dan,
Yes I have removed the *out* keyword from hbond command.
Regards
On Thu, Feb 12, 2015 at 11:22 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Try removing the 'out' keyword from your hbond command.
>
> On Thu, Feb 12, 2015 at 8:19 AM, Vijay Achari <glycoamber.gmail.com>
> wrote:
> > Dear Dan,
> >
> > Here attached the log file I generated during the command execution. Hope
> > this might help you as well.
> >
> > Regards
> > Vijay
> >
> > On Thu, Feb 12, 2015 at 10:51 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> This is strange, and may indicate a bug. I will try to reproduce the
> >> error on my end and get back to you.
> >>
> >> -Dan
> >>
> >> On Thu, Feb 12, 2015 at 2:19 AM, Vijay Achari <glycoamber.gmail.com>
> >> wrote:
> >> > Dear Dan,
> >> >
> >> > I ran this whole calculation in another machine which have 96GB of RAM
> >> and
> >> > 24 core processors running in CENTOS6.
> >> >
> >> > I created a input file which contains:
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > *trajin
> >> >
> >>
> /home/users/vijay/slot3/paper3-lyo-system-TRAJ-Only/onlyTraj-bcmLyo25perR/reImaged-bcmLyo25perR.nc
> >> > 15001 15010hbond MyHB :1-128 out nhb.dat dist 3.5 angle 120 avgout
> >> > avghb.dat \ nointramol series solventacceptor :WAT.O solventdonor
> >> :WAT
> >> > \ solvout solvent_avg.dat bridgeout bridge.datrunwritedata
> >> solutehb.dat
> >> > MyHB[solutehb]writedata solventhb.dat MyHB[solventhb]lifetime
> >> > MyHB[solutehb] out solute.lifetime.datlifetime MyHB[solventhb] out
> >> > solvent.lifetime.datrunanalysis*
> >> > and I executed this file using cpptraj command:
> >> >
> >> >
> >> > *cpptraj topology -i hb-cpptraj2.in <http://hb-cpptraj2.in>*
> >> > If you notice, I only choose 10 frames. and the calculation run fine.
> But
> >> > at the end it states as below:
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > * . . . . MyHB[solventhb]:12640 "BMR_121.O15-V"
> >> > (integer), size is 10 MyHB[solventhb]:8317 "BMR_80.O14-V"
> (integer),
> >> > size is 10 MyHB[solventhb]:8647 "BMR_83.O16-V" (integer), size is
> 10
> >> > MyHB[solventhb]:9574 "BMR_92.O25-V" (integer), size is 10
> >> > MyHB[solventhb]:964 "BMR_10.O25-V" (integer), size is 10
> >> > MyHB[solventhb]:3465 "BMR_34.O22-V" (integer), size is 10
> >> > MyHB[solventhb]:4531 "BMR_44.O26-V" (integer), size is 10
> >> > MyHB[solventhb]:3694 "BMR_36.O25-V" (integer), size is 10
> >> > MyHB[solventhb]:4324 "BMR_42.O25-V" (integer), size is 10DATAFILES:
> >> > nhb.dat (Standard Data File): MyHB[UU] MyHB[UV] MyHB[Bridge]
> >> > MyHB[ID]Segmentation fault (core dumped)*
> >> > I get three files avghb.dat, bridge.dat, *nhb.dat* and
> solvent_avg.dat.
> >> But
> >> > the nhb.dat file is empty. There is no data at all.
> >> >
> >> > Other files contains data in their respective formats.
> >> >
> >> > Why this happens and how to overcome?
> >> > Your help is much appreciated.
> >> >
> >> > Thank you.
> >> >
> >> > Vijay
> >> >
> >> >
> >> > On Thu, Feb 12, 2015 at 1:46 PM, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >> >
> >> >> Hi,
> >> >>
> >> >> On Wed, Feb 11, 2015 at 6:32 PM, Vijay Achari <glycoamber.gmail.com>
> >> >> wrote:
> >> >> > Is this showing some error?
> >> >> >
> >> >> >
> >> >> >
> >> >> > DATAFILES:
> >> >> > nhb.dat (Standard Data File): MyHB[UU] MyHB[UV] MyHB[Bridge]
> >> MyHB[ID]
> >> >> > *** buffer overflow detected ***: cpptraj terminated
> >> >>
> >> >> Interesting - this indicates a memory issue. What version of cpptraj
> >> >> are you using (cpptraj --version)? What happens if you write out in
> >> >> grace format instead (change nhb.dat to nhb.avg)? The hbond time
> >> >> series command can be very memory hungry since you essentially need
> an
> >> >> array of size N (where N is the number of frames) for each hydrogen
> >> >> bond detected. What happens if you run without the 'series' keyword?
> >> >>
> >> >> -Dan
> >> >>
> >> >> > ======= Backtrace: =========
> >> >> > /lib/x86_64-linux-gnu/libc.so.6(+0x73f1f)[0x7f917d6fdf1f]
> >> >> >
> /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f917d79582c]
> >> >> > /lib/x86_64-linux-gnu/libc.so.6(+0x10a6f0)[0x7f917d7946f0]
> >> >> > /lib/x86_64-linux-gnu/libc.so.6(+0x109bf9)[0x7f917d793bf9]
> >> >> >
> >> /lib/x86_64-linux-gnu/libc.so.6(_IO_default_xsputn+0xbc)[0x7f917d70629c]
> >> >> > /lib/x86_64-linux-gnu/libc.so.6(_IO_padn+0x6e)[0x7f917d6fa22e]
> >> >> >
> /lib/x86_64-linux-gnu/libc.so.6(_IO_vfprintf+0x2576)[0x7f917d6d6266]
> >> >> >
> /lib/x86_64-linux-gnu/libc.so.6(__vsprintf_chk+0x84)[0x7f917d793c84]
> >> >> > cpptraj[0x520100]
> >> >> > cpptraj[0x5335fb]
> >> >> > cpptraj[0x533ae2]
> >> >> > cpptraj[0x53655a]
> >> >> > cpptraj[0x526d93]
> >> >> > cpptraj[0x527aaf]
> >> >> > cpptraj[0x524a70]
> >> >> > cpptraj[0x516442]
> >> >> > cpptraj[0x51677b]
> >> >> > cpptraj[0x51e8f9]
> >> >> > cpptraj[0x51f3b5]
> >> >> > cpptraj[0x40a201]
> >> >> >
> >> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f917d6abec5]
> >> >> > cpptraj[0x40a26b]
> >> >> > ======= Memory map: ========
> >> >> > 00400000-0071c000 r-xp 00000000 08:06 420960
> >> >> > /usr/local/apps/amber14/bin/cpptraj
> >> >> > 0091c000-00969000 r--p 0031c000 08:06 420960
> >> >> > /usr/local/apps/amber14/bin/cpptraj
> >> >> > 00969000-00971000 rw-p 00369000 08:06 420960
> >> >> > /usr/local/apps/amber14/bin/cpptraj
> >> >> > 00971000-0098a000 rw-p 00000000 00:00 0
> >> >> > 02924000-107b1000 rw-p 00000000 00:00 0
> >> >> > [heap]
> >> >> > 7f917cb4c000-7f917d00d000 rw-p 00000000 00:00 0
> >> >> > 7f917d44e000-7f917d489000 r-xp 00000000 08:06 272697
> >> >> > /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> >> >> > 7f917d489000-7f917d688000 ---p 0003b000 08:06 272697
> >> >> > /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> >> >> > 7f917d688000-7f917d689000 r--p 0003a000 08:06 272697
> >> >> > /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> >> >> > 7f917d689000-7f917d68a000 rw-p 0003b000 08:06 272697
> >> >> > /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> >> >> > 7f917d68a000-7f917d845000 r-xp 00000000 08:06 683092
> >> >> > /lib/x86_64-linux-gnu/libc-2.19.so
> >> >> > 7f917d845000-7f917da45000 ---p 001bb000 08:06 683092
> >> >> > /lib/x86_64-linux-gnu/libc-2.19.so
> >> >> > 7f917da45000-7f917da49000 r--p 001bb000 08:06 683092
> >> >> > /lib/x86_64-linux-gnu/libc-2.19.so
> >> >> > 7f917da49000-7f917da4b000 rw-p 001bf000 08:06 683092
> >> >> > /lib/x86_64-linux-gnu/libc-2.19.so
> >> >> > 7f917da4b000-7f917da50000 rw-p 00000000 00:00 0
> >> >> > 7f917da50000-7f917da66000 r-xp 00000000 08:06 659472
> >> >> > /lib/x86_64-linux-gnu/libgcc_s.so.1
> >> >> > 7f917da66000-7f917dc65000 ---p 00016000 08:06 659472
> >> >> > /lib/x86_64-linux-gnu/libgcc_s.so.1
> >> >> > 7f917dc65000-7f917dc66000 rw-p 00015000 08:06 659472
> >> >> > /lib/x86_64-linux-gnu/libgcc_s.so.1
> >> >> > 7f917dc66000-7f917dd6b000 r-xp 00000000 08:06 683111
> >> >> > /lib/x86_64-linux-gnu/libm-2.19.so
> >> >> > 7f917dd6b000-7f917df6a000 ---p 00105000 08:06 683111
> >> >> > /lib/x86_64-linux-gnu/libm-2.19.so
> >> >> > 7f917df6a000-7f917df6b000 r--p 00104000 08:06 683111
> >> >> > /lib/x86_64-linux-gnu/libm-2.19.so
> >> >> > 7f917df6b000-7f917df6c000 rw-p 00105000 08:06 683111
> >> >> > /lib/x86_64-linux-gnu/libm-2.19.so./hb-Analysis.cpptraj: line 39:
> >> 2888
> >> >> > Aborted (core dumped) cpptraj $top <<EOF
> >> >> >
> >> >> >
> >> >> > trajin $trajpath/reImaged-$system.nc 15001 20000
> >> >> >
> >> >> >
> >> >> > # COMMAND
> >> >> >
> >> >> > hbond MyHB :1-128 out nhb.dat dist 3.5 angle 120 avgout avghb.dat
> >> >> > nointramol series solventacceptor :WAT.O solventdonor :WAT
> >> solvout
> >> >> > solvent_avg.dat bridgeout bridge.dat
> >> >> > run
> >> >> > writedata solutehb.dat MyHB[solutehb]
> >> >> > writedata solventhb.dat MyHB[solventhb]
> >> >> > lifetime MyHB[solutehb] out solute.lifetime.dat
> >> >> > lifetime MyHB[solventhb] out solvent.lifetime.dat
> >> >> > runanalysis
> >> >> >
> >> >> >
> >> >> > EOF
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> > Thank you
> >> >> > Vijay
> >> >> >
> >> >> > On Thu, Feb 12, 2015 at 2:21 AM, Daniel Roe <
> daniel.r.roe.gmail.com>
> >> >> wrote:
> >> >> >
> >> >> >> Hi,
> >> >> >>
> >> >> >> On Wed, Feb 11, 2015 at 10:35 AM, Vijay Achari <
> glycoamber.gmail.com
> >> >
> >> >> >> wrote:
> >> >> >> > So far I tried to execute a command as shown below:
> >> >> >> >
> >> >> >> > *hbond :1-128 out nhb.dat dist 3.5 angle 120 avgout avghb.dat
> >> >> nointramol
> >> >> >> > series*
> >> >> >> >
> >> >> >> > But I dont know what are the additional options I need to add in
> >> >> order to
> >> >> >> > calculate the solute-solvent (lipid-water) hydrogen bonding. And
> >> >> continue
> >> >> >> > with lifetime analysis, although you have mentioned about
> lifetime
> >> >> >> > calculation in your earlier email.
> >> >> >>
> >> >> >> You will need to use the 'solventdonor' and 'solventacceptor'
> >> >> >> keywords. I also recommend giving your hydrogen bond data set a
> name
> >> >> >> to make it easier to refer to when writing out and analyzing your
> >> time
> >> >> >> series data. So you may want to modify your input like so:
> >> >> >>
> >> >> >> hbond MyHB :1-128 out nhb.dat dist 3.5 angle 120 avgout
> avghb.dat \
> >> >> >> nointramol series solventacceptor :WAT.O solventdonor :WAT \
> >> >> >> solvout solvent_avg.dat bridgeout bridge.dat
> >> >> >> run
> >> >> >> writedata solutehb.dat MyHB[solutehb]
> >> >> >> writedata solventhb.dat MyHB[solventhb]
> >> >> >> lifetime MyHB[solutehb] out solute.lifetime.dat
> >> >> >> lifetime MyHB[solventhb] out solvent.lifetime.dat
> >> >> >> runanalysis
> >> >> >>
> >> >> >> The manual should definitely contain better examples, but it still
> >> has
> >> >> >> some useful information. I highly recommend going over the manual
> >> >> >> entries for the 'hbond' and 'lifetime' commands just to make sure
> you
> >> >> >> understand what each keyword is doing. Hope that this helps, let
> me
> >> >> >> know if you have any more questions.
> >> >> >>
> >> >> >> -Dan
> >> >> >>
> >> >> >> >
> >> >> >> > Could you kindly help me here?
> >> >> >> > Appreciate your help in advance.
> >> >> >> >
> >> >> >> > Thanks
> >> >> >> > Vijay
> >> >> >> >
> >> >> >> >
> >> >> >> > On Thu, Feb 12, 2015 at 12:44 AM, Daniel Roe <
> >> daniel.r.roe.gmail.com>
> >> >> >> wrote:
> >> >> >> >
> >> >> >> >> Hi,
> >> >> >> >>
> >> >> >> >> On Wed, Feb 11, 2015 at 3:18 AM, Vijay Achari <
> >> glycoamber.gmail.com>
> >> >> >> >> wrote:
> >> >> >> >> > I don't understand the meaning of <*dsetarg0*> file. despite
> it
> >> is
> >> >> >> saying
> >> >> >> >> > about data file. But which data file and how to obtain this
> >> file?
> >> >> >> >>
> >> >> >> >> As stated in the manual, this argument pertains to data sets:
> >> >> >> >>
> >> >> >> >> <dsetarg0> [<dsetarg1> ...] Argument(s) specifying datasets to
> be
> >> >> used.
> >> >> >> >>
> >> >> >> >> The data sets can be data that have been generated by cpptraj
> >> during
> >> >> a
> >> >> >> >> run, or previously read in with the 'readdata' command. For
> >> example,
> >> >> >> >> say you have a data file named solventlifetime.dat which
> contains
> >> >> >> >> hydrogen bond time series data (from 'hbond series') in
> columns,
> >> >> e.g.:
> >> >> >> >>
> >> >> >> >> #Frame DC5_1.N3-V DC5_1.O2-V
> >> >> >> >> 1 1.0000 1.0000
> >> >> >> >> 2 0.0000 1.0000
> >> >> >> >> ...
> >> >> >> >>
> >> >> >> >> You can read the data in and perform lifetime analysis (over
> >> windows
> >> >> >> >> of size 5000) using the following input:
> >> >> >> >>
> >> >> >> >> readdata solventlifetime.dat
> >> >> >> >> runanalysis lifetime out life.gnu solventlifetime.dat window
> 5000
> >> >> >> >>
> >> >> >> >> Note that since I didn't provide a data set name to the
> 'readdata'
> >> >> >> >> command (via 'name <set name>'), the file name is chosen as
> >> default.
> >> >> >> >> You can see what data sets are currently loaded with 'list
> >> dataset'.
> >> >> >> >>
> >> >> >> >> Note that the hydrogen bond time series data is not written out
> >> >> >> >> automatically - you need to save it using a 'writedata' command
> >> after
> >> >> >> >> 'hbond' is run, like so:
> >> >> >> >>
> >> >> >> >> parm ../DPDP.parm7
> >> >> >> >> trajin ../DPDP.nc
> >> >> >> >> hbond HB out hbond.dat .N,H,C,O series avgout hbavg.dat
> >> printatomnum
> >> >> >> >> run
> >> >> >> >> write solutehb.agr HB[solutehb]
> >> >> >> >> runanalysis lifetime HB[solutehb] out lifehb.gnu window 10
> >> >> >> >>
> >> >> >> >> There are two things to note in the above input. The first is
> >> that I
> >> >> >> >> am issuing a 'run' command before writing or performing
> analysis
> >> on
> >> >> >> >> the hydrogen bond time series data. This is because unlike some
> >> other
> >> >> >> >> commands (like e.g. 'distance'), cpptraj doesn't know if any
> data
> >> (in
> >> >> >> >> this case hydrogen bonds) is actually present in the system
> until
> >> the
> >> >> >> >> analysis is actually run. The second is that I'm using a data
> set
> >> >> >> >> aspect (in this case [solutehb]) to select only solute-solute
> >> >> hydrogen
> >> >> >> >> bonds.
> >> >> >> >>
> >> >> >> >> This should be explained better in the manual, and there is a
> >> >> tutorial
> >> >> >> >> in the works, but for now I recommend you read section 28.3 of
> the
> >> >> >> >> Amber 14 manual (Data Sets and Data Files), and maybe run
> through
> >> the
> >> >> >> >> two existing cpptraj tutorials
> >> >> >> >> (http://ambermd.org/tutorials/#analysis) to become more
> familiar
> >> >> with
> >> >> >> >> data sets etc in cpptraj.
> >> >> >> >>
> >> >> >> >> Hope this helps - let me know if you have any more questions,
> >> >> >> >>
> >> >> >> >> -Dan
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> >
> >> >> >> >> > Anyway I tried something like below:
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> > cpptraj topology << EOF
> >> >> >> >> >
> >> >> >> >> > *lifetime out hb-LifeTime-bcmLyo25perR.out
> >> >> >> >> > HB_inBothLayer_001_128-bcmLyo25perR.tbl cut 0.5 greater*
> >> >> >> >> >
> >> >> >> >> > EOF
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> > with *HB_inBothLayer_001_128-bcmLyo25perR.tbl * is the output
> >> file
> >> >> of
> >> >> >> >> > hydrogen bonding.
> >> >> >> >> >
> >> >> >> >> > But this fail to run.
> >> >> >> >> > I wish to get some here.
> >> >> >> >> >
> >> >> >> >> > Regards
> >> >> >> >> > Vijay
> >> >> >> >> > _______________________________________________
> >> >> >> >> > 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
> >> >>
> >> > _______________________________________________
> >> > 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 Thu Feb 12 2015 - 08:00:04 PST
