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)
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Received on Thu Feb 12 2015 - 07:30:03 PST
