On Thu, Feb 12, 2015 at 8:28 AM, Vijay Achari <glycoamber.gmail.com> wrote:
> With your latest code, the calculation run fine.
OK, this seems like it is a buffer overflow problem caused by long
bridge ID strings. I'll have to work on a patch for that.
> The *nhb.dat* file contains information as below
>
> *#Frame MyHB[UU] MyHB[UV] MyHB[Bridge]*
> 1 315 979 190
>
> Well, if I not mistaken this is the file called as *<dsetarg0>* (data set)
> for calculating the *lifetime*?
No, this is just the number of solute-solute hydrogen bonds,
solute-solvent hydrogen bonds, and solute-solvent bridges
respectively. The MyHB[solutehb] etc data sets contain the hydrogen
bond time series data that is used for the lifetime calculation (1 if
hydrogen bond is present, 0 if not).
-Dan
>
> Regards
> Vijay
>
>
>
> On Thu, Feb 12, 2015 at 11:06 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> OK, try it again but remove 'out nhb.dat' from your hbond command.
>> Then add one more command after 'run', e.g.:
>>
>> hbond MyHB :1-128 dist 3.5 angle 120 \
>> avgout avghb.dat nointramol series \
>> solventacceptor :WAT.O solventdonor :WAT \
>> solvout solvent_avg.dat bridgeout bridge.dat
>> run
>> writedata nhb.dat MyHB[UU] MyHB[UV] MyHB[Bridge]
>>
>> See if that works,
>>
>> -Dan
>>
>> On Thu, Feb 12, 2015 at 7:51 AM, 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)
>>
>>
>>
>> --
>> -------------------------
>> 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 - 08:00:04 PST
