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)
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Received on Thu Feb 12 2015 - 07:30:02 PST
