Dear Dan,
With your latest code, the calculation run fine.
Now I get four files
*avghb.dat, bridge.dat, solvent_avg.dat *and *nhb.dat. *
The *nhb.dat* file contains information as below
*#Frame MyHB[UU] MyHB[UV] MyHB[Bridge]*
1 315 979 190
2 308 997 199
3 301 994 209
4 320 967 213
5 312 1001 215
6 326 987 198
7 324 967 201
8 328 983 200
9 335 983 195
10 321 986 205
Well, if I not mistaken this is the file called as *<dsetarg0>* (data set)
for calculating the *lifetime*?
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
>
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Received on Thu Feb 12 2015 - 07:30:04 PST
