Dear Dan,
I have executed as your sample code for about 5000 frames for testing. But
at the end of the processing I get something as below :
Is this showing some error?
DATAFILES:
nhb.dat (Standard Data File): MyHB[UU] MyHB[UV] MyHB[Bridge] MyHB[ID]
*** buffer overflow detected ***: cpptraj terminated
======= 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
>
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Received on Wed Feb 11 2015 - 18:00:02 PST
