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
Received on Wed Feb 11 2015 - 09:00:02 PST
