Dear Dan,
Thanks for your detail explanation. After reading above notes I realized
that I need to run the hbond calculation at first.
By the way, after reading some extra notes I became little dizzy although I
used to use ptraj for calculating HB. Now I am trying to use cpptraj.
Considering my system directly, which is a hydrated bilayer constitute with
glycolipids, I wish to calculate the hydrogen bonding between 1) lipid to
lipid and 2) lipid to solvent(water)
Basically the hydrogen bond occur between hydroxyl (donor) and hydrogen or
oxygen atoms (acceptor). My glycolipid have 7 hydroxyl groups.
The part I find *difficult *is to write the proper command with appropriate
options for my need.
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.
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
>
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Received on Wed Feb 11 2015 - 10:00:02 PST
