Re: [AMBER] hbond lifetime

From: George Tzotzos <gtzotzos.me.com>
Date: Wed, 10 Sep 2014 17:52:46 -0300

Thank you for the quick reply. Actually the output I get is:

ACTION OUTPUT:

DATASETS:
  5 data sets:
        H1[UU] "H1[UU]" (integer), size is 2000
        HB_00001[UU] "HB_00001[UU]" (integer), size is 2000
        HB_00001[UV] "HB_00001[UV]" (integer), size is 2000
        HB_00001[Bridge] "HB_00001[Bridge]" (integer), size is 2000
        HB_00001[ID] "HB_00001[ID]" (string), size is 2000
DATAFILE OUTPUT:
  hb.dat: HB_00001[UU] HB_00001[UV] HB_00001[Bridge] HB_00001[ID]
hb.dat: Writing 2000 frames.
  [runanalysis lifetime H1 [UU] out life.dat]
Error: lifetime: No data sets selected.

I find it a bit difficult to interpret the bracketed terms and use the right dataset.

George



On 10Sep, 2014, at 5:27 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> Hi,
>
> On Wed, Sep 10, 2014 at 2:13 PM, George Tzotzos <gtzotzos.me.com> wrote:
>> trajin prod_0-20ns.nc
>> hbond H1 series acceptormask :126&.N*,O* donormask :1-125&@N*,O*
>> hbond out hb.dat dist 3.0 avgout avg.dat \
>> bridgeout bridgeout.dat solventdonor :WAT solventacceptor :WAT&.O
>> go
>> runanalysis lifetime H1 [hb.dat] out life.dat
>
> The data set aspects generated by 'hbond series' are [solutehb] for
> solute-solute hydrogen bonds and [solventhb] for solvent-solute
> hydrogen bonds (note that aspect information is listed for all actions
> that use them in the cpptraj section of the Amber 14 manual). Since
> you have named your data set H1 and you are looking for solute-solute
> hydrogen bonds, you should refer to the data set as 'H1[solutehb]'. If
> you're ever unsure as to how data sets are named you can refer to your
> cpptraj output after a run. You should see a summary of data set names
> etc in the DATASETS: part of the output, e.g.:
>
> DATASETS:
> 20 data sets:
> H1[UU] "H1[UU]" (integer), size is 100
> H1[solutehb]:24 "GLU_13.O-VAL_2.N-H" (integer), size is 100
> H1[solutehb]:104 "TYR_11.O-ILE_4.N-H" (integer), size is 100
> ...
>
> So in summary the analysis command you want should look like:
>
> runanalysis lifetime H1[solutehb] out life.dat
>
> Hope this helps,
>
> -Dan
>
>>
>> The script produces: avg.dat; bridgeout.dat and hb.dat. If fails to produce life.dat due to Error: lifetime: No datasets selected.
>>
>> Any help in improving the script will be much appreciated.
>>
>> Regards
>>
>> George
>>
>>
>>
>> _______________________________________________
>> 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
Received on Wed Sep 10 2014 - 14:00:03 PDT
Custom Search