Re: [AMBER] hbond lifetime

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 10 Sep 2014 20:51:06 -0600

Hi,

On Wed, Sep 10, 2014 at 2:52 PM, George Tzotzos <gtzotzos.me.com> wrote:
> DATASETS:
> 5 data sets:
> H1[UU] "H1[UU]" (integer), size is 2000

This data set is from your first 'hbond' command that you named H1.
Since there are no other data sets and you used the 'series' keyword
it appears no hydrogen bonds were detected. Is this the case? If so
the data in H1[UU] should be all zeros. You can check this by adding
an 'out <filename>' keyword to your first hbond command or a 'create
<filename> H1[UU]' command.

> 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

These data sets are from your second 'hbond' command, where you did
not specify 'series', so no hydrogen bond lifetime data sets were
saved. You also did not specify a data set name in the second command
so it defaulted to 'HB_00001'.

Unless there is some obvious reason I'm overlooking you probably want
to just use one 'hbond' command, something like:

hbond H1 series acceptormask :126.N*,O* donormask :1-125.N*,O* \
    out hb.dat dist 3.0 avgout avg.dat \
    bridgeout bridgeout.dat solventdonor :WAT solventacceptor :WAT.O

This will create data sets H1[UU], H1[UV], H1[Bridge], H1[ID], and if
hydrogen bonds are detected H1[solutehb] and H1[solventhb] for
solute-solute and solute-solvent hydrogen bonds respectively.

(Note that masks of the form ':<res>.<atom>' imply the '&', which is
why I omitted it).

Hope this helps, let me know if you have any more issues.

-Dan

> 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)
>>
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>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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-- 
-------------------------
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)
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Received on Wed Sep 10 2014 - 20:00:03 PDT
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