On Fri, Mar 27, 2015 at 10:28 AM, James Starlight
<jmsstarlight.gmail.com> wrote:
> use :
> multidihedral chi_toogle chip resrange 1-10 out dihedral.agr
>
> or it should to provide precise atom names like
>
> multidihedral chi_toogle :.CA:.CB:.CG:.CD1 resrange 1-10 out dihedral.agr
The former should work. As always, you should run this on a small
subset of your data (say no more than 100 frames) before trying
production, and examine your output carefully for any 'Warning:' or
'Error:' messages. Make sure you get all of the dihedrals you expect.
-Dan
>
> James
>
> 2015-03-27 16:39 GMT+01:00 Daniel Roe <daniel.r.roe.gmail.com>:
>> Hi,
>>
>> You'll need to use the 'dihedral' or 'multidihedral' commands to
>> generate the dihedral data. If using 'multidihedral' it's important to
>> issue a 'run' command before any analysis. Then use the 'hist', 'kde
>> or 'multihist' analysis commands to generate histograms (either same
>> step or subsequent step). In addition you can use the 'stat' analysis
>> command to obtain more detailed info on the dihedrals. For example, to
>> look at all phi distributions for residues 1-10:
>>
>> parm myparm.parm7
>> trajin mytraj.nc
>> multidihedral MyDihedral phi resrange 1-10 out dihedral.agr
>> run
>> multihist MyDihedral[*] out hist.dihedral.agr normint min -180 max 180 step 1
>> stat all out stat.dihedral.dat
>>
>> Hope this helps,
>>
>> -Dan
>>
>> On Fri, Mar 27, 2015 at 9:13 AM, James Starlight <jmsstarlight.gmail.com> wrote:
>>> Dear Amber users!
>>>
>>> I need to analyze several md trajectories of the receptor-ligand
>>> complexes to obtain some structural information on level of receptor's
>>> individual residues. For each of the trajectory I need to calculate
>>> distributions of dihedral angles within specified receptor's residues
>>> and obtain the information in histogram form to compare such outputs
>>> and to see how the presence of different ligands alter its equilibrium
>>> dynamics. I'll be expecially thankful for example of cpptraj commands
>>> sequence for such kind of the analysis as well as its additional tools
>>> which could produce relevant information in my task.
>>>
>>> Thanks alot!
>>>
>>> James
>>>
>>> _______________________________________________
>>> 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)
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Received on Fri Mar 27 2015 - 10:00:04 PDT
