Hi Dan,
thanks you very much for help!
one question- to choose chi-1 of the side-chains of 1-10 residues ( to
see how side chains flip-flop during the md run) will it be enough to
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
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
>>
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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 Fri Mar 27 2015 - 09:30:02 PDT
