Re: [AMBER] Histogram analysis of the dihedral distributions using cpptraj

From: Daniel Roe <>
Date: Fri, 27 Mar 2015 09:39:26 -0600


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
multidihedral MyDihedral phi resrange 1-10 out dihedral.agr
multihist MyDihedral[*] out hist.dihedral.agr normint min -180 max 180 step 1
stat all out stat.dihedral.dat

Hope this helps,


On Fri, Mar 27, 2015 at 9:13 AM, James Starlight <> 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

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Fri Mar 27 2015 - 09:00:04 PDT
Custom Search