[AMBER] radial distribution function results

From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Date: Thu, 8 Mar 2018 17:52:45 +0000


I am studying interactions between glycans on the surface of a glycoprotein and used the radial function in cpptraj

here is an example of my input:

parm md_stripped.prmtop
trajin md2_9_append_stripped.nc
radial glycan1_glycan2.out 0.1 15.0 :650-661 :602-613 noimage volume nointramol glycan1_glycan2

The results appear strange (Average density is 0.000000 distances / Ang^3) and I'm not sure why. Should I rather use the default density instead of volume? From Volmaps over time and inspection of individual frames I can see that these glycans do interact. Any help on how to obtain an appropriate RDF curve would be much appreciated.

The .dat file only contains -nan for all lines up until 14.95
#Distance_(Ang) :602-613_=>_:638-649
          0.050 -nan
         14.950 -nan

Here is some of my cpptraj log output:

        Reading 'CDOM_CPLX_rnb_stripped_box.prmtop' as Amber Topology
INPUT: Reading Input from file cpptraj_rdf.in
  [trajin md2_9_append_stripped.nc]
        Reading 'md2_9_append_stripped.nc' as Amber NetCDF
Warning: Trajectory box type is 'Trunc. Oct.' but topology box type is 'None'.
Warning: Setting topology box information from trajectory.
  [radial N36_54.out 0.1 15.0 :650-661 :602-613 noimage volume nointramol N36_54]
    RADIAL: Calculating RDF for atoms in mask [:650-661] to atoms in mask [:602-613]
            Output to N36_54.out.
            Histogram max 15.000000, spacing 0.100000, bins 150.
            Normalizing based on cell volume.
            Imaging disabled.
---------- RUN BEGIN -------------------------------------------------

 0: 'CDOM_CPLX_rnb_stripped_box.prmtop', 11273 atoms, 665 res, box: Trunc. Oct., 4 mol, 3000 frames

 0: 'md2_9_append_stripped.nc' is a NetCDF AMBER trajectory, Parm CDOM_CPLX_rnb_stripped_box.prmtop (Trunc. Oct. box) (reading 3000 of 3000)
  Coordinate processing will occur on 3000 frames.
TIME: Run Initialization took 0.0000 seconds.

ACTION SETUP FOR PARM 'CDOM_CPLX_rnb_stripped_box.prmtop' (4 actions):
  0: [radial N36_54.out 0.1 15.0 :650-661 :602-613 noimage volume nointramol N36_54]
        Ignoring 93636 intra-molecular distances.
    RADIAL: 306 atoms in Mask1, 306 atoms in Mask2, Imaging off.

----- md2_9_append_stripped.nc (1-3000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 3000 frames and processed 3000 frames.
TIME: Trajectory processing: 2.3625 s
TIME: Avg. throughput= 1269.8348 frames / second.

    RADIAL: 3000 frames, # in mask1= 306, # in mask2 = 306, # in common = 93636
            Average volume is 1027665.163006 Ang^3.
            Average density is 0.000000 distances / Ang^3.

  4 data sets:
        N36_54 ":650-661 => :602-613" (double), size is 150

  N36_54.out (Standard Data File): :650-661 => :602-613

Lizelle Lubbe

PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
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Received on Thu Mar 08 2018 - 10:00:03 PST
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