Hi,
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 -------------------------------------------------
PARAMETER FILES:
0: 'CDOM_CPLX_rnb_stripped_box.prmtop', 11273 atoms, 665 res, box: Trunc. Oct., 4 mol, 3000 frames
INPUT TRAJECTORIES:
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.
BEGIN TRAJECTORY PROCESSING:
.....................................................
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.
ACTION OUTPUT:
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.
DATASETS:
4 data sets:
N36_54 ":650-661 => :602-613" (double), size is 150
DATAFILES:
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
