Thanks Daniel,
Excluding nointramol solved the problem and produced a proper curve
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Tuesday, March 13, 2018 7:44:04 PM
To: AMBER Mailing List
Subject: Re: [AMBER] radial distribution function results
Hi,
The issue is that you've specified 'nointramol' to ignore
intramolecular distances, but according to cpptraj the number of
intramolecular distances (reported as "# in common") is 93636,
indicating everything select by the two masks is in the same molecule.
Is this the case? If not, can you send me off-list the topology file
and a single trajectory frame so I can test it? If everything is part
of the same molecule, remove the 'nointramol' keyword.
-Dan
On Thu, Mar 8, 2018 at 12:52 PM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote:
> 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
> Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Mar 13 2018 - 12:30:02 PDT
