I’m running cpptraj volmap to generate a peakfile for subsequent SPAM analysis. The solvent is water.
The cpptraj volmap.in file that I used is:
volmap volmap.xplor 0.5 0.5 0.5 :WAT.O radscale 1.36 name GRID size 5,5,5 center -54.5,-13.5,-18.5 peakcut 0.01 peakfile peaks
I assume the grid size (5,5,5) is in angstrom along the X,Y,Z dimensions. Is it legitimate instead of the center argument above to use centermask :1-125?
In either case the generated peakfile contained no data, even at a very small peakcut (0.001).
Thank you in advance for any suggestions
George
INPUT: Reading input from 'volmap.in'
[parm subA_solv.prmtop]
Reading 'subA_solv.prmtop' as Amber Topology
Radius Set: H(N)-modified Bondi radii (mbondi2)
[trajin prod_100ns.nc]
Reading 'prod_100ns.nc' as Amber NetCDF
[volmap volmap.xplor 0.5 0.5 0.5 :WAT.O radscale 1.36 name GRID size 5,5,5 centermask :1-125 peakcut 0.001 peakfile peaks]
VOLMAP: Grid spacing will be 0.50x0.50x0.50 Angstroms
Grid centered at origin.
Gridding atoms in mask ':WAT.O'
Dividing radii by 1.360000
Density will wrtten to 'volmap.xplor'
Grid dataset name is 'GRID'
Density peaks above 0.001 will be printed to peaks in XYZ-format
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: subA_solv.prmtop, 13140 atoms, 3847 res, box: Trunc. Oct., 3723 mol, 3713 solvent
INPUT TRAJECTORIES (1 total):
0: 'prod_100ns.nc' is a NetCDF AMBER trajectory, Parm subA_solv.prmtop (Trunc. Oct. box) (reading 10000 of 10000)
Coordinate processing will occur on 10000 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'subA_solv.prmtop' (1 actions):
0: [volmap volmap.xplor 0.5 0.5 0.5 :WAT.O radscale 1.36 name GRID size 5,5,5 centermask :1-125 peakcut 0.001 peakfile peaks]
Volmap: Grid mask [:WAT.O] selects 3713 atoms.
----- prod_100ns.nc (1-10000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 10000 frames and processed 10000 frames.
TIME: Avg. throughput= 3651.9995 frames / second.
ACTION OUTPUT:
No peaks found with a density greater than 0.001
DATASETS (1 total):
GRID "GRID" (float grid), size is 1000
DATAFILES (2 total):
volmap.xplor (Xplor File): GRID
peaks (Volmap Peaks)
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Received on Fri Sep 15 2017 - 07:00:02 PDT
