Hi,
If your intention is to look for peaks which you can use as input for
'spam' you probably want to use an 'rms' command to remove
translation/rotation from your solute of interest, then 'center' to
ensure your system is centered on the grid, i.e. you want the system
oriented such that the solute is your reference frame. Otherwise with
the overall translational motion present in your system it is entirely
possible for there to be no solvent peaks.
For example (assuming residues 1-125 are the solute):
rms first :1-125
center :1-125 mass origin
volmap volmap.xplor 0.5 0.5 0.5 :WAT.O radscale 1.36 name GRID size
5,5,5peakcut 0.001 peakfile peaks
Hope this helps.
-Dan
On Fri, Sep 15, 2017 at 9:54 AM, George Tzotzos <gtzotzos.me.com> wrote:
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 Wed Sep 20 2017 - 09:30:03 PDT
