Hi,
You're using the old syntax which can be easy to make a small mistake
(also 'solv' appears to be unneeded). Try:
grid out 1P3_5ns_COM.xplor 100 0.5 100 0.5 100 0.5 name 1P3 :1P3 origin max 0.9
Hope this helps,
-Dan
On Fri, Jan 18, 2019 at 10:47 AM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
>
> Hi,
> I have been trying to use teh grid command to find out occupancies of probe molecules. My system is a equilibrated box of water + Pyrimidine
> I have used this input
> parm 1P3_WAT_box.prmtop
> trajin prod_total.mdcrd 1 5000 1
> center mass origin
> image origin center familiar
>
> #Write out grid count of probe occupancy
>
> grid WAT_1P3_5ns_COM.xplor solv WAT 100 0.5 100 0.5 100 0.5 :WAT origin max 0.9
>
> grid 1P3_5ns_COM.xplor solv 1P3 100 0.5 100 0.5 100 0.5 :1P3 origin max 0.9
>
> #Correct for systematic error induced by ptraj grid function
> translate x -0.25 y -0.25 z -0.25
>
>
>
> I get the WAT_1P3_5ns_COM.xplor file but I am not able to generate 1P3_5ns_COM.xplor
>
> This is my error.
> Any help will be very useful
>
> CPPTRAJ: Trajectory Analysis. V18.01
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 01/18/19 10:08:46
> | Available memory: 155.466 GB
>
> INPUT: Reading input from 'STDIN'
> [parm 1P3_WAT_box.prmtop]
> Reading '1P3_WAT_box.prmtop' as Amber Topology
> Radius Set: modified Bondi radii (mbondi)
> [trajin prod_total.mdcrd 1 5000 1]
> Reading 'prod_total.mdcrd' as Amber Trajectory
> [center mass origin]
> CENTER: Centering coordinates using center of mass of atoms in mask (*) to
> coordinate origin.
> [image origin center familiar]
> IMAGE: By molecule to origin based on center of mass using all atoms
> Triclinic On, familiar shape.
> [grid 1P3_5ns_COM.xplor solv 1P3 100 0.5 100 0.5 100 0.5 :1P3 origin max 0.9]
> GRID:
> Calculating positive density.
> -=Grid Dims=- X Y Z
> Bins: 100 100 100
> Origin: -50 -50 -25
> Spacing: 1 1 0.5
> Center: 0 0 0
> Grid data set: 'GRID_00001'
> Mask expression: [:1P3]
> Pseudo-PDB will be printed to STDOUT
> Error: [grid] Not all arguments handled: [ solv 0.5 0.5 ]
> 1 errors encountered reading input.
> TIME: Total execution time: 0.1149 seconds.
> Error: Error(s) occurred during execution.
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Received on Thu Jan 24 2019 - 08:30:01 PST
