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 Fri Jan 18 2019 - 08:00:03 PST
