Check the version - you’re using version 1.0.5 which is *old*. Check your
PATH variable to make sure you’re including your Amber 14 install. Better
yet, upgrade to AmberTools 18 or use cpptraj from github.
-Dan
On Wed, Feb 27, 2019 at 5:12 PM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:
> I want to do some xplor file generation using AMBER14 version of cpptraj.
>
> However, it says Unknown Command GRID??
>
> Any help will be appreciated.
> Thanks
> Debarati
>
>
>
> CPPTRAJ: Trajectory Analysis. V1.0.5
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
> > > [parm 3kfa_layer_1P3_H2O_5-95vv.prmtop]
> > [trajin New4E_production.1.crd 1 1250 1]
> > > [center :1-286 mass origin]
> > [image origin familiar com :1-286]
> > > > [strip :Cl-,Na+]
> > > > [grid 3kfa_1P3_19.0-20.0ns_1P3_center.xplor solv 1P3 200 0.5 200
> 0.5 200 0.5 :1P3 origin max 0.9]
> Warning: Unknown Command grid.
> > > > > > >
> TRAJECTORIES:
> [New4E_production.1.crd] is an AMBER trajectory, Parm 0 (with box info)
> (reading 1250 of 1250)
> Coordinate processing will occur on 1250 frames.
>
> PARAMETER FILES:
> 0: 3kfa_layer_1P3_H2O_5-95vv.prmtop, 83688 atoms, 25958 res, box 1, 25673
> mol, 25660 solvent mol, 1250 frames.
>
> REFERENCE COORDS:
> No reference coordinates.
> No frames defined.
>
> OUTPUT TRAJECTORIES:
> No files.
>
> ACTIONS: Initializing 3 actions:
> 0: [center :1-286 mass origin]
> CENTER: To origin via center of mass using atoms in mask :1-286
>
> 1: [image origin familiar com :1-286]
> IMAGE: To origin based on first atom position using atoms in mask *
> Triclinic On, familiar shape centering on atoms in mask :1-286.
>
> 2: [strip :Cl-,Na+]
> STRIP: Stripping atoms in mask [:Cl-,Na+]
>
> BEGIN TRAJECTORY PROCESSING:
> ----- [New4E_production.1.crd] (1-1250, 1) -----
> .... Setting up 3 actions for 3kfa_layer_1P3_H2O_5-95vv.prmtop ....
> STRIP: Stripping 12 atoms.
> New parm: First solvent molecule is 2
> New parmtop contains 83676 atoms.
> 25946 residues.
> 25661 molecules.
> 25660 solvent molcules.
> ...................................................
> [||------------------------------------------^C----]
> [debarati.fino 3kfa_md_2pmemdcuda]$
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 27 2019 - 14:30:02 PST
