I would like to know if Center of Mass binning is included in Amber18 latest version of cpptraj grid command
Instead of per atom binning can we ask it to grid as per the center of mass ?
One of my colleagues modified the cpptraj code to get Center of mass binning that was done 3 years back.. SO I am trying to use his modified version of cpptraj
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Thursday, February 28, 2019 3:51 AM
To: AMBER Mailing List
Subject: Re: [AMBER] CPPTRAJ grid unknown command
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]$
>
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>
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Received on Thu Feb 28 2019 - 08:00:02 PST
