Thanks Dan!
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Friday, March 1, 2019 8:38 PM
To: AMBER Mailing List
Subject: Re: [AMBER] CPPTRAJ grid unknown command
Hi,
OK, I think I see what you want - you want to bin the center of mass
of residues/molecules rather than bin each atom? If so, there's no
option to do it directly, but you can do it with cpptraj with a few
extra steps. For example, the following script creates a
pseudo-trajectory from the centers of mass of solute residues, then
grids it.
parm tz2.ortho.parm7
trajin tz2.ortho.nc
# Autoimage trajectory, create center of mass vector traj for each res
autoimage origin
for residues RES inmask !:WAT i=1;i++
vector v$i center $RES
done
run
writedata res.com.nc vectraj trajfmt netcdf parmout vecdata.parm7 noorigin v*
# Grid the vector traj
clear trajin
parm vecdata.parm7
trajin res.com.nc parm vecdata.parm7
grid out test.dx 20 .5 20 .5 20 .5 origin *
run
Hope this helps,
-Dan
PS - If you'd like to make a feature request, the best place to do so
is on the cpptraj GitHub repository:
https://github.com/Amber-MD/cpptraj/issues
On Thu, Feb 28, 2019 at 10:31 AM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
>
> 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]$
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Mar 01 2019 - 09:30:02 PST
