Hi,
Gridding by residue/by molecule is now implemented in the current
GitHub version of cpptraj.
-Dan
On Fri, Mar 1, 2019 at 12:41 PM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
>
> Hi Daniel,
>
> This is my modified file (input) as instructed.
>
> parm 3kfa_layer_ACN_H2O_5-95vv.prmtop
>
> trajin production.1.crd 1 1250 1
>
> strip :Cl-,Na+
>
> autoimage origin
>
> for residues C3N inmask !:WAT i=1;i++
>
> vector v$i center $C3N
>
> done
>
> run
>
> writedata res_com.mdcrd vectraj trajfmt netcdf parmout vecdata.prmtop noorigin v*
>
> # Grid the vector traj
>
> clear trajin
>
> parm vecdata.prmtop
>
> trajin res_com.mdcrd parm vecdata.prmtop
>
> #Write out grid count of probe occupancy
>
> grid out 3kfa_ACN_10-15ns_C3N_center.xplor 200 0.5 200 0.5 200 0.5 :C3N origin *
>
> grid out 3kfa_ACN_10-15ns_WAT.xplor 200 0.5 200 0.5 200 0.5 :WAT origin *
>
> run
>
> My intention is "The center of mass of acetonitrile probe to be binned in a 0.5 A grid spacing using Amber18 cpptraj"
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Friday, March 1, 2019 8:38 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] CPPTRAJ grid unknown command
>
> Hi,
>
> OK, I think I see what you want - you want to bin the center of mass
> of residues/molecules rather than bin each atom? If so, there's no
> option to do it directly, but you can do it with cpptraj with a few
> extra steps. For example, the following script creates a
> pseudo-trajectory from the centers of mass of solute residues, then
> grids it.
>
>
> parm tz2.ortho.parm7
> trajin tz2.ortho.nc
> # Autoimage trajectory, create center of mass vector traj for each res
> autoimage origin
> for residues RES inmask !:WAT i=1;i++
> vector v$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]$
> > >
> > > _______________________________________________
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Received on Mon Mar 11 2019 - 12:30:06 PDT
