Re: [AMBER] Error-Calculating distance between two atoms in CPPTRAJ

From: Jag Silwal <jagsilwal.gmail.com>
Date: Fri, 11 Aug 2017 13:00:21 -0400

Dan,

Thank you. That works.

ambermd website and any tutorials are not loading today. I don't know why.

 I always look at manual first but today it is not loading either.

So I found this in one from the email archives:

 Anyway, thank you for your quick response.

From: Billy Miller III <brmilleriii.gmail.com
<brmilleriii.gmail.com?Subject=Re%3A%20%5BAMBER%5D%20Distance%20between%20two%20atoms%20vs%20time>
>
Date: Mon, 22 Mar 2010 08:57:13 -0400

Once you trajin the correct trajectory file, the general command for
calculating the distance between two atoms should be something like this:

distance DIST .atom_number1 .atom_number2 out dist.out

Or for your specific case, it should be:

distance DIST .256 .399 out dist.out

You could also use the residues numbers and atom types:

distance DIST :154.OE1 :45.OD2

Either of these last two commands should give you the exact same results
for
your system.

Good luck!

-Bill Miller

On Fri, Aug 11, 2017 at 12:52 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> Hi,
>
> On Fri, Aug 11, 2017 at 12:42 PM, Jag Silwal <jagsilwal.gmail.com> wrote:
> >
> > distance DIST1 .3981.3092 out dist1.out
> >
> > distance DIST :3981.O :3092.OH
>
> None of your mask expressions are valid. The symbol for atom is '.'.
> You want something like:
>
> distance DIST1 .3981 @3092 out dist1.out
>
> The cpptraj section of the Amber manual has a good explanation of
> Amber mask syntax (28.2.2 Atom Mask Selection Syntax, page 555). The
> tutorials are also a good place to start:
> http://ambermd.org/tutorials/#analysis
>
> Out of curiosity, what example were you using that recommended using a
> period in the atom mask?
>
> -Dan
>
> >
> > And I got no output with the following message :
> >
> > parm x.prmtop
> > Reading 'x.prmtop' as Amber Topology
> >> trajin Prod.mdcrd
> > Reading 'Prod.mdcrd' as Amber NetCDF
> >> distance DIST :3981.O :3092.OH
> > DISTANCE: :3981.O to :3092.OH, center of mass.
> >> run
> > ---------- RUN BEGIN -------------------------------------------------
> >
> > PARAMETER FILES (1 total):
> > 0: x.prmtop, 55934 atoms, 17450 res, box: Orthogonal, 17179 mol, 17171
> > solvent
> >
> > INPUT TRAJECTORIES (1 total):
> > 0: 'Prod.mdcrd' is a NetCDF AMBER trajectory, Parm x.prmtop (Orthogonal
> > box) (reading 9000 of 9000)
> > Coordinate processing will occur on 9000 frames.
> >
> > BEGIN TRAJECTORY PROCESSING:
> > .....................................................
> > ACTION SETUP FOR PARM 'x.prmtop' (1 actions):
> > 0: [distance DIST :3981.O :3092.OH]
> > :3981.O (0 atoms) to :3092.OH (0 atoms)
> > Warning: One or both masks have no atoms.
> > Warning: Setup incomplete for [distance]: Skipping
> > ----- Prod.mdcrd (1-9000, 1) -----
> > 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> >
> > Read 9000 frames and processed 9000 frames.
> > TIME: Avg. throughput= 203.0209 frames / second.
> >
> > ACTION OUTPUT:
> >
> > DATASETS (1 total):
> > DIST "DIST" (double, distance), size is 0
> >
> > RUN TIMING:
> > TIME: Init : 0.0000 s ( 0.00%)
> > TIME: Trajectory Process : 44.3304 s (100.00%)
> > TIME: Action Post : 0.0000 s ( 0.00%)
> > TIME: Analysis : 0.0000 s ( 0.00%)
> > TIME: Data File Write : 0.0000 s ( 0.00%)
> > TIME: Other : 0.0000 s ( 0.00%)
> > TIME: Run Total 44.3305 s
> > ---------- RUN END ---------------------------------------------------
> >> quit
> > ------------------------------------------------------------
> --------------------
> > To cite CPPTRAJ use:
> > Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software
> for
> > Processing and Analysis of Molecular Dynamics Trajectory Data". J.
> Chem.
> >
> >
> >
> > Any inputs would be greatly appreciated.
> >
> >
> > Jag S
> >
> > Michigan State U
> > Chemistry
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Aug 11 2017 - 10:30:02 PDT
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