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

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Fri, 11 Aug 2017 12:52:39 -0400

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
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> 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
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Received on Fri Aug 11 2017 - 10:00:04 PDT
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